# Index

A B C D E F G H I J K L M N O P Q R S T U V W X Y Z
All Classes and Interfaces|All Packages|Constant Field Values|Serialized Form

## A

A(int[], int) - Static method in class ij.process.AutoThresholder
ABGR - Static variable in class ij.io.FileInfo
  32-bit interleaved ABGR.
abort() - Static method in class ij.Macro
  Aborts the currently running macro or any plugin using IJ.run().
abort() - Static method in class ij.macro.Interpreter
  Aborts currently running macro.
abort() - Method in class ij.measure.Minimizer
  Aborts minimization.
abort(Interpreter) - Static method in class ij.macro.Interpreter
  Absolete, replaced by abortMacro().
abort(String) - Method in class ij.macro.Interpreter
ABORTED - Static variable in class ij.measure.Minimizer
  Status returned: aborted by call to abort method.
abortMacro() - Method in class ij.macro.Interpreter
  Aborts this macro.
abortModification(ImagePlus) - Method in class ij.gui.Roi
  Aborts constructing or modifying the roi (called by the ImageJ class on escape)
abortPaste() - Method in class ij.gui.Roi
ABOUT_MENU - Static variable in class ij.Menus
AboutBox - Class in ij.plugin
  This plugin implements the Help/About ImageJ command by opening about.jpg in ij.jar, scaling it 600% and adding text to an overlay.
AboutBox() - Constructor for class ij.plugin.AboutBox
abs() - Method in class ij.process.FloatProcessor
abs() - Method in class ij.process.ImageProcessor
  If this is a 32-bit or signed 16-bit image, performs an absolute value transform, otherwise does nothing.
abs() - Method in class ij.process.ShortProcessor
ABS - Static variable in interface ij.macro.MacroConstants
accept(File, String) - Method in class ij.plugin.Compiler
ACOS - Static variable in interface ij.macro.MacroConstants
actionPerformed(ActionEvent) - Method in class ij.gui.GenericDialog
actionPerformed(ActionEvent) - Method in class ij.gui.HistogramWindow
actionPerformed(ActionEvent) - Method in class ij.gui.HTMLDialog
actionPerformed(ActionEvent) - Method in class ij.gui.MessageDialog
actionPerformed(ActionEvent) - Method in class ij.gui.NonBlockingGenericDialog
actionPerformed(ActionEvent) - Method in class ij.gui.PlotWindow
  Called if user has activated a button or popup menu item
actionPerformed(ActionEvent) - Method in class ij.gui.SaveChangesDialog
actionPerformed(ActionEvent) - Method in class ij.gui.StackWindow
actionPerformed(ActionEvent) - Method in class ij.gui.Toolbar
actionPerformed(ActionEvent) - Method in class ij.gui.WaitForUserDialog
actionPerformed(ActionEvent) - Method in class ij.gui.YesNoCancelDialog
actionPerformed(ActionEvent) - Method in class ij.ImageJ
  Handle menu events.
actionPerformed(ActionEvent) - Method in class ij.macro.FunctionFinder
actionPerformed(ActionEvent) - Method in class ij.measure.ResultsTableMacros
actionPerformed(ActionEvent) - Method in class ij.plugin.BatchConverter
actionPerformed(ActionEvent) - Method in class ij.plugin.BatchProcessor
actionPerformed(ActionEvent) - Method in class ij.plugin.CommandFinder
actionPerformed(ActionEvent) - Method in class ij.plugin.filter.Calibrator
actionPerformed(ActionEvent) - Method in class ij.plugin.filter.Convolver
actionPerformed(ActionEvent) - Method in class ij.plugin.frame.Channels
actionPerformed(ActionEvent) - Method in class ij.plugin.frame.ColorThresholder
actionPerformed(ActionEvent) - Method in class ij.plugin.frame.Commands
actionPerformed(ActionEvent) - Method in class ij.plugin.frame.ContrastAdjuster
actionPerformed(ActionEvent) - Method in class ij.plugin.frame.Editor
actionPerformed(ActionEvent) - Method in class ij.plugin.frame.Fitter
actionPerformed(ActionEvent) - Method in class ij.plugin.frame.Recorder
actionPerformed(ActionEvent) - Method in class ij.plugin.frame.RoiManager
actionPerformed(ActionEvent) - Method in class ij.plugin.frame.SyncWindows
  Implementation of ActionListener interface.
actionPerformed(ActionEvent) - Method in class ij.plugin.frame.ThresholdAdjuster
actionPerformed(ActionEvent) - Method in class ij.plugin.LUT_Editor
actionPerformed(ActionEvent) - Method in class ij.plugin.MacroInstaller
actionPerformed(ActionEvent) - Method in class ij.plugin.Orthogonal_Views
actionPerformed(ActionEvent) - Method in class ij.text.TextPanel
actionPerformed(ActionEvent) - Method in class ij.text.TextWindow
activateImage(ImagePlus) - Static method in class ij.macro.Interpreter
add(double) - Method in class ij.process.FloatProcessor
add(double) - Method in class ij.process.ImageProcessor
  Adds 'value' to each pixel in the image or ROI.
add(double) - Method in class ij.process.ShortProcessor
add(float) - Method in class ij.util.FloatArray
  Appends the specified value to the end of this FloatArray.
add(float[], int) - Method in class ij.util.FloatArray
  Appends the first n values from the specified array to this FloatArray.
add(int) - Method in class ij.process.FloatProcessor
add(int) - Method in class ij.process.ImageProcessor
  Adds 'value' to each pixel in the image or ROI.
add(int) - Method in class ij.process.ShortProcessor
add(Overlay) - Method in class ij.gui.Overlay
  Adds the ROIs in 'overlay2' to this overlay.
add(Roi) - Method in class ij.gui.Overlay
  Adds an ROI to this Overlay.
add(Roi, int) - Method in class ij.plugin.frame.RoiManager
  Adds the specified ROI to the list.
add(Roi, String) - Method in class ij.gui.Overlay
  Adds an ROI to this Overlay using the specified name.
add(ImagePlus, Roi, int) - Method in class ij.plugin.frame.RoiManager
  Adds the specified ROI to the list.
add(ImageProcessor, double) - Method in class ij.plugin.filter.SaltAndPepper
add(Component) - Method in class ij.gui.ImageWindow
add(String, double[]) - Method in class ij.gui.Plot
  Adds a curve, set of points or error bars to this plot, where 'type' is "line", "connected circle", "filled", "bar", "separated bar", "circle", "box", "triangle", "diamond", "cross", "x", "dot", "error bars" or "xerror bars".
add(String, double[], double[]) - Method in class ij.gui.Plot
  Adds a curve or set of points to this plot, where 'type' is "line", "connected circle", "filled", "bar", "separated bar", "circle", "box", "triangle", "diamond", "cross", "x" or "dot".
add(String, String) - Static method in class ij.Menus
  Adds a command to the ImageJ menu bar.
ADD - Static variable in interface ij.process.Blitter
  dst=dst+src
ADD_FIT - Static variable in class ij.gui.PlotContentsDialog
  Types of dialog (ERROR suppresses the dialog after an invalid call of a constructor)
ADD_FROM_ARRAYS - Static variable in class ij.gui.PlotContentsDialog
  Types of dialog (ERROR suppresses the dialog after an invalid call of a constructor)
ADD_FROM_PLOT - Static variable in class ij.gui.PlotContentsDialog
  Types of dialog (ERROR suppresses the dialog after an invalid call of a constructor)
ADD_FROM_TABLE - Static variable in class ij.gui.PlotContentsDialog
  Types of dialog (ERROR suppresses the dialog after an invalid call of a constructor)
ADD_TO_MANAGER - Static variable in class ij.plugin.filter.ParticleAnalyzer
  Add particles to ROI Manager.
ADD_TO_OVERLAY - Static variable in interface ij.measure.Measurements
addAdjustmentListener(AdjustmentListener) - Method in class ij.gui.ScrollbarWithLabel
addBatchModeImage(ImagePlus) - Static method in class ij.macro.Interpreter
addButton(String, ActionListener) - Method in class ij.gui.GenericDialog
  Add button to the dialog
addChar(char) - Method in class ij.gui.TextRoi
  This method is used by the text tool to add typed characters to displayed text selections.
addCheckbox(String, boolean) - Method in class ij.gui.GenericDialog
  Adds a checkbox.
addCheckboxGroup(int, int, String[], boolean[]) - Method in class ij.gui.GenericDialog
  Adds a group of checkboxs using a grid layout.
addCheckboxGroup(int, int, String[], boolean[], String[]) - Method in class ij.gui.GenericDialog
  Adds a group of checkboxs using a grid layout.
addChoice(String, String[], String) - Method in class ij.gui.GenericDialog
  Adds a popup menu.
addColumns() - Method in class ij.measure.ResultsTable
  Obsolete; the addValue() method automatically adds columns as needed.
addCommandListener(CommandListener) - Static method in class ij.Executer
  Adds the specified command listener.
addDialogListener(DialogListener) - Method in class ij.gui.GenericDialog
  Add an Object implementing the DialogListener interface.
addDirectoryField(String, String) - Method in class ij.gui.GenericDialog
  Adds a directory text field and "Browse" button, where the field width is determined by the length of 'defaultPath', with a minimum of 25 columns.
addDirectoryField(String, String, int) - Method in class ij.gui.GenericDialog
addElement(Roi) - Method in class ij.gui.Overlay
  Adds an ROI to this Overlay.
addEnumChoice(String, E) - Method in class ij.gui.GenericDialog
  Adds a group of choices to the dialog with menu items taken from the `enum` class of the specified default item (enum constant).
addEnumChoice(String, E[], E) - Method in class ij.gui.GenericDialog
  Adds a group of choices to the dialog with menu items taken from the supplied array of `enum` elements.
addErrorBars(double[]) - Method in class ij.gui.Plot
  Adds vertical error bars to the last data passed to the plot (via the constructor or addPoints).
addErrorBars(float[]) - Method in class ij.gui.Plot
  Adds vertical error bars to the last data passed to the plot (via the constructor or addPoints).
addErrorBars(float[]) - Method in class ij.gui.PlotWindow
  Deprecated.
  use the corresponding method of the Plot class
addErrorBars(String, float[]) - Method in class ij.gui.Plot
addEventListener(IJEventListener) - Static method in class ij.IJ
addFileField(String, String) - Method in class ij.gui.GenericDialog
  Adds a file text field and "Browse" button, where the field width is determined by the length of 'defaultPath', with a minimum of 25 columns.
addFileField(String, String, int) - Method in class ij.gui.GenericDialog
addHelp(String) - Method in class ij.gui.GenericDialog
  Adds a "Help" button that opens the specified URL in the default browser.
addHistogram(double[]) - Method in class ij.gui.Plot
  Plots a histogram from an array using auto-binning.
addHistogram(double[], double) - Method in class ij.gui.Plot
  Plots a histogram from an array using the specified bin width.
addHistogram(double[], double, double) - Method in class ij.gui.Plot
  Plots a histogram of the value distribution (bin counts) from an array
addHorizontalErrorBars(double[]) - Method in class ij.gui.Plot
  Adds horizontal error bars to the last data passed to the plot (via the constructor or addPoints).
addHorizontalErrorBars(float[]) - Method in class ij.gui.Plot
  Adds horizontal error bars to the last data passed to the plot (via the constructor or addPoints).
addImage(ImagePlus) - Method in class ij.gui.GenericDialog
  Adds an image to the dialog.
addImage(FileInfo) - Method in class ij.plugin.FileInfoVirtualStack
  Adds an image to this stack.
addImageChoice(String, String) - Method in class ij.gui.GenericDialog
  Adds a popup menu that lists the currently open images.
addImageListener(ImageListener) - Static method in class ij.ImagePlus
addKeyListener(KeyListener) - Method in class ij.gui.ScrollbarWithLabel
addKeyListener(KeyListener) - Method in class ij.text.TextPanel
  Unused keyPressed and keyTyped events will be passed to 'listener'.
addLabel(double, double, String) - Method in class ij.gui.Plot
  Draws text at the specified location, where (0,0) is the upper left corner of the the plot frame and (1,1) is the lower right corner.
addLabel(double, double, String) - Method in class ij.gui.PlotWindow
  Deprecated.
  use the corresponding method of the Plot class
addLabel(String) - Method in class ij.measure.ResultsTable
  Adds a label to the beginning of the current row.
addLabel(String, String) - Method in class ij.measure.ResultsTable
  Deprecated.
  Replaced by setValue(String,int,String)
addLayoutComponent(String, Component) - Method in class ij.gui.ImageLayout
  Not used by this class.
addLegend(String) - Method in class ij.gui.Plot
  Adds an automatically positioned legend, where 'labels' can be a tab-delimited or newline-delimited list of curve or point labels in the sequence these data were added.
addLegend(String, String) - Method in class ij.gui.Plot
  Adds a legend at the position given in 'options', where 'labels' can be tab-delimited or newline-delimited list of curve or point labels in the sequence these data were added.
addMacroTool(String, MacroInstaller) - Method in class ij.gui.Toolbar
  Used by the MacroInstaller class to add a macro tool to the toolbar.
addMacroTool(String, MacroInstaller, int) - Method in class ij.gui.Toolbar
  Used by the MacroInstaller class to install a set of macro tools.
addMessage(String) - Method in class ij.gui.GenericDialog
  Adds a message consisting of one or more lines of text.
addMessage(String, Font) - Method in class ij.gui.GenericDialog
  Adds a message consisting of one or more lines of text, which will be displayed using the specified font.
addMessage(String, Font, Color) - Method in class ij.gui.GenericDialog
  Adds a message consisting of one or more lines of text, which will be displayed using the specified font and color.
addMouseListener(MouseListener) - Method in class ij.text.TextPanel
addNotify() - Method in class ij.gui.MultiLineLabel
addNumericField(String, double) - Method in class ij.gui.GenericDialog
  Adds a numeric field.
addNumericField(String, double, int) - Method in class ij.gui.GenericDialog
  Adds a numeric field.
addNumericField(String, double, int, int, String) - Method in class ij.gui.GenericDialog
  Adds a numeric field.
addObjectFromPlot(Plot, int) - Method in class ij.gui.Plot
  Add the i-th PlotObject (in the sequence how they were added, including hidden ones) from another plot to this one.
addOffset() - Method in class ij.gui.PolygonRoi
addOpenRecentItem(String) - Static method in class ij.Menus
  Adds a file path to the beginning of the File/Open Recent submenu.
addPanel(Panel) - Method in class ij.gui.GenericDialog
  Adds a Panel to the dialog.
addPanel(Panel, int, Insets) - Method in class ij.gui.GenericDialog
  Adds a Panel to the dialog with custom contraint and insets.
addPlot(Plot) - Method in class ij.gui.PlotVirtualStack
  Adds a plot to the end of the stack.
addPlugInTool(PlugInTool) - Static method in class ij.gui.Toolbar
  Adds a plugin tool to the first available toolbar slot, or to the last slot if the toolbar is full.
addPoint(double, double) - Method in class ij.gui.PointRoi
  Adds a point to this PointRoi.
addPoint(double, double) - Method in class ij.process.FloatPolygon
addPoint(double, double, int) - Method in class ij.gui.PointRoi
  Adds a point at the specified stack position.
addPoint(float, float) - Method in class ij.process.FloatPolygon
addPoint(ImagePlus, double, double) - Method in class ij.gui.PointRoi
  Adds a point to this PointRoi.
addPoints(double[], double[], double[], int) - Method in class ij.gui.Plot
  Adds a set of points to the plot or adds a curve if shape is set to LINE.
addPoints(double[], double[], int) - Method in class ij.gui.Plot
  Adds a set of points to the plot using double arrays.
addPoints(double[], double[], int) - Method in class ij.gui.PlotWindow
  Deprecated.
  use the corresponding method of the Plot class
addPoints(float[], float[], float[], int, String) - Method in class ij.gui.Plot
  Adds a set of points to the plot or adds a curve if shape is set to LINE.
addPoints(float[], float[], int) - Method in class ij.gui.Plot
  Adds a set of points to the plot or adds a curve if shape is set to LINE.
addPoints(float[], float[], int) - Method in class ij.gui.PlotWindow
  Deprecated.
  use the corresponding method of the Plot class
addPoints(String, float[], float[], int) - Method in class ij.gui.Plot
addPoints(ArrayList, ArrayList, int) - Method in class ij.gui.Plot
  Adds a set of points to the plot using double ArrayLists.
addPoints(ArrayList, ArrayList, ArrayList, int) - Method in class ij.gui.Plot
  Adds a set of points to the plot using double ArrayLists.
addPreviewCheckbox(PlugInFilterRunner) - Method in class ij.gui.GenericDialog
  Adds a checkbox labelled "Preview" for "automatic" preview.
addPreviewCheckbox(PlugInFilterRunner, String) - Method in class ij.gui.GenericDialog
  Add the preview checkbox with user-defined label; for details see the addPreviewCheckbox method with standard "Preview" label.
addRadioButtonGroup(String, String[], int, int, String) - Method in class ij.gui.GenericDialog
  Adds a radio button group.
addResults() - Method in class ij.measure.ResultsTable
  Adds the last row in this table to the Results window without updating it.
addRoi(Roi) - Method in class ij.plugin.frame.RoiManager
  Adds the specified ROI.
addRoiListener(RoiListener) - Static method in class ij.gui.Roi
addRow() - Method in class ij.measure.ResultsTable
  Adds a row to the table.
addSeparator(String) - Static method in class ij.IJ
addSlice(ImageProcessor) - Method in class ij.ImageStack
  Adds the image in 'ip' to the end of the stack.
addSlice(String) - Method in class ij.VirtualStack
  Adds an image to the end of a virtual stack created using the VirtualStack(w,h,cm,path) constructor.
addSlice(String, ImageProcessor) - Method in class ij.ImageStack
  Adds the image in 'ip' to the end of the stack, setting the string 'sliceLabel' as the slice metadata.
addSlice(String, ImageProcessor) - Method in class ij.VirtualStack
  Does nothing..
addSlice(String, ImageProcessor, int) - Method in class ij.ImageStack
  Adds the image in 'ip' to the stack following slice 'n'.
addSlice(String, ImageProcessor, int) - Method in class ij.VirtualStack
  Does noting.
addSlice(String, Object) - Method in class ij.ImageStack
  Adds an image in the form of a pixel array to the end of the stack.
addSlice(String, Object) - Method in class ij.VirtualStack
  Does nothing.
addSlider(String, double, double, double) - Method in class ij.gui.GenericDialog
  Adds a slider (scroll bar) to the dialog box.
addSlider(String, double, double, double, double) - Method in class ij.gui.GenericDialog
  This vesion of addSlider() adds a 'stepSize' argument.
  Example: http://wsr.imagej.net/macros/SliderDemo.txt
addStringField(String, String) - Method in class ij.gui.GenericDialog
  Adds an 8 column text field.
addStringField(String, String, int) - Method in class ij.gui.GenericDialog
  Adds a text field.
addText(String, double, double) - Method in class ij.gui.Plot
addTextAreas(String, String, int, int) - Method in class ij.gui.GenericDialog
  Adds one or two (side by side) text areas.
addToArray(float[], float) - Static method in class ij.util.Tools
  Adds a number to all array elements
addToManager - Variable in class ij.plugin.filter.ParticleAnalyzer
addTool(String) - Method in class ij.gui.Toolbar
  Adds a tool to the toolbar.
addToOverlay() - Method in class ij.gui.PointRoi
addToOverlay() - Static method in class ij.plugin.filter.Analyzer
addToSameRow() - Method in class ij.gui.GenericDialog
  Makes the next item appear in the same row as the previous.
addToStack() - Method in class ij.gui.Plot
  Appends the current plot to a virtual stack and resets allPlotObjects for next slice N.
addUnsignedShortSlice(String, Object) - Method in class ij.ImageStack
  Deprecated.
  Short images are always unsigned.
addUserPoint(ImagePlus, double, double) - Method in class ij.gui.PointRoi
addValue(int, double) - Method in class ij.measure.ResultsTable
  Adds a numeric value to the specified column, on the last table row.
addValue(String, double) - Method in class ij.measure.ResultsTable
  Adds a numeric value to the specified column, on the last table row.
addValue(String, String) - Method in class ij.measure.ResultsTable
  Adds a string value to the specified column, on the last table row.
addWindow(Frame) - Static method in class ij.WindowManager
  Adds the specified Frame to the Window menu.
addWindow(Window) - Static method in class ij.WindowManager
  Adds the specified window to the Window menu.
adjustCalibration(Calibration) - Method in class ij.gui.Plot
  Adjusts a Calibration object to fit the current axes.
adjustmentValueChanged(AdjustmentEvent) - Method in class ij.gui.ColorChooser
adjustmentValueChanged(AdjustmentEvent) - Method in class ij.gui.GenericDialog
adjustmentValueChanged(AdjustmentEvent) - Method in class ij.gui.ScrollbarWithLabel
adjustmentValueChanged(AdjustmentEvent) - Method in class ij.gui.StackWindow
adjustmentValueChanged(AdjustmentEvent) - Method in class ij.plugin.frame.ColorThresholder
adjustmentValueChanged(AdjustmentEvent) - Method in class ij.plugin.frame.ContrastAdjuster
adjustmentValueChanged(AdjustmentEvent) - Method in class ij.plugin.frame.LineWidthAdjuster
adjustmentValueChanged(AdjustmentEvent) - Method in class ij.plugin.frame.ThresholdAdjuster
adjustmentValueChanged(AdjustmentEvent) - Method in class ij.plugin.Orthogonal_Views
adjustmentValueChanged(AdjustmentEvent) - Method in class ij.text.TextPanel
ALL_KEYS - Static variable in class ij.IJ
ALL_STATS - Static variable in interface ij.measure.Measurements
  All measurement options
allowRecording(boolean) - Method in class ij.plugin.frame.RoiManager
allPoints() - Static method in class ij.gui.Wand
  Returns 'true' if output contains intermediate points for straight lines longer than one pixel.
altKeyDown() - Static method in class ij.IJ
  Returns true if the alt key is down.
alwaysOnTop - Static variable in class ij.Prefs
  "ImageJ" window is always on top.
analyze(ImagePlus) - Method in class ij.plugin.filter.LineGraphAnalyzer
  Uses extracts a set of coordinate pairs from a digitized line graph.
analyze(ImagePlus) - Method in class ij.plugin.filter.ParticleAnalyzer
  Performs particle analysis on the current slice of the specified image.
analyze(ImagePlus, ImageProcessor) - Method in class ij.plugin.filter.ParticleAnalyzer
  Performs particle analysis on the specified ImagePlus and ImageProcessor.
analyzer - Variable in class ij.plugin.filter.ParticleAnalyzer
Analyzer - Class in ij.plugin.filter
  This plugin implements ImageJ's Analyze/Measure and Analyze/Set Measurements commands.
Analyzer() - Constructor for class ij.plugin.filter.Analyzer
Analyzer(ImagePlus) - Constructor for class ij.plugin.filter.Analyzer
  Constructs a new Analyzer using the specified ImagePlus object and the current measurement options and default results table.
Analyzer(ImagePlus, int, ResultsTable) - Constructor for class ij.plugin.filter.Analyzer
  Construct a new Analyzer using an ImagePlus object and private measurement options and a ResultsTable.
Analyzer(ImagePlus, ResultsTable) - Constructor for class ij.plugin.filter.Analyzer
  Construct a new Analyzer using an ImagePlus object and a ResultsTable.
and(int) - Method in class ij.process.FloatProcessor
and(int) - Method in class ij.process.ImageProcessor
  Binary AND of each pixel in the image or ROI with 'value'.
and(int) - Method in class ij.process.ShortProcessor
and(ShapeRoi) - Method in class ij.gui.ShapeRoi
  Unary intersection operator.
AND - Static variable in interface ij.process.Blitter
  dst=dst AND src
angle - Variable in class ij.process.EllipseFitter
  Angle in degrees
angle - Variable in class ij.process.ImageStatistics
  Angle in degrees of fitted ellipse
ANGLE - Static variable in class ij.gui.Roi
ANGLE - Static variable in class ij.gui.Toolbar
ANGLE - Static variable in class ij.measure.ResultsTable
angstromSymbol - Static variable in class ij.IJ
animationSelector - Variable in class ij.gui.StackWindow
Animator - Class in ij.plugin
  This plugin animates stacks.
Animator() - Constructor for class ij.plugin.Animator
antialiasedText - Static variable in class ij.Prefs
  No longer used
antialiasedText - Variable in class ij.process.ImageProcessor
antialiasedTools - Static variable in class ij.Prefs
  Draw tool icons using antialiasing (always true).
AppearanceOptions - Class in ij.plugin
  This plugin implements the Edit/Options/Appearance command.
AppearanceOptions() - Constructor for class ij.plugin.AppearanceOptions
append(String) - Method in class ij.plugin.frame.Editor
append(String) - Method in class ij.text.TextPanel
  Adds one or more lines to the end of this TextPanel.
append(String) - Method in class ij.text.TextWindow
  Adds one or more lines of text to the window.
append(String, String) - Static method in class ij.IJ
  Appends a string to the end of a file.
append(ArrayList) - Method in class ij.text.TextPanel
  Adds strings contained in an ArrayList to the end of this TextPanel.
appendLine(String) - Method in class ij.text.TextPanel
  Adds a single line to the end of this TextPanel.
appendToStack() - Method in class ij.gui.Plot
appendWithoutUpdate(String) - Method in class ij.text.TextPanel
  Adds a single line to the end of this TextPanel without updating the display.
applyLut() - Method in class ij.process.ByteProcessor
applyMacro(ImageProcessor, String, boolean) - Static method in class ij.plugin.filter.ImageMath
applyMacro(String) - Method in class ij.measure.ResultsTable
  Applies a macro to each row of the table; the columns are assigned variable names as given by getHeadingsAsVaribleNames().
applyMacro(String) - Method in class ij.process.ImageProcessor
  Uses the Process/Math/Macro command to apply macro code to this image.
applyTable(int[]) - Method in class ij.process.ByteProcessor
applyTable(int[]) - Method in class ij.process.ColorProcessor
applyTable(int[]) - Method in class ij.process.FloatProcessor
applyTable(int[]) - Method in class ij.process.ImageProcessor
  Transforms the image or ROI using a lookup table.
applyTable(int[]) - Method in class ij.process.ShortProcessor
  Transforms the pixel data using a 65536 entry lookup table.
applyTable(int[]) - Method in class ij.process.StackProcessor
applyTable(int[], int) - Method in class ij.process.ColorProcessor
area - Variable in class ij.process.ImageStatistics
AREA - Static variable in interface ij.measure.Measurements
AREA - Static variable in class ij.measure.ResultsTable
AREA_FRACTION - Static variable in interface ij.measure.Measurements
AREA_FRACTION - Static variable in class ij.measure.ResultsTable
areaFraction - Variable in class ij.process.ImageStatistics
ARG_ARRAY - Static variable in interface ij.macro.MacroExtension
ARG_NUMBER - Static variable in interface ij.macro.MacroExtension
ARG_OPTIONAL - Static variable in interface ij.macro.MacroExtension
ARG_OUTPUT - Static variable in interface ij.macro.MacroExtension
ARG_STRING - Static variable in interface ij.macro.MacroExtension
ARGB - Static variable in class ij.io.FileInfo
  32-bit interleaved ARGB.
argTypes - Variable in class ij.macro.ExtensionDescriptor
ARRAY - Static variable in interface ij.macro.MacroConstants
ARRAY_FUNC - Static variable in interface ij.macro.MacroConstants
ARRAY_FUNCTION - Static variable in interface ij.macro.MacroConstants
arrayFunctionIDs - Static variable in interface ij.macro.MacroConstants
arrayFunctions - Static variable in interface ij.macro.MacroConstants
ArrayUtil - Class in ij.util
ArrayUtil(float[]) - Constructor for class ij.util.ArrayUtil
  constructeur
ArrayUtil(int) - Constructor for class ij.util.ArrayUtil
  constructeur
Arrow - Class in ij.gui
  This is an Roi subclass for creating and displaying arrows.
Arrow(double, double, double, double) - Constructor for class ij.gui.Arrow
Arrow(int, int, ImagePlus) - Constructor for class ij.gui.Arrow
ARROW - Static variable in class ij.io.RoiDecoder
ARROW_HEAD_SIZE - Static variable in class ij.io.RoiDecoder
ARROW_STYLE - Static variable in class ij.io.RoiDecoder
ArrowTool - Class in ij.plugin.tool
ArrowTool() - Constructor for class ij.plugin.tool.ArrowTool
ArrowToolOptions - Class in ij.plugin
  This plugin implements the Edit/Options/Arrow Tool command.
ArrowToolOptions() - Constructor for class ij.plugin.ArrowToolOptions
ARTIST - Static variable in class ij.io.TiffDecoder
ASIN - Static variable in interface ij.macro.MacroConstants
asp_bk - Variable in class ij.gui.Roi
aspect - Variable in class ij.gui.Roi
ASPECT_RATIO - Static variable in class ij.measure.ResultsTable
ATAN - Static variable in interface ij.macro.MacroConstants
ATAN2 - Static variable in interface ij.macro.MacroConstants
AUTO_FORMAT - Static variable in class ij.measure.ResultsTable
AUTO_POSITION - Static variable in class ij.gui.Plot
  Legend positions
AUTO_UPDATE - Static variable in interface ij.macro.MacroConstants
autoClose - Static variable in class ij.gui.PlotWindow
  Automatically close window after saving values.
autoContrast - Static variable in class ij.Prefs
  Adjust contrast when scrolling stacks
autoLivePlots - Static variable in class ij.Prefs
  Turn live display on plots automatically
autoOutline(int, int) - Method in class ij.gui.Wand
  Traces the boundary of an area of uniform color, where 'startX' and 'startY' are somewhere inside the area.
autoOutline(int, int, double, double) - Method in class ij.gui.Wand
  Traces an object defined by lower and upper threshold values or an interior hole; whatever is found first ('legacy mode').
autoOutline(int, int, double, double, int) - Method in class ij.gui.Wand
  Traces an object defined by lower and upper threshold values.
autoOutline(int, int, double, int) - Method in class ij.gui.Wand
  Traces the boundary of the area with pixel values within 'tolerance' of the value of the pixel at the starting location.
autoOutline(int, int, int, int) - Method in class ij.gui.Wand
  This is a variation of legacy autoOutline that uses int threshold arguments.
autoRun() - Static method in class ij.plugin.MacroInstaller
  Runs the StartupMacros AutoRun macro on the current thread.
autoRunExamples - Static variable in class ij.Prefs
  Automatically run examples in Help/Examples menu.
autoThreshold() - Method in class ij.process.ColorProcessor
autoThreshold() - Method in class ij.process.FloatProcessor
  Not implemented.
autoThreshold() - Method in class ij.process.ImageProcessor
  Converts the image to binary using an automatically determined threshold.
AutoThresholder - Class in ij.process
  Autothresholding methods (limited to 256 bin histograms) from the Auto_Threshold plugin (http://fiji.sc/Auto_Threshold) by G.Landini at bham dot ac dot uk).
AutoThresholder() - Constructor for class ij.process.AutoThresholder
AutoThresholder.Method - Enum Class in ij.process
AVERAGE - Static variable in class ij.plugin.Binner
AVERAGE - Static variable in interface ij.process.Blitter
  dst=(dst+src)/2
AVG_METHOD - Static variable in class ij.plugin.ZProjector
AVI - Static variable in class ij.io.Opener
AVI_Reader - Class in ij.plugin
  ImageJ Plugin for reading an AVI file into an image stack (one slice per video frame) Restrictions and Notes: - Only few formats supported: - uncompressed 8 bit with palette (=LUT) - uncompressed 8 invalid input: '&' 16 bit grayscale - uncompressed 24 invalid input: '&' 32 bit RGB (alpha channel ignored) - uncompressed 32 bit AYUV (alpha channel ignored) - various YUV 4:2:2 and 4:2:0 compressed formats (i.e., formats with full luminance resolution, but reduced chroma resolution - png or jpeg-encoded individual frames.
AVI_Reader() - Constructor for class ij.plugin.AVI_Reader
AVI_Writer - Class in ij.plugin.filter
  This plugin implements the File/Save As/AVI command.
AVI_Writer() - Constructor for class ij.plugin.filter.AVI_Writer
avoidResliceInterpolation - Static variable in class ij.Prefs
  Avoid interpolation when re-slicing
AXIS_OPTIONS - Static variable in class ij.gui.PlotDialog
  Types of dialog.

## B

B(int[], int) - Static method in class ij.process.AutoThresholder
BACKGROUND_COLOR_CHANGED - Static variable in interface ij.IJEventListener
backgroundColor - Static variable in class ij.ImageJ
backgrounds - Static variable in class ij.plugin.Thresholder
BackgroundSubtracter - Class in ij.plugin.filter
  Implements ImageJ's Subtract Background command.
BackgroundSubtracter() - Constructor for class ij.plugin.filter.BackgroundSubtracter
BAR - Static variable in class ij.gui.Arrow
BAR - Static variable in class ij.gui.Plot
  Draw a histogram bar for each point (bars touch each other unless the x axis has categories set via the axis label.
BARE_OUTLINES - Static variable in class ij.plugin.filter.ParticleAnalyzer
BARG - Static variable in class ij.io.FileInfo
  32-bit interleaved BARG (MCID).
baseCM - Variable in class ij.process.ImageProcessor
BatchConverter - Class in ij.plugin
  This plugin implements the File/ /Convert command, which converts the images in a folder to a specified format.
BatchConverter() - Constructor for class ij.plugin.BatchConverter
BatchMeasure - Class in ij.plugin
  This plugin implements the File/Batch/Measure command, which measures all the images in a user-specified folder.
BatchMeasure() - Constructor for class ij.plugin.BatchMeasure
batchMode - Static variable in class ij.macro.Interpreter
BatchProcessor - Class in ij.plugin
  This plugin implements the File/Batch/Macro and File/Batch/Virtual Stack commands.
BatchProcessor() - Constructor for class ij.plugin.BatchProcessor
BCOLOR - Static variable in class ij.Prefs
beep() - Static method in class ij.IJ
  Emits an audio beep.
BEEP - Static variable in interface ij.macro.MacroConstants
Benchmark - Class in ij.plugin
  Implements the Plugins/Utilities/Run Benchmark command.
Benchmark - Class in ij.plugin.filter
  Implements the Plugins/Utilities/Run Benchmark command when the current image is 512x512 and RGB.
Benchmark() - Constructor for class ij.plugin.Benchmark
Benchmark() - Constructor for class ij.plugin.filter.Benchmark
BGR - Static variable in class ij.io.FileInfo
  24-bit interleaved BGR.
BICUBIC - Static variable in class ij.process.ImageProcessor
  Interpolation methods
bilevel(int[]) - Method in class ij.process.AutoThresholder
BILINEAR - Static variable in class ij.process.ImageProcessor
  Interpolation methods
bimodalTest(double[]) - Static method in class ij.process.AutoThresholder
bin(int) - Method in class ij.process.ImageProcessor
  Returns a copy of this image that has been reduced in size using binning.
Binary - Class in ij.plugin.filter
  Implements the Erode, Dilate, Open, Close, Outline, Skeletonize and Fill Holes commands in the Process/Binary submenu.
Binary() - Constructor for class ij.plugin.filter.Binary
BinaryInterpolator - Class in ij.process
BinaryInterpolator() - Constructor for class ij.process.BinaryInterpolator
BinaryProcessor - Class in ij.process
  This class processes binary images.
BinaryProcessor(ByteProcessor) - Constructor for class ij.process.BinaryProcessor
  Creates a BinaryProcessor from a ByteProcessor.
Binner - Class in ij.plugin
  This plugin implements the Image/Transform/Bin command.
Binner() - Constructor for class ij.plugin.Binner
binSize - Variable in class ij.process.ImageStatistics
BIT_DEPTH - Static variable in interface ij.macro.MacroConstants
BitBuffer - Class in ij.io
  A class for reading arbitrary numbers of bits from a byte array.
BitBuffer(byte[]) - Constructor for class ij.io.BitBuffer
BITMAP - Static variable in class ij.io.FileInfo
  1-bit black and white.
BITS_PER_SAMPLE - Static variable in class ij.io.TiffDecoder
BLACK - Static variable in class ij.process.ImageProcessor
  Value of pixels included in masks.
BLACK_AND_WHITE_LUT - Static variable in class ij.process.ImageProcessor
blackBackground - Static variable in class ij.Prefs
  Backgound is black in binary images
blackCanvas - Static variable in class ij.Prefs
  Use black image border.
Blitter - Interface in ij.process
  ImageJ bit blitting classes must implement this interface.
blue - Variable in class ij.plugin.filter.RGBStackSplitter
blues - Variable in class ij.io.FileInfo
blur(ImagePlus, double, double, double) - Static method in class ij.plugin.GaussianBlur3D
blur(ImageProcessor, double) - Method in class ij.plugin.filter.GaussianBlur
  Deprecated.
BLUR_MORE - Static variable in class ij.process.ImageProcessor
blur1Direction(FloatProcessor, double, double, boolean, int) - Method in class ij.plugin.filter.GaussianBlur
  Blur an image in one direction (x or y) by a Gaussian, using multiple threads on multiprocessor machines
blurFloat(FloatProcessor, double, double, double) - Method in class ij.plugin.filter.GaussianBlur
  Gaussian Filtering of a FloatProcessor.
blurGaussian(double) - Method in class ij.process.ImageProcessor
  Blurs the image by convolving with a Gaussian function.
blurGaussian(ImageProcessor, double) - Method in class ij.plugin.filter.GaussianBlur
  Gaussian Filtering of an ImageProcessor
blurGaussian(ImageProcessor, double, double, double) - Method in class ij.plugin.filter.GaussianBlur
  Gaussian Filtering of an ImageProcessor
bLUT1 - Variable in class ij.process.ImageProcessor
bLUT2 - Variable in class ij.process.ImageProcessor
BMP - Static variable in class ij.io.FileInfo
BMP - Static variable in class ij.io.Opener
BMP_Reader - Class in ij.plugin
  This plugin reads BMP files.
BMP_Reader() - Constructor for class ij.plugin.BMP_Reader
BMP_Writer - Class in ij.plugin
  Implements the File/Save As/BMP command.
BMP_Writer() - Constructor for class ij.plugin.BMP_Writer
boldFont - Variable in class ij.process.ImageProcessor
BOTTOM - Static variable in class ij.io.RoiDecoder
BOTTOM_LEFT - Static variable in class ij.gui.Plot
  Legend positions
BOTTOM_MARGIN - Static variable in class ij.gui.Plot
  Deprecated.
  Not a fixed value any more, use getDrawingFrame() to get the drawing area
BOTTOM_RIGHT - Static variable in class ij.gui.Plot
  Legend positions
boundingRect(int, int, int, int) - Method in class ij.plugin.frame.SyncWindows
  Compute bounding rectangle given current and old cursor locations.
BOX - Static variable in class ij.gui.Plot
  Display points using a square box-shaped mark.
BOX - Static variable in class ij.gui.PlotWindow
  Deprecated.
BREAK - Static variable in interface ij.macro.MacroConstants
BRIGHT_OUTLIERS - Static variable in class ij.plugin.filter.RankFilters
BrowserLauncher - Class in ij.plugin
  This plugin implements the File/Import/URL command and the commands in the Help menu that open web pages.
BrowserLauncher() - Constructor for class ij.plugin.BrowserLauncher
BRUSH_ROI - Static variable in class ij.gui.Toolbar
BrushTool - Class in ij.plugin.tool
  This class implements the Paintbrush Tool, which allows the user to draw on an image, or on an Overlay if "Paint on overlay" is enabled.
BrushTool() - Constructor for class ij.plugin.tool.BrushTool
bSyncAll - Variable in class ij.plugin.frame.SyncWindows
  Buttons for user control.
BUILD - Static variable in class ij.ImageJ
buildControlDialog(int, int) - Method in class ij.plugin.ZProjector
  Builds dialog to query users for projection parameters.
buildControlPanel() - Method in class ij.plugin.frame.SyncWindows
  Builds panel containing control buttons.
buildWindowList() - Method in class ij.plugin.frame.SyncWindows
  Builds list of open ImageWindows
builtInTools - Static variable in class ij.gui.Toolbar
bUnsyncAll - Variable in class ij.plugin.frame.SyncWindows
  Buttons for user control.
button - Variable in class ij.gui.MessageDialog
button - Variable in class ij.gui.WaitForUserDialog
BYTE - Static variable in class ij.plugin.filter.EDM
  Output type: new 8-bit image
BYTE_OVERWRITE - Static variable in class ij.plugin.filter.EDM
  Output type: overwrite current 8-bit image
ByteBlitter - Class in ij.process
  This class does bit blitting of byte images.
ByteBlitter(ByteProcessor) - Constructor for class ij.process.ByteBlitter
  Constructs a ByteBlitter from a ByteProcessor.
ByteProcessor - Class in ij.process
  This is an 8-bit image and methods that operate on that image.
ByteProcessor(int, int) - Constructor for class ij.process.ByteProcessor
  Creates a blank ByteProcessor of the specified dimensions.
ByteProcessor(int, int, byte[]) - Constructor for class ij.process.ByteProcessor
  Creates a ByteProcessor from a byte array.
ByteProcessor(int, int, byte[], ColorModel) - Constructor for class ij.process.ByteProcessor
  Creates a ByteProcessor from a pixel array and IndexColorModel.
ByteProcessor(ImageProcessor, boolean) - Constructor for class ij.process.ByteProcessor
  Creates a ByteProcessor from an ImageProcessor.
ByteProcessor(Image) - Constructor for class ij.process.ByteProcessor
  Creates a ByteProcessor from an AWT Image.
ByteProcessor(BufferedImage) - Constructor for class ij.process.ByteProcessor
  Creates a ByteProcessor from a TYPE_BYTE_GRAY BufferedImage.
ByteStatistics - Class in ij.process
  8-bit image statistics, including histogram.
ByteStatistics(ImageProcessor) - Constructor for class ij.process.ByteStatistics
  Construct an ImageStatistics object from a ByteProcessor using the standard measurement options (area, mean, mode, min and max) and no calibration.
ByteStatistics(ImageProcessor, int, Calibration) - Constructor for class ij.process.ByteStatistics
  Constructs a ByteStatistics object from a ByteProcessor using the specified measurement and calibration.

## C

C(int[], int) - Static method in class ij.process.AutoThresholder
C_POSITION - Static variable in class ij.io.RoiDecoder
c2hex(Color) - Static method in class ij.util.Tools
  Converts a Color to an 7 byte hex string starting with '#'.
cachedMask - Variable in class ij.gui.Roi
cal - Variable in class ij.gui.HistogramWindow
cal - Variable in class ij.process.ImageStatistics
calculate(String, ImagePlus, ImagePlus) - Method in class ij.plugin.ImageCalculator
  Deprecated.
  replaced by run(String,ImagePlus,ImagePlus)
calculateDistance(int, int, int, int) - Static method in class ij.gui.Plot
CALCULATOR - Static variable in interface ij.macro.MacroConstants
calibrate(ImagePlus) - Method in class ij.plugin.filter.Calibrator
  Calibrate an image with the function type defined previously.
CALIBRATE - Static variable in interface ij.macro.MacroConstants
calibrateConversions - Static variable in class ij.Prefs
  Calibrate image type conversions
calibrated() - Method in class ij.measure.Calibration
  Returns true if this image is density calibrated.
Calibration - Class in ij.measure
  Calibration objects contain an image's spatial and density calibration data.
Calibration() - Constructor for class ij.measure.Calibration
  Constructs a new Calibration object using the default values.
Calibration(ImagePlus) - Constructor for class ij.measure.Calibration
  Constructs a new Calibration object using the default values.
CalibrationBar - Class in ij.plugin
  This plugin implements the Analyze/Tools/Calibration Bar command.
CalibrationBar() - Constructor for class ij.plugin.CalibrationBar
calibrationFunction - Variable in class ij.io.FileInfo
Calibrator - Class in ij.plugin.filter
  Implements the Analyze/Calibrate command.
Calibrator() - Constructor for class ij.plugin.filter.Calibrator
CALL - Static variable in interface ij.macro.MacroConstants
cancelButton - Variable in class ij.gui.WaitForUserDialog
CANCELED - Static variable in class ij.IJ
cancelPressed() - Method in class ij.gui.SaveChangesDialog
  Returns true if the user dismissed dialog by pressing "Cancel".
cancelPressed() - Method in class ij.gui.YesNoCancelDialog
  Returns true if the user dismissed dialog by pressing "Cancel".
canEnlarge(int, int) - Method in class ij.gui.ImageCanvas
  Returns the size to which the window can be enlarged, or null if it can't be enlarged.
canImport(JComponent, DataFlavor[]) - Method in class ij.io.DragAndDropHandler
  Returns whether any of the transfer flavors is supported
CanvasResizer - Class in ij.plugin
  This plugin implements the Image/Adjust/Canvas Size command.
CanvasResizer() - Constructor for class ij.plugin.CanvasResizer
captureImage() - Method in class ij.plugin.ScreenGrabber
  Captures the active image window and returns it as an ImagePlus.
captureScreen() - Method in class ij.plugin.ScreenGrabber
  Captures the entire screen and returns it as an ImagePlus.
caSnapshot() - Method in class ij.process.ColorProcessor
  Used by the ContrastAdjuster
caSnapshot(boolean) - Method in class ij.process.ColorProcessor
  Used by the ContrastAdjuster
cChannel - Variable in class ij.plugin.frame.SyncWindows
  Checkboxes for user control.
cCoords - Variable in class ij.plugin.frame.SyncWindows
  Checkboxes for user control.
cCursor - Variable in class ij.plugin.frame.SyncWindows
  Checkboxes for user control.
center - Variable in class ij.gui.Roi
center(Window) - Static method in class ij.gui.GUI
center(Window, Component) - Static method in class ij.gui.GUI
  Positions the specified window in the center of the screen that contains target.
CENTER - Static variable in class ij.gui.Plot
  Text justification.
CENTER - Static variable in class ij.gui.TextRoi
CENTER_JUSTIFY - Static variable in class ij.process.ImageProcessor
  Center justify text.
CENTER_OF_MASS - Static variable in interface ij.measure.Measurements
centerDialog(boolean) - Method in class ij.gui.GenericDialog
  Display dialog centered on the primary screen.
centerNextImage() - Static method in class ij.gui.ImageWindow
  Causes the next image to be opened to be centered on the screen and displayed without informational text above the image.
centerOnImageJScreen(Window) - Static method in class ij.gui.GUI
  Positions the specified window in the center of the screen containing the "ImageJ" window.
CENTROID - Static variable in interface ij.measure.Measurements
cFrame - Variable in class ij.plugin.frame.SyncWindows
  Checkboxes for user control.
CHANGE_VALUES - Static variable in interface ij.macro.MacroConstants
changeFont(Font) - Method in class ij.gui.Plot
changeFont(Font) - Method in class ij.gui.PlotWindow
  Deprecated.
  use the corresponding method of the Plot class
changes - Variable in class ij.ImagePlus
  True if any changes have been made to this image.
changes - Variable in class ij.plugin.frame.Editor
CHANNEL - Static variable in class ij.measure.ResultsTable
ChannelArranger - Class in ij.plugin
  This plugin implements the Image/Colors/Arrange Channels command, which allows the user to change the order of channels.
ChannelArranger() - Constructor for class ij.plugin.ChannelArranger
channelLuts - Variable in class ij.io.FileInfo
Channels - Class in ij.plugin.frame
  Displays the ImageJ "Channels" dialog.
Channels() - Constructor for class ij.plugin.frame.Channels
ChannelSplitter - Class in ij.plugin
  This plugin implements the Image/Color/Split Channels command.
ChannelSplitter() - Constructor for class ij.plugin.ChannelSplitter
CHAPMAN - Static variable in class ij.measure.CurveFitter
  Constants for the built-in fit functions
CHAR_CODE_AT - Static variable in interface ij.macro.MacroConstants
CHECK_AVAILABLE_MEMORY - Static variable in class ij.gui.NewImage
checkArguments(Object[]) - Method in class ij.macro.ExtensionDescriptor
checkbox - Variable in class ij.gui.GenericDialog
checkForDuplicateName - Static variable in class ij.WindowManager
choice - Variable in class ij.gui.GenericDialog
chromaD50 - Variable in class ij.process.ColorSpaceConverter
  reference white in xyY coordinates
chromaD55 - Variable in class ij.process.ColorSpaceConverter
chromaD65 - Variable in class ij.process.ColorSpaceConverter
chromaD75 - Variable in class ij.process.ColorSpaceConverter
chromaWhitePoint - Variable in class ij.process.ColorSpaceConverter
CIRCLE - Static variable in class ij.gui.Plot
  Display points using a circle (5 pixels in diameter if line thicknessinvalid input: '<'=1, otherwise 7).
CIRCLE - Static variable in class ij.gui.PlotWindow
  Deprecated.
CIRCLE - Static variable in class ij.gui.PointRoi
CIRCULARITY - Static variable in interface ij.measure.Measurements
CIRCULARITY - Static variable in class ij.measure.ResultsTable
CircularRoiMaker - Class in ij.plugin
  This class implements the Process/FFT/Make Circular Selection command.
CircularRoiMaker() - Constructor for class ij.plugin.CircularRoiMaker
ClassChecker - Class in ij.plugin
  Checks for duplicate class and JAR files in the plugins folders.
ClassChecker() - Constructor for class ij.plugin.ClassChecker
clear() - Method in class ij.gui.Overlay
  Removes all the ROIs in this Overlay.
clear() - Method in class ij.text.TextPanel
  Deletes all the lines.
clear() - Method in class ij.util.FloatArray
  Removes all elements form this FloatArray.
clear(ImageProcessor) - Method in class ij.gui.TextRoi
clear(ImageProcessor) - Method in class ij.plugin.filter.Filler
CLEAR_WORKSHEET - Static variable in class ij.plugin.filter.ParticleAnalyzer
  Clear "Results" window before starting.
clearOutside(ImageProcessor) - Method in class ij.plugin.filter.Filler
  Deprecated.
  replaced by ImageProcessor.fillOutside(Roi)
clearSelection() - Method in class ij.text.TextPanel
  Deletes the selected lines.
clipboard - Variable in class ij.gui.Roi
Clipboard - Class in ij.plugin
  Copies/pastes images to/from the system clipboard.
Clipboard() - Constructor for class ij.plugin.Clipboard
clipHeight - Variable in class ij.gui.Roi
clipRectMargin() - Method in class ij.gui.Arrow
clipRectMargin() - Method in class ij.gui.Line
clipRectMargin() - Method in class ij.gui.PolygonRoi
clipRectMargin() - Method in class ij.gui.Roi
clipWidth - Variable in class ij.gui.Roi
clipX - Variable in class ij.gui.Roi
clipXMax - Variable in class ij.process.ImageProcessor
clipXMin - Variable in class ij.process.ImageProcessor
clipY - Variable in class ij.gui.Roi
clipYMax - Variable in class ij.process.ImageProcessor
clipYMin - Variable in class ij.process.ImageProcessor
clone() - Method in class ij.gui.ImageRoi
clone() - Method in class ij.gui.PointRoi
  Returns a copy of this PointRoi.
clone() - Method in class ij.gui.PolygonRoi
  Returns a copy of this PolygonRoi.
clone() - Method in class ij.gui.Roi
  Returns a copy of this roi.
clone() - Method in class ij.gui.ShapeRoi
  Returns a deep copy of this.
clone() - Method in class ij.gui.TextRoi
  Returns a copy of this TextRoi.
clone() - Method in class ij.ImagePlus
  Returns a shallow copy of this ImagePlus.
clone() - Method in class ij.io.FileInfo
clone() - Method in class ij.macro.Variable
clone() - Method in class ij.measure.Calibration
clone() - Method in class ij.measure.ResultsTable
  Duplicates this ResultsTable.
clone() - Method in class ij.process.ImageProcessor
  Returns a shallow copy of this ImageProcessor, where this image and the copy share pixel data.
clone() - Method in class ij.process.LUT
close() - Method in class ij.CompositeImage
close() - Method in class ij.gui.ImageWindow
  Removes this window from the window list and disposes of it.
close() - Method in class ij.gui.StackWindow
close() - Method in class ij.gui.WaitForUserDialog
close() - Method in class ij.ImagePlus
  Closes this image and sets the ImageProcessor to null.
close() - Method in class ij.io.LogStream
close() - Method in class ij.io.RandomAccessStream
close() - Method in class ij.macro.FunctionFinder
close() - Method in class ij.plugin.frame.Channels
close() - Method in class ij.plugin.frame.ColorPicker
close() - Method in class ij.plugin.frame.ColorThresholder
close() - Method in class ij.plugin.frame.Commands
  Overrides PlugInFrame.close().
close() - Method in class ij.plugin.frame.ContrastAdjuster
  Overrides close() in PlugInDialog.
close() - Method in class ij.plugin.frame.Editor
  Overrides close() in PlugInFrame.
close() - Method in class ij.plugin.frame.LineWidthAdjuster
  Overrides close() in PlugInFrame.
close() - Method in class ij.plugin.frame.MemoryMonitor
close() - Method in class ij.plugin.frame.PasteController
close() - Method in class ij.plugin.frame.PlugInDialog
  Closes this window.
close() - Method in class ij.plugin.frame.PlugInFrame
  Closes this window.
close() - Method in class ij.plugin.frame.Recorder
close() - Method in class ij.plugin.frame.RoiManager
  Overrides PlugInFrame.close().
close() - Method in class ij.plugin.frame.SyncWindows
close() - Method in class ij.plugin.frame.ThresholdAdjuster
  Overrides close() in PlugInFrame.
close() - Method in class ij.text.TextWindow
close(boolean) - Method in class ij.text.TextWindow
  Closes this TextWindow.
CLOSE - Static variable in interface ij.macro.MacroConstants
CLOSE - Static variable in class ij.plugin.filter.RankFilters
closeAll() - Static method in class ij.plugin.Commands
  Closes all image windows, or returns 'false' if the user cancels the unsaved changes dialog box.
closeAllWindows() - Static method in class ij.WindowManager
  Closes all windows.
closeAndRefocus() - Method in class ij.macro.FunctionFinder
closed - Variable in class ij.gui.ImageWindow
CLOSED - Static variable in class ij.ImagePlus
closingAll - Static variable in class ij.Prefs
  "Close All" command running
cm - Variable in class ij.process.ImageProcessor
cm2 - Variable in class ij.process.ImageProcessor
CMDS_KEY - Static variable in class ij.plugin.frame.Commands
CMYK - Static variable in class ij.io.FileInfo
  32-bit interleaved CMYK.
coefficients - Variable in class ij.io.FileInfo
COLOR - Static variable in class ij.CompositeImage
  Display modes (note: TRANSPARENT mode has not yet been implemented)
COLOR - Static variable in class ij.IJ
  Image display modes
COLOR - Static variable in interface ij.macro.MacroConstants
COLOR_256 - Static variable in class ij.ImagePlus
  8-bit indexed color
COLOR_MAP - Static variable in class ij.io.TiffDecoder
COLOR_PICKER_CLOSED - Static variable in interface ij.IJEventListener
COLOR_RGB - Static variable in class ij.ImagePlus
  32-bit RGB color
COLOR8 - Static variable in class ij.io.FileInfo
  8-bit unsigned integer with color lookup table.
ColorBlitter - Class in ij.process
  This class does bit blitting of RGB images.
ColorBlitter(ColorProcessor) - Constructor for class ij.process.ColorBlitter
  Constructs a ColorBlitter from a ColorProcessor.
ColorChooser - Class in ij.gui
  Displays a dialog that allows the user to select a color using three sliders.
ColorChooser(String, Color, boolean) - Constructor for class ij.gui.ColorChooser
  Constructs a ColorChooser using the specified title and initial color.
ColorChooser(String, Color, boolean, Frame) - Constructor for class ij.gui.ColorChooser
ColorPicker - Class in ij.plugin.frame
  Implements the Image/Color/Color Picker command.
ColorPicker() - Constructor for class ij.plugin.frame.ColorPicker
ColorProcessor - Class in ij.process
  This is an 32-bit RGB image and methods that operate on that image..
ColorProcessor(int, int) - Constructor for class ij.process.ColorProcessor
  Creates a blank ColorProcessor of the specified dimensions.
ColorProcessor(int, int, int[]) - Constructor for class ij.process.ColorProcessor
  Creates a ColorProcessor from a pixel array.
ColorProcessor(Image) - Constructor for class ij.process.ColorProcessor
  Creates a ColorProcessor from an AWT Image or BufferedImage.
colors - Static variable in class ij.CompositeImage
colors - Static variable in class ij.plugin.Colors
Colors - Class in ij.plugin
  This plugin implements most of the Edit/Options/Colors command.
Colors() - Constructor for class ij.plugin.Colors
ColorSpaceConverter - Class in ij.process
  ColorSpaceConverter
ColorSpaceConverter() - Constructor for class ij.process.ColorSpaceConverter
  Default constructor; uses D65 for the white point
ColorSpaceConverter(String) - Constructor for class ij.process.ColorSpaceConverter
  Constructor for setting a non-default white point
ColorStatistics - Class in ij.process
  RGB image statistics, including histogram.
ColorStatistics(ImageProcessor) - Constructor for class ij.process.ColorStatistics
  Construct an ImageStatistics object from a ColorProcessor using the standard measurement options (area, mean, mode, min and max).
ColorStatistics(ImageProcessor, int, Calibration) - Constructor for class ij.process.ColorStatistics
  Constructs a ColorStatistics object from a ColorProcessor using the specified measurement options.
ColorThresholder - Class in ij.plugin.frame
  Selects pixels according to hsb or rgb components.
ColorThresholder() - Constructor for class ij.plugin.frame.ColorThresholder
colorToString(Color) - Static method in class ij.plugin.Colors
  Converts a Color into a lowercase string ("red", "green", "#aa55ff", etc.).
colorToString2(Color) - Static method in class ij.plugin.Colors
  Converts a Color into a string ("Red", "Green", #aa55ff, etc.).
COLUMN_IN_USE - Static variable in class ij.measure.ResultsTable
COLUMN_NOT_FOUND - Static variable in class ij.measure.ResultsTable
columnDeleted() - Method in class ij.measure.ResultsTable
columnExists(int) - Method in class ij.measure.ResultsTable
  Returns 'true' if the specified column exists and is not empty.
columnExists(String) - Method in class ij.measure.ResultsTable
  Returns 'true' if the specified column exists and is not emptly.
combineHorizontally(ImageStack, ImageStack) - Method in class ij.plugin.StackCombiner
combineVertically(ImageStack, ImageStack) - Method in class ij.plugin.StackCombiner
COMMAND_IN_USE - Static variable in class ij.Menus
COMMAND_NOT_FOUND - Static variable in class ij.Menus
commandExecuting(String) - Method in interface ij.CommandListener
commandExecuting(String) - Method in class ij.plugin.EventListener
commandExecuting(String) - Method in class ij.plugin.frame.Commands
commandExecuting(String) - Method in class ij.plugin.frame.SyncWindows
commandExecuting(String) - Method in class ij.plugin.Orthogonal_Views
CommandFinder - Class in ij.plugin
CommandFinder() - Constructor for class ij.plugin.CommandFinder
commandInUse(String) - Static method in class ij.Menus
commandLineMacro() - Static method in class ij.Prefs
CommandListener - Interface in ij
  Plugins that implement this interface are notified when ImageJ is about to run a menu command.
CommandLister - Class in ij.plugin
  This class is used by the Plugins/Shortcuts/List Shortcuts command to display a list keyboard shortcuts.
CommandLister() - Constructor for class ij.plugin.CommandLister
commandPrefix - Static variable in class ij.plugin.MacroInstaller
Commands - Class in ij.plugin
  Runs miscellaneous File and Window menu commands.
Commands - Class in ij.plugin.frame
  This plugin implements the Plugins>Utiltiees>Recent Commands command.
Commands() - Constructor for class ij.plugin.Commands
Commands() - Constructor for class ij.plugin.frame.Commands
Compiler - Class in ij.plugin
  Compiles and runs plugins using the javac compiler.
Compiler() - Constructor for class ij.plugin.Compiler
COMPLETED - Static variable in interface ij.gui.RoiListener
completeReset() - Method in class ij.CompositeImage
COMPOSITE - Static variable in class ij.CompositeImage
  Display modes (note: TRANSPARENT mode has not yet been implemented)
COMPOSITE - Static variable in class ij.gui.Roi
COMPOSITE - Static variable in class ij.IJ
  Image display modes
COMPOSITE_ROIS - Static variable in class ij.plugin.filter.ParticleAnalyzer
  Use composite ROIs for particles with holes.
CompositeConverter - Class in ij.plugin
  This plugin implements the Image/Color/Make Composite command.
CompositeConverter() - Constructor for class ij.plugin.CompositeConverter
compositeImage - Variable in class ij.ImagePlus
CompositeImage - Class in ij
CompositeImage(ImagePlus) - Constructor for class ij.CompositeImage
CompositeImage(ImagePlus, int) - Constructor for class ij.CompositeImage
compositeRois - Variable in class ij.plugin.filter.ParticleAnalyzer
COMPOUND_FILTER - Static variable in class ij.Undo
COMPOUND_FILTER_DONE - Static variable in class ij.Undo
compression - Variable in class ij.io.FileInfo
COMPRESSION - Static variable in class ij.io.TiffDecoder
COMPRESSION_NONE - Static variable in class ij.io.FileInfo
COMPRESSION_UNKNOWN - Static variable in class ij.io.FileInfo
concatenate(ImagePlus[], boolean) - Method in class ij.plugin.Concatenator
  Concatenates two or more images or stacks.
concatenate(ImagePlus, ImagePlus, boolean) - Method in class ij.plugin.Concatenator
  Concatenate two images or stacks.
concatenateHyperstacks(ImagePlus[], String, boolean) - Method in class ij.plugin.Concatenator
  Obsolete, replaced by concatenate(images,keep) and Concatenator.run(images).
Concatenator - Class in ij.plugin
  This plugin, which concatenates two or more images or stacks, implements the Image/Stacks/Tools/Concatenate command.
Concatenator() - Constructor for class ij.plugin.Concatenator
conjugateMultiply(FHT) - Method in class ij.process.FHT
  Returns the image resulting from the point by point Hartley conjugate multiplication of this image and the specified image.
CONNECTED_CIRCLES - Static variable in class ij.gui.Plot
  Draw black lines between the dots and a circle with the given color at each dot
constrain - Variable in class ij.gui.Roi
CONSTRUCTING - Static variable in class ij.gui.Roi
containedPoints(Roi) - Method in class ij.gui.PointRoi
  Returns the points of this Roi that are contained in the specified area ROI.
contains(double, double) - Method in class ij.process.FloatPolygon
  Returns 'true' if the point (x,y) is inside this polygon.
contains(float, float) - Method in class ij.process.FloatPolygon
  A version of contains() that accepts float arguments.
contains(int, int) - Method in class ij.gui.Arrow
contains(int, int) - Method in class ij.gui.Line
contains(int, int) - Method in class ij.gui.OvalRoi
  Tests whether the center of the specified pixel is inside the boundary of this OvalRoi.
contains(int, int) - Method in class ij.gui.PointRoi
  Returns true if (x,y) is one of the points in this collection.
contains(int, int) - Method in class ij.gui.PolygonRoi
  Returns whether the center of pixel (x,y) is contained in the Roi.
contains(int, int) - Method in class ij.gui.Roi
  Returns whether the center of pixel (x,y) is contained in the Roi.
contains(int, int) - Method in class ij.gui.ShapeRoi
  Checks whether the center of the specified pixel inside of this ROI's shape boundaries.
contains(Roi) - Method in class ij.gui.Overlay
  Returns 'true' if this Overlay contains the specified ROI.
containsPoint(double, double) - Method in class ij.gui.OvalRoi
  Returns whether coordinate (x,y) is contained in the Roi.
containsPoint(double, double) - Method in class ij.gui.PolygonRoi
  Returns whether coordinate (x,y) is contained in the Roi.
containsPoint(double, double) - Method in class ij.gui.Roi
  Returns whether coordinate (x,y) is contained in the Roi.
containsPoint(double, double) - Method in class ij.gui.ShapeRoi
  Returns whether coordinate (x,y) is contained in the Roi.
containsRegex(String, String, boolean) - Static method in class ij.plugin.FolderOpener
CONTINUE - Static variable in interface ij.macro.MacroConstants
ContrastAdjuster - Class in ij.plugin.frame
  This plugin implements the Brightness/Contrast, Window/level and Color Balance commands, all in the Image/Adjust sub-menu.
ContrastAdjuster() - Constructor for class ij.plugin.frame.ContrastAdjuster
ContrastEnhancer - Class in ij.plugin
  Implements ImageJ's Process/Enhance Contrast command.
ContrastEnhancer() - Constructor for class ij.plugin.ContrastEnhancer
controlKeyDown() - Static method in class ij.IJ
  Returns true if the control key is down.
controlPanel() - Method in class ij.plugin.frame.SyncWindows
  Build window list display and button controls.
ControlPanel - Class in ij.plugin
  ControlPanel.
ControlPanel() - Constructor for class ij.plugin.ControlPanel
convert(int) - Method in class ij.process.MedianCut
  Uses Heckbert's median-cut algorithm to divide the color space defined by "hist" into "maxcubes" cubes.
convert(ImageProcessor) - Method in class ij.plugin.filter.ThresholdToSelection
  Returns a selection created from the thresholded pixels in the specified image, or null if there are no thresholded pixels.
convert(String) - Method in class ij.plugin.Converter
  Converts the ImagePlus to the specified image type.
CONVERT_TO_FLOAT - Static variable in interface ij.plugin.filter.PlugInFilter
  Set this flag to have the ImageProcessor that is passed to the run() method converted to a FloatProcessor.
convertAndCalibrate(ImagePlus, String) - Static method in class ij.process.ImageConverter
Converter - Class in ij.plugin
  Implements the conversion commands in the Image/Type submenu.
Converter() - Constructor for class ij.plugin.Converter
convertGrayJpegTo8Bits(ImagePlus) - Static method in class ij.io.Opener
  Converts the specified RGB image to 8-bits if the 3 channels are identical.
convertHSB32ToRGB() - Method in class ij.process.ImageConverter
  Converts a 3-slice (hue, saturation, brightness) 32-bit stack to RGB.
convertHSBToRGB() - Method in class ij.process.ImageConverter
  Converts a 3-slice (hue, saturation, brightness) 8-bit stack to RGB.
convertHyperstack(ImagePlus, ImagePlus) - Method in class ij.plugin.RGBStackConverter
convertImagesToStack() - Method in class ij.plugin.ImagesToStack
convertImagesToStack() - Method in class ij.plugin.StackEditor
convertIndexToPosition(int) - Method in class ij.ImagePlus
  Converts the stack index 'n' (one-based) into a hyperstack position (channel, slice, frame).
convertLabToRGB() - Method in class ij.process.ImageConverter
  Converts a Lab stack to RGB.
convertLineToArea(Roi) - Static method in class ij.gui.Roi
  Converts a line selection into an area (polygon or composite) selection.
  Author: Michael Schmid
convertOutputType(Variable, Object) - Static method in class ij.macro.ExtensionDescriptor
convertRGBStackToRGB() - Method in class ij.process.ImageConverter
  Converts a 2 or 3 slice 8-bit stack to RGB.
convertRGBtoIndexedColor(int) - Method in class ij.process.ImageConverter
  Converts an RGB image to 8-bits indexed color.
convertShortcutToCode(String) - Static method in class ij.Menus
convertStackToImages(ImagePlus) - Method in class ij.plugin.StackEditor
convertToByte() - Method in class ij.process.TypeConverter
  Converts processor to a ByteProcessor.
convertToByte(boolean) - Method in class ij.process.ImageProcessor
  Returns an 8-bit version of this image as a ByteProcessor.
convertToByte(int) - Method in class ij.process.MedianCut
  This is a version of convert that returns a ByteProcessor.
convertToByteProcessor() - Method in class ij.process.ImageProcessor
  Returns an 8-bit version of this image as a ByteProcessor.
convertToByteProcessor(boolean) - Method in class ij.process.ImageProcessor
  Returns an 8-bit version of this image as a ByteProcessor.
convertToColorProcessor() - Method in class ij.process.ImageProcessor
  Returns an RGB version of this image as a ColorProcessor.
convertToFloat() - Method in class ij.ImageStack
  Creates a float version of this stack.
convertToFloat() - Method in class ij.process.ImageProcessor
  Returns a 32-bit float version of this image as a FloatProcessor.
convertToFloat(float[]) - Method in class ij.process.TypeConverter
  Converts processor to a FloatProcessor.
convertToFloatProcessor() - Method in class ij.process.ImageProcessor
  Returns a 32-bit float version of this image as a FloatProcessor.
convertToGray16() - Method in class ij.process.ImageConverter
  Converts this ImagePlus to 16-bit grayscale.
convertToGray16() - Method in class ij.process.StackConverter
  Converts this Stack to 16-bit grayscale.
convertToGray32() - Method in class ij.process.ImageConverter
  Converts this ImagePlus to 32-bit grayscale.
convertToGray32() - Method in class ij.process.StackConverter
  Converts this Stack to 32-bit (float) grayscale.
convertToGray8() - Method in class ij.process.ImageConverter
  Converts this ImagePlus to 8-bit grayscale.
convertToGray8() - Method in class ij.process.StackConverter
  Converts this Stack to 8-bit grayscale.
convertToHSB() - Method in class ij.process.ImageConverter
  Converts an RGB image to a HSB (hue, saturation and brightness) stack.
convertToHSB32() - Method in class ij.process.ImageConverter
  Converts an RGB image to a 32-bit HSB (hue, saturation and brightness) stack.
convertToHSB32Hyperstack() - Method in class ij.process.StackConverter
  Converts the stack (which must be RGB) to a 3 channel (hue, saturation and brightness) 32-bit hyperstack.
convertToHSBHyperstack() - Method in class ij.process.StackConverter
  Converts the stack (which must be RGB) to a 3 channel (hue, saturation and brightness) hyperstack.
convertToImageProcessor(BufferedImage, int) - Static method in class ij.ImagePlus
  Extract pixels as an ImageProcessor from a single band of a BufferedImage.
convertToIndexedColor(int) - Method in class ij.process.StackConverter
  Converts the stack to 8-bits indexed color.
convertToLab() - Method in class ij.process.ImageConverter
  Converts an RGB image to a Lab stack.
convertToLabHyperstack() - Method in class ij.process.StackConverter
  Converts the stack (which must be RGB) to a 3 channel Lab hyperstack.
convertToMicrons - Static variable in class ij.Prefs
  Convert tiff units to microns if pixel width is less than 0.0001 cm.
convertToPolygon() - Method in class ij.gui.Roi
  Deprecated.
convertToRGB() - Method in class ij.process.ImageConverter
  Converts this ImagePlus to RGB.
convertToRGB() - Method in class ij.process.ImageProcessor
  Returns an RGB version of this image as a ColorProcessor.
convertToRGB() - Method in class ij.process.StackConverter
  Converts the Stack to RGB.
convertToRGB() - Method in class ij.process.TypeConverter
  Converts processor to a ColorProcessor.
convertToRGB(ImagePlus) - Static method in class ij.plugin.RGBStackConverter
  Converts the specified multi-channel (composite) image to RGB.
convertToRGBHyperstack() - Method in class ij.process.StackConverter
  Converts the stack (which must be RGB) to a 3 channel (red, green and blue) hyperstack.
convertToRGBStack() - Method in class ij.process.ImageConverter
  Converts an RGB image to an RGB (red, green and blue) stack.
convertToShort() - Method in class ij.process.TypeConverter
  Converts processor to a ShortProcessor.
convertToShort(boolean) - Method in class ij.process.ImageProcessor
  Returns a 16-bit version of this image as a ShortProcessor.
convertToShortProcessor() - Method in class ij.process.ImageProcessor
  Returns a 16-bit version of this image as a ShortProcessor.
convertToShortProcessor(boolean) - Method in class ij.process.ImageProcessor
  Returns a 16-bit version of this image as a ShortProcessor.
convertVariable(Interpreter, int, Variable) - Static method in class ij.macro.ExtensionDescriptor
convolve(float[], int, int) - Method in class ij.process.ByteProcessor
  Performs a convolution operation using the specified kernel.
convolve(float[], int, int) - Method in class ij.process.ColorProcessor
  Performs a convolution operation using the specified kernel.
convolve(float[], int, int) - Method in class ij.process.FloatProcessor
  Performs a convolution operation using the specified kernel.
convolve(float[], int, int) - Method in class ij.process.ImageProcessor
  Performs a convolution operation using the specified kernel.
convolve(float[], int, int) - Method in class ij.process.ShortProcessor
  Performs a convolution operation using the specified kernel.
convolve(ImageProcessor, float[], int, int) - Method in class ij.plugin.filter.Convolver
  Convolves `ip` with a kernel of width `kw` and height `kh`.
CONVOLVE - Static variable in class ij.process.ImageProcessor
convolve3x3(int[]) - Method in class ij.process.ByteProcessor
convolve3x3(int[]) - Method in class ij.process.ColorProcessor
  3x3 convolution contributed by Glynne Casteel.
convolve3x3(int[]) - Method in class ij.process.FloatProcessor
  Does 3x3 convolution.
convolve3x3(int[]) - Method in class ij.process.ImageProcessor
  Convolves the image or ROI with the specified 3x3 integer convolution kernel.
convolve3x3(int[]) - Method in class ij.process.ShortProcessor
  Does 3x3 convolution.
convolveFloat(ImageProcessor, float[], int, int) - Method in class ij.plugin.filter.Convolver
  Convolves the float image `ip` with a kernel of width `kw` and height `kh`.
convolveFloat1D(FloatProcessor, float[], int, int) - Method in class ij.plugin.filter.Convolver
  Convolves the image `ip` with a kernel of width `kw` and height `kh`.
convolveFloat1D(FloatProcessor, float[], int, int, double) - Method in class ij.plugin.filter.Convolver
  Convolves the image `ip` with a kernel of width `kw` and height `kh`.
Convolver - Class in ij.plugin.filter
  This plugin convolves images using user user defined kernels.
Convolver() - Constructor for class ij.plugin.filter.Convolver
Coordinates - Class in ij.plugin
  The plugin implements the Image/Adjust/Coordinates command.
Coordinates() - Constructor for class ij.plugin.Coordinates
COORDINATES - Static variable in class ij.io.RoiDecoder
copy - Variable in class ij.gui.HistogramWindow
copy() - Method in class ij.ImagePlus
  Copies the contents of the current selection, or the entire image if there is no selection, to the internal clipboard.
copy() - Method in class ij.measure.Calibration
  Returns a clone of this object.
copy(boolean) - Method in class ij.gui.ImageWindow
  Copies the current ROI to the clipboard.
copy(boolean) - Method in class ij.ImagePlus
  Copies the contents of the current selection to the internal clipboard.
COPY - Static variable in interface ij.process.Blitter
  dst=src
COPY_AXIS_STYLE - Static variable in class ij.gui.Plot
  Flag for copying from a template: copy axis style
COPY_CONTENTS_STYLE - Static variable in class ij.gui.Plot
  Flag for copying from a template: copy contents style
COPY_EXTRA_OBJECTS - Static variable in class ij.gui.Plot
  Flag for copying PlotObjects (curves...) from a template if the template has more PlotObjects than the Plot to copy to.
COPY_INVERTED - Static variable in interface ij.process.Blitter
  dst=255-src (8-bits and RGB)
COPY_LABELS - Static variable in class ij.gui.Plot
  Flag for copying from a template: copy style invalid input: '&' text of axis labels
COPY_LEGEND - Static variable in class ij.gui.Plot
  Flag for copying from a template: copy legend
COPY_SIZE - Static variable in class ij.gui.Plot
  Flag for copying from a template: copy plot size
COPY_TRANSPARENT - Static variable in interface ij.process.Blitter
  Copies with white pixels transparent.
COPY_ZERO_TRANSPARENT - Static variable in interface ij.process.Blitter
  Copies with zero pixels transparent.
copyAttributes(Roi) - Method in class ij.gui.Arrow
copyAttributes(Roi) - Method in class ij.gui.PointRoi
copyAttributes(Roi) - Method in class ij.gui.Roi
  Copy the attributes (outline color, fill color, outline width) of 'roi2' to the this selection.
copyAttributes(ImagePlus) - Method in class ij.ImagePlus
  Used internally.
copyBits(ImageStack, int, int, int) - Method in class ij.process.StackProcessor
copyBits(ImageProcessor, int, int, int) - Method in interface ij.process.Blitter
  Copies the image in 'src' to (x,y) using the specified mode.
copyBits(ImageProcessor, int, int, int) - Method in class ij.process.ByteBlitter
  Copies the byte image in 'ip' to (x,y) using the specified mode.
copyBits(ImageProcessor, int, int, int) - Method in class ij.process.ByteProcessor
  Copies the image contained in 'ip' to (xloc, yloc) using one of the transfer modes defined in the Blitter interface.
copyBits(ImageProcessor, int, int, int) - Method in class ij.process.ColorBlitter
  Copies the RGB image in 'ip' to (x,y) using the specified mode.
copyBits(ImageProcessor, int, int, int) - Method in class ij.process.ColorProcessor
  Copies the image contained in 'ip' to (xloc, yloc) using one of the transfer modes defined in the Blitter interface.
copyBits(ImageProcessor, int, int, int) - Method in class ij.process.FloatBlitter
  Copies the float image in 'ip' to (x,y) using the specified mode.
copyBits(ImageProcessor, int, int, int) - Method in class ij.process.FloatProcessor
  Copies the image contained in 'ip' to (xloc, yloc) using one of the transfer modes defined in the Blitter interface.
copyBits(ImageProcessor, int, int, int) - Method in class ij.process.ImageProcessor
  Copies the image contained in 'ip' to (xloc, yloc) using one of the transfer modes defined in the Blitter interface.
copyBits(ImageProcessor, int, int, int) - Method in class ij.process.ShortBlitter
  Copies the 16-bit image in 'ip' to (x,y) using the specified mode.
copyBits(ImageProcessor, int, int, int) - Method in class ij.process.ShortProcessor
  Copies the image contained in 'ip' to (xloc, yloc) using one of the transfer modes defined in the Blitter interface.
copyBits(ImageProcessor, int, int, int) - Method in class ij.process.StackProcessor
copyColumnHeaders - Static variable in class ij.Prefs
  Include column headers when copying tables to clipboard.
copyFile(File, File) - Static method in class ij.macro.Functions
copyFile(String, String) - Static method in class ij.util.Tools
  Copies the contents of the file at 'path1' to 'path2', returning an error message (as a non-empty string) if there is an error.
copyLuts(ImagePlus) - Method in class ij.CompositeImage
  Copies the LUTs and display mode of 'imp' to this image.
copyScale(ImagePlus) - Method in class ij.ImagePlus
  Copies the calibration of the specified image to this image.
copySelection() - Method in class ij.text.TextPanel
  Copies the current selection to the system clipboard.
copyToClipboard() - Method in class ij.gui.HistogramWindow
copyToSystem() - Method in class ij.ImagePlus
  Copies the contents of the current selection, or the entire image if there is no selection, to the system clipboard.
copyToSystem(ImagePlus) - Static method in class ij.plugin.Clipboard
  Copies the contents of the specified image, or selection, to the system clicpboard.
CORNER_DIAMETER - Static variable in class ij.gui.Toolbar
COS - Static variable in interface ij.macro.MacroConstants
count - Variable in class ij.gui.HistogramWindow
COUNT - Static variable in class ij.plugin.filter.MaximumFinder
  Do not create an image, just count maxima and add count to Results table
COUNTERS_OFFSET - Static variable in class ij.io.RoiDecoder
create() - Method in class ij.gui.Overlay
  Returns a new Overlay that has the same properties as this one.
create(double, double, double, double) - Static method in class ij.gui.Line
  Creates a new straight line selection using the specified starting and ending offscreen coordinates.
create(double, double, double, double) - Static method in class ij.gui.OvalRoi
  Creates an OvalRoi.
create(double, double, double, double) - Static method in class ij.gui.Roi
  Creates a rectangular ROI.
create(double, double, double, double, int) - Static method in class ij.gui.Roi
  Creates a rounded rectangular ROI.
create(double, double, String, Font) - Static method in class ij.gui.TextRoi
  Obsolete.
create(int, int, int, int) - Static method in class ij.ImageStack
  Creates a new ImageStack.
create(ImagePlus[]) - Static method in class ij.ImageStack
  Creates an ImageStack from an ImagePlus array.
create(String, double, double, Font) - Static method in class ij.gui.TextRoi
  Creates a TextRoi using the specified text and location.
create(String, String) - Method in class ij.plugin.frame.Editor
createBlankImage(int, int) - Static method in class ij.gui.GUI
  Obsolete
createByteImage(String, int, int, int, int) - Static method in class ij.gui.NewImage
createColorModel(FileInfo) - Method in class ij.io.FileOpener
  Returns an IndexColorModel for the image specified by this FileInfo.
createComposite(int, int, int, ImageStack[], boolean) - Method in class ij.plugin.RGBStackMerge
  Deprecated; replaced by mergeChannels().
CREATED - Static variable in interface ij.gui.RoiListener
createEmptyStack() - Method in class ij.ImagePlus
  Returns an empty image stack that has the same width, height and color table as this image.
createFloatImage(String, int, int, int, int) - Static method in class ij.gui.NewImage
createGrayscaleColorModel(boolean) - Static method in class ij.LookUpTable
createHyperStack(String, int, int, int, int) - Method in class ij.ImagePlus
  This method has been replaced by IJ.createHyperStack().
createHyperStack(String, int, int, int, int, int, int) - Static method in class ij.IJ
  Creates a new hyperstack.
createImage() - Method in class ij.process.ByteProcessor
createImage() - Method in class ij.process.ColorProcessor
createImage() - Method in class ij.process.FloatProcessor
  Create an 8-bit AWT image by scaling pixels in the range min-max to 0-255.
createImage() - Method in class ij.process.ImageProcessor
  Returns a copy of this image is the form of an AWT Image.
createImage() - Method in class ij.process.IntProcessor
  Create an 8-bit AWT image by scaling pixels in the range min-max to 0-255.
createImage() - Method in class ij.process.ShortProcessor
  Create an 8-bit AWT image by scaling pixels in the range min-max to 0-255.
createImage() - Method in class ij.process.SignedShortProcessor
  Create an 8-bit AWT image by scaling pixels in the range min-max to 0-255.
createImage(IndexColorModel) - Static method in class ij.plugin.LutLoader
  Creates a 256x32 image from an IndexColorModel.
createImage(String, int, int, int, int) - Static method in class ij.IJ
  Creates a new image.
createImage(String, int, int, int, int, int) - Static method in class ij.gui.NewImage
createImage(String, String, int, int, int) - Static method in class ij.IJ
  Creates a new imagePlus.
createImage(String, String, int, int, int, int, int) - Static method in class ij.IJ
  Creates a new hyperstack.
createImagePlus() - Method in class ij.ImagePlus
  Returns a new ImagePlus with this image's attributes (e.g.
createInputStream(FileInfo) - Method in class ij.io.FileOpener
  Returns an InputStream for the image described by this FileInfo.
createIntImage(String, int, int, int, int) - Static method in class ij.gui.NewImage
createInvertedLut() - Method in class ij.process.LUT
createLut() - Method in class ij.ImagePlus
  Creates a LookUpTable object that corresponds to this image.
createLutFromColor(Color) - Method in class ij.CompositeImage
createLutFromColor(Color) - Static method in class ij.process.LUT
  Creates a color LUT from a Color.
createMacro(String) - Method in class ij.plugin.NewPlugin
createMacro(String, String) - Method in class ij.plugin.frame.Editor
createMask() - Method in class ij.process.ByteProcessor
  Returns a binary mask, or null if a threshold is not set.
createMask() - Method in class ij.process.FloatProcessor
  Returns a binary mask, or null if a threshold is not set.
createMask() - Method in class ij.process.ImageProcessor
  Returns a binary mask, or null if a threshold is not set or this is an RGB image.
createMask() - Method in class ij.process.ShortProcessor
  Returns a binary mask, or null if a threshold is not set.
createMask(ImagePlus) - Static method in class ij.plugin.Thresholder
  Returns an 8-bit binary (0 and 255) threshold mask that has the same dimensions as this image.
createNewRoi(int, int) - Method in class ij.ImagePlus
  Starts the process of creating a new selection, where sx and sy are the starting screen coordinates.
createOverlay() - Static method in class ij.plugin.OverlayLabels
  Creates an empty Overlay that has the current label settings.
createPlugin(String, int, String) - Method in class ij.plugin.NewPlugin
createProcessor(int, int) - Method in class ij.process.ByteProcessor
  Returns a new, blank ByteProcessor with the specified width and height.
createProcessor(int, int) - Method in class ij.process.ColorProcessor
  Returns a new, blank ColorProcessor with the specified width and height.
createProcessor(int, int) - Method in class ij.process.FloatProcessor
  Returns a new, blank FloatProcessor with the specified width and height.
createProcessor(int, int) - Method in class ij.process.ImageProcessor
  Returns a new, blank processor with the specified width and height.
createProcessor(int, int) - Method in class ij.process.ShortProcessor
  Returns a new, blank ShortProcessor with the specified width and height.
createRGBImage(String, int, int, int, int) - Static method in class ij.gui.NewImage
createRoiMask() - Method in class ij.ImagePlus
  Returns an 8-bit binary (foreground=255, background=0) ROI or overlay mask that has the same dimensions as this image.
createShortImage(String, int, int, int, int) - Static method in class ij.gui.NewImage
  Creates an unsigned short image.
createStackOverlay(Roi[]) - Static method in class ij.gui.Overlay
createSubtitle() - Method in class ij.gui.ImageWindow
  Creates the subtitle.
createSubtitle() - Method in class ij.gui.StackWindow
createTableFromImage(ImageProcessor) - Static method in class ij.measure.ResultsTable
  Creates a ResultsTable from an image or image selection.
createThreadArray() - Static method in class ij.util.ThreadUtil
createThreadArray(int) - Static method in class ij.util.ThreadUtil
createThresholdMask() - Method in class ij.ImagePlus
  Returns an 8-bit binary threshold mask (foreground=255, background=0) that has the same dimensions as this image.
createUnsignedShortImage(String, int, int, int, int) - Static method in class ij.gui.NewImage
  Deprecated.
  Short images are always unsigned.
createWindow() - Method in class ij.gui.ProfilePlot
  Displays this profile plot in a window.
crop() - Method in class ij.ImagePlus
  Returns a copy this image or stack slice, cropped if there is an ROI.
crop() - Method in class ij.process.ByteProcessor
crop() - Method in class ij.process.ColorProcessor
crop() - Method in class ij.process.FloatProcessor
crop() - Method in class ij.process.ImageProcessor
  Returns a new processor containing an image that corresponds to the current ROI.
crop() - Method in class ij.process.ShortProcessor
crop(int, int) - Method in class ij.gui.Overlay
  Removes ROIs having positions outside of the interval defined by firstSlice and lastSlice.
crop(int, int, int, int) - Method in class ij.process.StackProcessor
  Crops the stack to the specified rectangle.
crop(int, int, int, int, int, int) - Method in class ij.gui.Overlay
  Removes ROIs having a C, Z or T coordinate outside the volume defined by firstC, lastC, firstZ, lastZ, firstT and lastT.
crop(int, int, int, int, int, int) - Method in class ij.ImageStack
  Creates a new stack by cropping this one.
crop(Roi) - Method in class ij.gui.PointRoi
crop(Roi[]) - Method in class ij.ImagePlus
  Multi-roi cropping with default "slice" option.
crop(Roi[], String) - Method in class ij.ImagePlus
  Returns an array of cropped images based on the provided list of rois.
crop(ImagePlus) - Method in class ij.plugin.Duplicator
  Returns a copy the current image or stack slice, cropped if there is a selection.
crop(Rectangle) - Method in class ij.gui.Overlay
crop(String) - Method in class ij.ImagePlus
  Returns a cropped copy this image or stack, where 'options' can be "stack", "slice", "whole-slice" or a range (e.g., "20-30").
cropAndSave(Roi[], String, String) - Method in class ij.ImagePlus
  Saves the contents of the ROIs in this overlay as separate images, where 'directory' is the directory path and 'format' is "tif", "png" or "jpg".
cropOverlay(Overlay, Rectangle) - Static method in class ij.plugin.Duplicator
CROSS - Static variable in class ij.gui.Plot
  Display points using an cross-shaped mark.
CROSS - Static variable in class ij.gui.PlotWindow
  Deprecated.
CROSS - Static variable in class ij.gui.PointRoi
CROSSHAIR - Static variable in class ij.gui.PointRoi
CROSSHAIR - Static variable in class ij.gui.Toolbar
crosshairCursor - Static variable in class ij.gui.ImageCanvas
cScaling - Variable in class ij.plugin.frame.SyncWindows
  Checkboxes for user control.
cSelector - Variable in class ij.gui.StackWindow
cSlice - Variable in class ij.plugin.frame.SyncWindows
  Checkboxes for user control.
cTable - Variable in class ij.ImageStack
cTable - Variable in class ij.process.ImageProcessor
CTZ - Static variable in class ij.plugin.HyperStackConverter
cubic(double) - Static method in class ij.process.ImageProcessor
currentMacroEditor - Static variable in class ij.plugin.frame.Editor
currentMemory() - Static method in class ij.IJ
  Returns the amount of memory currently being used by ImageJ.
currentSlice - Variable in class ij.ImagePlus
cursorOverImage() - Method in class ij.gui.ImageCanvas
  Returns 'true' if the cursor is over this image.
CurveFitter - Class in ij.measure
  Curve fitting class based on the Simplex method in the Minimizer class Notes on fitting polynomial functions: (i) The range of x values should not be too far from 0, especially for higher-order polynomials.
CurveFitter(double[], double[]) - Constructor for class ij.measure.CurveFitter
  Construct a new CurveFitter.
CUSTOM - Static variable in class ij.gui.Plot
  Draw shape using macro code
CUSTOM - Static variable in class ij.io.Opener
CUSTOM - Static variable in class ij.measure.Calibration
CUSTOM1 - Static variable in class ij.gui.Toolbar
CUSTOM2 - Static variable in class ij.gui.Toolbar
CUSTOM3 - Static variable in class ij.gui.Toolbar
CUSTOM4 - Static variable in class ij.gui.Toolbar
CUSTOM5 - Static variable in class ij.gui.Toolbar
CUSTOM6 - Static variable in class ij.gui.Toolbar
CUSTOM7 - Static variable in class ij.gui.Toolbar
cut() - Method in class ij.ImagePlus
  Copies the contents of the current selection to the internal clipboard and then clears the selection.
cx - Variable in class ij.process.ImageProcessor
cy - Variable in class ij.process.ImageProcessor
CZT - Static variable in class ij.plugin.HyperStackConverter

## D

d2s(double) - Static method in class ij.IJ
  Converts a number to a formatted string using 2 digits to the right of the decimal point.
d2s(double, int) - Static method in class ij.IJ
  Converts a number to a rounded formatted string.
d2s(double, int) - Static method in class ij.measure.ResultsTable
  This is a version of IJ.d2s() that uses scientific notation for small numbes that would otherwise display as zero.
d2s(double, int, int) - Static method in class ij.IJ
  Converts a number to a rounded formatted string.
D2S - Static variable in interface ij.macro.MacroConstants
D50 - Variable in class ij.process.ColorSpaceConverter
  reference white in XYZ coordinates
D55 - Variable in class ij.process.ColorSpaceConverter
D65 - Variable in class ij.process.ColorSpaceConverter
D75 - Variable in class ij.process.ColorSpaceConverter
DARK_BACKGROUND - Static variable in class ij.plugin.frame.ThresholdAdjuster
DARK_OUTLIERS - Static variable in class ij.plugin.filter.RankFilters
darkBlue - Static variable in class ij.plugin.filter.Analyzer
DATE_TIME - Static variable in class ij.io.TiffDecoder
debug(Interpreter, int) - Method in interface ij.macro.Debugger
debug(Interpreter, int) - Method in class ij.plugin.frame.Editor
DEBUG - Static variable in class ij.ImageJ
  Run ImageJ in debug mode.
DEBUG - Static variable in interface ij.macro.MacroConstants
DEBUG_LOC_KEY - Static variable in class ij.text.TextWindow
Debugger - Interface in ij.macro
debugInfo - Variable in class ij.io.FileInfo
debugMode - Static variable in class ij.IJ
  Use setDebugMode(boolean) to enable/disable debug mode.
debugMode - Variable in class ij.io.TiffDecoder
decimalPlaces - Variable in class ij.gui.HistogramWindow
decode(String) - Static method in class ij.plugin.Colors
  Converts a String with the color name or the hexadecimal representation of a color with 6 or 8 hex digits to a Color.
decode(String, Color) - Static method in class ij.plugin.Colors
  Converts a String with the color name or the hexadecimal representation of a color with 6 or 8 hex digits to a Color.
decodeDescriptionString(FileInfo) - Method in class ij.io.FileOpener
decodeEscaped(String, char) - Static method in class ij.util.Tools
  Decodes backslash-escaped characters from the String until the character 'delim' is found.
decodeToken(int) - Method in class ij.macro.Program
Default - Enum constant in enum class ij.process.AutoThresholder.Method
DEFAULT_FLAGS - Static variable in class ij.gui.Plot
  The default axisFlags, will be modified by PlotWindow.noGridLines and PlotWindow.noTicks (see getDefaultFlags)
DEFAULT_JPEG_QUALITY - Static variable in class ij.io.FileSaver
DEFAULT_PORT - Static variable in class ij.ImageJ
  Address of socket where Image accepts commands
DEFAULT_QUALITY - Static variable in class ij.plugin.JpegWriter
DEFAULT_VALUE_UNIT - Static variable in class ij.measure.Calibration
defaultChoiceIndexes - Variable in class ij.gui.GenericDialog
defaultColor - Static variable in class ij.gui.Roi
defaultColorModel - Static variable in class ij.process.ImageProcessor
defaultCursor - Static variable in class ij.gui.ImageCanvas
defaultDirectory - Static variable in class ij.gui.HistogramWindow
defaultFillColor - Static variable in class ij.gui.Roi
defaultResultsExtension() - Static method in class ij.Prefs
defaultStrings - Variable in class ij.gui.GenericDialog
defaultText - Variable in class ij.gui.GenericDialog
defaultValues - Variable in class ij.gui.GenericDialog
degreeSymbol - Static variable in class ij.IJ
deleteColumn(String) - Method in class ij.measure.ResultsTable
  Deletes the specified column.
DELETED - Static variable in interface ij.gui.RoiListener
deleteHandle(double, double) - Method in class ij.gui.PolygonRoi
deleteLastSlice() - Method in class ij.ImageStack
  Deletes the last slice in the stack.
deleteLastSlice() - Method in class ij.VirtualStack
  Deletes the last slice in the stack.
deletePoint(int) - Method in class ij.gui.PointRoi
deletePoint(int) - Method in class ij.gui.PolygonRoi
deleteRoi() - Method in class ij.ImagePlus
  Deletes the current region of interest.
deleteRow(int) - Method in class ij.measure.ResultsTable
  Deletes the specified row.
deleteRows(int, int) - Static method in class ij.IJ
  Deletes 'row1' through 'row2' of the "Results" window, where 'row1' and 'row2' must be in the range 0-Analyzer.getCounter()-1.
deleteRows(int, int) - Method in class ij.measure.ResultsTable
  Deletes the specified rows.
deleteSlice(int) - Method in class ij.gui.PlotVirtualStack
  Deletes the specified slice, where 1<=n<=nslices.
deleteSlice(int) - Method in class ij.ImageStack
  Deletes the specified slice, where 1<=n<=nslices.
deleteSlice(int) - Method in class ij.plugin.AVI_Reader
  Deletes the specified image from this virtual stack (if it is one), where 1<=n<=nslices.
deleteSlice(int) - Method in class ij.plugin.FileInfoVirtualStack
  Deletes the specified image, where 1<=n<=nImages.
deleteSlice(int) - Method in class ij.plugin.ListVirtualStack
  Deletes the specified image, where 1<=n<=nslices.
deleteSlice(int) - Method in class ij.VirtualStack
  Deletes the specified slice, where 1<=n<=nslices.
descaleX(int) - Method in class ij.gui.Plot
  Converts pixels to calibrated coordinates.
descaleY(int) - Method in class ij.gui.Plot
  Converts pixels to calibrated coordinates.
description - Variable in class ij.io.FileInfo
deselect() - Method in class ij.plugin.frame.RoiManager
deselect(Roi) - Method in class ij.plugin.frame.RoiManager
  Deselect the specified ROI if it is the only one selected.
deserialize(byte[]) - Method in class ij.io.Opener
  Deserialize a byte array that was serialized using the FileSaver.serialize().
DESPECKLE - Static variable in class ij.plugin.filter.RankFilters
destroy() - Method in class ij.ImageJApplet
dfht3(float[], int, boolean, int) - Method in class ij.process.FHT
  Performs an optimized 1D FHT of an array or part of an array.
DIALOG - Static variable in interface ij.macro.MacroConstants
dialogCancelButtonOnRight - Static variable in class ij.Prefs
  Dialog "Cancel" button is on right on Linux
dialogItemChanged(GenericDialog, AWTEvent) - Method in interface ij.gui.DialogListener
  This method is invoked by a Generic Dialog if any of the inputs have changed (CANCEL does not trigger it; OK and running the dialog from a macro only trigger the first DialogListener added to a GenericDialog).
dialogItemChanged(GenericDialog, AWTEvent) - Method in class ij.gui.PlotContentsDialog
dialogItemChanged(GenericDialog, AWTEvent) - Method in class ij.gui.PlotDialog
  This method is called when the user changes something in the dialog.
dialogItemChanged(GenericDialog, AWTEvent) - Method in class ij.gui.RoiDefaultsDialog
dialogItemChanged(GenericDialog, AWTEvent) - Method in class ij.measure.ResultsTableMacros
dialogItemChanged(GenericDialog, AWTEvent) - Method in class ij.plugin.AppearanceOptions
dialogItemChanged(GenericDialog, AWTEvent) - Method in class ij.plugin.ArrowToolOptions
dialogItemChanged(GenericDialog, AWTEvent) - Method in class ij.plugin.CircularRoiMaker
dialogItemChanged(GenericDialog, AWTEvent) - Method in class ij.plugin.Coordinates
dialogItemChanged(GenericDialog, AWTEvent) - Method in class ij.plugin.filter.BackgroundSubtracter
dialogItemChanged(GenericDialog, AWTEvent) - Method in class ij.plugin.filter.Binary
dialogItemChanged(GenericDialog, AWTEvent) - Method in class ij.plugin.filter.Convolver
dialogItemChanged(GenericDialog, AWTEvent) - Method in class ij.plugin.filter.GaussianBlur
  Listener to modifications of the input fields of the dialog
dialogItemChanged(GenericDialog, AWTEvent) - Method in class ij.plugin.filter.ImageMath
dialogItemChanged(GenericDialog, AWTEvent) - Method in class ij.plugin.filter.MaximumFinder
  Read the parameters (during preview or after showing the dialog)
dialogItemChanged(GenericDialog, AWTEvent) - Method in class ij.plugin.filter.PlugInFilterRunner
  The listener to any change in the dialog.
dialogItemChanged(GenericDialog, AWTEvent) - Method in class ij.plugin.filter.RankFilters
dialogItemChanged(GenericDialog, AWTEvent) - Method in class ij.plugin.filter.Rotator
dialogItemChanged(GenericDialog, AWTEvent) - Method in class ij.plugin.filter.StackLabeler
dialogItemChanged(GenericDialog, AWTEvent) - Method in class ij.plugin.filter.Translator
dialogItemChanged(GenericDialog, AWTEvent) - Method in class ij.plugin.filter.UnsharpMask
dialogItemChanged(GenericDialog, AWTEvent) - Method in class ij.plugin.Grid
dialogItemChanged(GenericDialog, AWTEvent) - Method in class ij.plugin.HyperStackReducer
dialogItemChanged(GenericDialog, AWTEvent) - Method in class ij.plugin.OverlayLabels
dialogItemChanged(GenericDialog, AWTEvent) - Method in class ij.plugin.PointToolOptions
dialogItemChanged(GenericDialog, AWTEvent) - Method in class ij.plugin.RectToolOptions
dialogItemChanged(GenericDialog, AWTEvent) - Method in class ij.plugin.RGBStackConverter
dialogItemChanged(GenericDialog, AWTEvent) - Method in class ij.plugin.RoiEnlarger
dialogItemChanged(GenericDialog, AWTEvent) - Method in class ij.plugin.SpecifyROI
dialogItemChanged(GenericDialog, AWTEvent) - Method in class ij.plugin.Text
dialogItemChanged(GenericDialog, AWTEvent) - Method in class ij.plugin.WandToolOptions
DialogListener - Interface in ij.gui
  PlugIns or PlugInFilters that want to listen to changes in a GenericDialog without adding listeners for each dialog field should implementthis method.
DIAMOND - Static variable in class ij.gui.Plot
  Display points using an diamond-shaped mark.
DICOM - Class in ij.plugin
  This plugin decodes DICOM files.
DICOM - Static variable in class ij.io.FileInfo
DICOM - Static variable in class ij.io.Opener
DICOM() - Constructor for class ij.plugin.DICOM
  Default constructor.
DICOM(BufferedInputStream) - Constructor for class ij.plugin.DICOM
  Constructs a DICOM reader that using an BufferredInputStream.
DICOM(InputStream) - Constructor for class ij.plugin.DICOM
  Constructs a DICOM reader that using an InputStream.
DicomTools - Class in ij.util
  DICOM utilities
DicomTools() - Constructor for class ij.util.DicomTools
DIFFERENCE - Static variable in interface ij.process.Blitter
  dst=abs(dst-src)
digits - Variable in class ij.gui.HistogramWindow
dilate() - Method in class ij.process.ByteProcessor
dilate() - Method in class ij.process.ColorProcessor
dilate() - Method in class ij.process.FloatProcessor
  Not implemented.
dilate() - Method in class ij.process.ImageProcessor
  Dilates the image or ROI using a 3x3 minimum filter.
dilate() - Method in class ij.process.ShortProcessor
  Not implemented.
dilate(int, int) - Method in class ij.process.ByteProcessor
dimensionsSet - Variable in class ij.ImagePlus
DIR_IMAGE - Static variable in class ij.Prefs
directory - Variable in class ij.io.FileInfo
DirectoryChooser - Class in ij.io
  This class displays a dialog box that allows the user can select a directory.
DirectoryChooser(String) - Constructor for class ij.io.DirectoryChooser
  Display a dialog using the specified title.
disableChromaSubsampling(boolean) - Static method in class ij.plugin.JpegWriter
disableCommandRecording() - Static method in class ij.plugin.frame.Recorder
disableDensityCalibration() - Method in class ij.measure.Calibration
disablePathRecording() - Static method in class ij.plugin.frame.Recorder
  Temporarily disables path recording.
disablePopupMenu(boolean) - Method in class ij.gui.ImageCanvas
  Disable/enable popup menu.
disableReset(boolean) - Method in class ij.plugin.filter.Analyzer
  Used by RoiManager.multiMeasure() to suppress save as dialogs.
disableRowLabels() - Method in class ij.measure.ResultsTable
  Set the row label column to null if the column label is "Label".
disableUndo - Static variable in class ij.Prefs
  Disable Edit/Undo command.
dispatch(Functions) - Method in class ij.macro.ExtensionDescriptor
display(String, String) - Method in class ij.plugin.frame.Editor
DISPLAY_SUMMARY - Static variable in class ij.plugin.filter.ParticleAnalyzer
  Display a summary.
displayChanged(DisplayChangeEvent) - Method in class ij.plugin.frame.SyncWindows
  Method to pass on changes of the z-slice of a stack.
displayComplex - Static variable in class ij.plugin.FFT
displayCounts() - Method in class ij.gui.PointRoi
displayDialog(boolean) - Method in class ij.plugin.AVI_Reader
displayFHT - Static variable in class ij.plugin.FFT
displayRanges - Variable in class ij.io.FileInfo
displayRawPS - Static variable in class ij.plugin.FFT
displayResults() - Method in class ij.plugin.filter.Analyzer
  Writes the last row in the system results table to the Results window.
displaySummary - Variable in class ij.plugin.filter.ParticleAnalyzer
dispose() - Method in class ij.gui.GenericDialog
  Closes the dialog; records the options
dispose() - Method in class ij.gui.HTMLDialog
dispose() - Method in class ij.gui.NonBlockingGenericDialog
dispose() - Method in class ij.gui.Plot
  Releases the ImageProcessor and ImagePlus associated with the plot.
dispose() - Method in class ij.gui.PlotWindow
  Releases the resources used by this PlotWindow
Distribution - Class in ij.plugin
  This plugin implements the Analyze/Distribution command.
Distribution() - Constructor for class ij.plugin.Distribution
DIV_BY_ZERO_VALUE - Static variable in class ij.Prefs
DIV_EQUAL - Static variable in interface ij.macro.MacroConstants
divide(FHT) - Method in class ij.process.FHT
  Returns the image resulting from the point by point Hartley division of this image by the specified image.
DIVIDE - Static variable in interface ij.process.Blitter
  dst=dst/src
divideByZeroValue - Static variable in class ij.process.FloatBlitter
dmode - Variable in class ij.process.ImageStatistics
  Mode
DO - Static variable in interface ij.macro.MacroConstants
DO_COMMAND - Static variable in interface ij.macro.MacroConstants
DO_WAND - Static variable in interface ij.macro.MacroConstants
doClear() - Method in class ij.text.TextPanel
  Implements the Clear command.
doCommand(ImagePlus, String) - Static method in class ij.IJ
  Runs a menu command on a separete thread, using the specified image.
doCommand(String) - Static method in class ij.IJ
  Runs a menu command on a separete thread and returns immediately.
doCustomFit(UserFunction, int, String, double[], double[], boolean) - Method in class ij.measure.CurveFitter
  Fit a function defined in a user plugin implementing the UserFunction interface Use getStatus() and/or getStatusString() to see whether fitting was (probably) successful and getParams() to access the result.
doCustomFit(String, double[], boolean) - Method in class ij.measure.CurveFitter
  Fit a function defined as a macro String like "y = a + b*x + c*x*x".
DOES_16 - Static variable in interface ij.plugin.filter.PlugInFilter
  Set this flag if the filter handles 16-bit images.
DOES_32 - Static variable in interface ij.plugin.filter.PlugInFilter
  Set this flag if the filter handles float images.
DOES_8C - Static variable in interface ij.plugin.filter.PlugInFilter
  Set this flag if the filter handles 8-bit indexed color images.
DOES_8G - Static variable in interface ij.plugin.filter.PlugInFilter
  Set this flag if the filter handles 8-bit grayscale images.
DOES_ALL - Static variable in interface ij.plugin.filter.PlugInFilter
  Set this flag if the filter handles all types of images.
DOES_RGB - Static variable in interface ij.plugin.filter.PlugInFilter
  Set this flag if the filter handles RGB images.
DOES_STACKS - Static variable in interface ij.plugin.filter.PlugInFilter
  Set this flag if the filter wants its run() method to be called for all the slices in a stack.
doFit(int) - Method in class ij.measure.CurveFitter
  Perform curve fitting with one of the built-in functions doFit(fitType) does the fit quietly Use getStatus() and/or getStatusString() to see whether fitting was (probably) successful and getParams() to access the result.
doFit(int) - Method in class ij.plugin.frame.Fitter
  Fit data in the textArea, show result in log and create plot.
doFit(int, boolean) - Method in class ij.measure.CurveFitter
  Perform curve fitting with one of the built-in functions doFit(fitType, true) pops up a dialog allowing the user to set the initial fit parameters and various numbers controlling the Minimizer Use getStatus() and/or getStatusString() to see whether fitting was (probably) successful and getParams() to access the result.
doHyperStackProjection(boolean) - Method in class ij.plugin.ZProjector
doInclude(String) - Static method in class ij.plugin.frame.Editor
  Process optional #include statment at begining of macro.
doMath(ImagePlus, ImagePlus) - Method in class ij.plugin.FFTMath
done - Variable in class ij.gui.StackWindow
done() - Method in class ij.macro.Interpreter
DONE - Static variable in interface ij.plugin.filter.PlugInFilter
  Set this flag if the filter does not want its run method called.
doNotSaveWindowLocations - Static variable in class ij.Prefs
  Enable this option to workaround a bug with some Linux window managers that causes windows to wander down the screen.
dontSaveHeaders - Static variable in class ij.Prefs
  Don't save Results table column headers
dontSaveRowNumbers - Static variable in class ij.Prefs
  Don't save Results table row numbers
doOptions() - Method in class ij.plugin.Profiler
doProjection() - Method in class ij.plugin.ZProjector
  Performs actual projection using specified method.
doProjection(boolean) - Method in class ij.plugin.ZProjector
  Performs actual projection using specified method.
doRGBProjection() - Method in class ij.plugin.ZProjector
doRGBProjection(boolean) - Method in class ij.plugin.ZProjector
DOT - Static variable in class ij.gui.Plot
  Display points using a single pixel.
DOT - Static variable in class ij.gui.PointRoi
DOUBLE_CLICK_THRESHOLD - Static variable in class ij.gui.Toolbar
DOUBLE_HEADED - Static variable in class ij.io.RoiDecoder
DOUBLE_HEADED_KEY - Static variable in class ij.gui.Arrow
doubleBuffer - Static variable in class ij.Prefs
  No longer used
doWand(int, int) - Static method in class ij.IJ
  Equivalent to clicking on the current image at (x,y) with the wand tool.
doWand(int, int, double, String) - Static method in class ij.IJ
  Traces the boundary of the area with pixel values within 'tolerance' of the value of the pixel at the starting location.
doWand(ImagePlus, int, int, double, String) - Static method in class ij.IJ
  This version of doWand adds an ImagePlus argument.
download(String, String) - Static method in class ij.plugin.PluginInstaller
downloadJar(String) - Static method in class ij.plugin.Macro_Runner
DownsizeTable - Class in ij.process
  A table for easier downsizing by convolution with a kernel.
DragAndDrop - Class in ij.plugin
  This class opens images, roi's, luts and text files dragged and dropped on the "ImageJ" window.
DragAndDrop() - Constructor for class ij.plugin.DragAndDrop
DragAndDropHandler - Class in ij.io
  This class handles draginvalid input: '&drop' onto JFileChoosers.
DragAndDropHandler(JFileChooser) - Constructor for class ij.io.DragAndDropHandler
  Given a JFileChooser 'fc', this is how to use this class:
dragEnter(DropTargetDragEvent) - Method in class ij.plugin.DragAndDrop
dragExit(DropTargetEvent) - Method in class ij.plugin.DragAndDrop
dragOver(DropTargetDragEvent) - Method in class ij.plugin.DragAndDrop
draw() - Method in class ij.gui.Plot
  Draws the plot specified for the first time.
draw() - Method in class ij.gui.PlotWindow
  Displays the plot.
draw() - Method in class ij.ImagePlus
  Draws the image.
draw(int, int, int, int) - Method in class ij.ImagePlus
  Draws image and roi outline using a clip rect.
draw(Roi) - Method in class ij.process.ImageProcessor
  Draws the specified ROI on this image using the line width and color defined by ip.setLineWidth() and ip.setColor().
draw(ImagePlus, int, double, double, int) - Method in class ij.gui.HistogramPlot
  Plots a histogram using the specified title, number of bins and histogram range.
draw(ImagePlus, ImageStatistics) - Method in class ij.gui.HistogramPlot
  Draws the histogram using the specified title and ImageStatistics.
draw(ImageProcessor) - Method in class ij.plugin.filter.Filler
  Deprecated.
  replaced by ImageProcessor.draw(Roi)
draw(Graphics) - Method in class ij.gui.Arrow
  Draws this arrow on the image.
draw(Graphics) - Method in class ij.gui.EllipseRoi
draw(Graphics) - Method in class ij.gui.ImageRoi
draw(Graphics) - Method in class ij.gui.Line
  Draws this line on the image.
draw(Graphics) - Method in class ij.gui.OvalRoi
draw(Graphics) - Method in class ij.gui.PointRoi
  Draws the points on the image.
draw(Graphics) - Method in class ij.gui.PolygonRoi
draw(Graphics) - Method in class ij.gui.Roi
draw(Graphics) - Method in class ij.gui.RotatedRectRoi
draw(Graphics) - Method in class ij.gui.ShapeRoi
  Non-destructively draws the shape of this object on the associated ImagePlus.
draw(Graphics) - Method in class ij.gui.TextRoi
  Draws the text on the screen, clipped to the ROI.
draw(String, ImagePlus, int) - Method in class ij.gui.HistogramPlot
  Plots a histogram using the specified title and number of bins.
DRAW_LINE - Static variable in interface ij.macro.MacroConstants
DRAW_OFFSET - Static variable in class ij.io.RoiDecoder
DRAW_OVAL - Static variable in interface ij.macro.MacroConstants
DRAW_RECT - Static variable in interface ij.macro.MacroConstants
DRAW_STRING - Static variable in interface ij.macro.MacroConstants
drawArrow(int, int, int, int, double) - Method in class ij.gui.Plot
  Deprecated.
  Use as a public method is not supported any more because it is incompatible with rescaling
drawBackgrounds(boolean) - Method in class ij.gui.Overlay
drawColorBar(Graphics, int, int, int, int) - Method in class ij.LookUpTable
drawDot(int, int) - Method in class ij.process.ImageProcessor
  Draws a dot using the current line width and fill/draw value.
drawDot2(int, int) - Method in class ij.process.ImageProcessor
  Deprecated.
drawDottedLine(double, double, double, double, int) - Method in class ij.gui.Plot
  Draws a line using the coordinate system defined by setLimits().
drawEllipse(ImageProcessor) - Method in class ij.process.EllipseFitter
  Draws the ellipse on the specified image.
drawEllipse(ImageProcessor) - Method in class ij.process.ImageStatistics
drawHistogram(ImageProcessor, boolean) - Method in class ij.gui.HistogramPlot
drawHistogram(ImageProcessor, boolean) - Method in class ij.gui.HistogramWindow
drawInfo(Graphics) - Method in class ij.gui.ImageWindow
  Draws the subtitle.
drawingColor - Variable in class ij.process.ImageProcessor
drawLabel(ImagePlus, ImageProcessor, int, Rectangle) - Method in class ij.plugin.filter.Filler
drawLabels(boolean) - Method in class ij.gui.Overlay
drawLabels(boolean) - Static method in class ij.plugin.filter.Analyzer
drawLine(double, double, double, double) - Method in class ij.gui.Plot
  Draws a line using the coordinate system defined by setLimits().
drawLine(int, int) - Method in class ij.gui.Line
drawLine(int, int, int, int) - Method in class ij.process.ImageProcessor
  Draws a line from (x1,y1) to (x2,y2).
drawLine4(int, int, int, int) - Method in class ij.process.ImageProcessor
drawNames(boolean) - Method in class ij.gui.Overlay
drawNormalizedLine(double, double, double, double) - Method in class ij.gui.Plot
  Draws a line using a normalized 0-1, 0-1 coordinate system, with (0,0) at the top left and (1,1) at the lower right corner.
drawOval(int, int, int, int) - Method in class ij.process.ImageProcessor
  Draws an elliptical shape.
drawOverlay(Overlay) - Method in class ij.process.ImageProcessor
  Draws the specified Overlay on this image.
drawOverlay(Graphics) - Method in class ij.gui.Roi
drawOverlay(Graphics) - Method in class ij.gui.TextRoi
drawParticle(ImageProcessor, Roi, ImageStatistics, ImageProcessor) - Method in class ij.plugin.filter.ParticleAnalyzer
  Draws a selected particle in a separate image.
drawPixel(int, int) - Method in class ij.process.ByteProcessor
  Draws a pixel in the current foreground color.
drawPixel(int, int) - Method in class ij.process.ColorProcessor
  Draws a pixel in the current foreground color.
drawPixel(int, int) - Method in class ij.process.FloatProcessor
  Draws a pixel in the current foreground color.
drawPixel(int, int) - Method in class ij.process.ImageProcessor
  Sets the pixel at (x,y) to the current fill/draw value.
drawPixel(int, int) - Method in class ij.process.ShortProcessor
  Draws a pixel in the current foreground color.
drawPixels() - Method in class ij.gui.Roi
  Deprecated.
  replaced by drawPixels(ImageProcessor)
drawPixels(ImageProcessor) - Method in class ij.gui.Arrow
drawPixels(ImageProcessor) - Method in class ij.gui.Line
  If the width of this line is less than or equal to one, draws the line.
drawPixels(ImageProcessor) - Method in class ij.gui.OvalRoi
  Draws an outline of this OvalRoi on the image.
drawPixels(ImageProcessor) - Method in class ij.gui.PointRoi
drawPixels(ImageProcessor) - Method in class ij.gui.PolygonRoi
drawPixels(ImageProcessor) - Method in class ij.gui.Roi
  Draws the selection outline on the specified ImageProcessor.
drawPixels(ImageProcessor) - Method in class ij.gui.ShapeRoi
  Draws the shape of this object onto the specified ImageProcessor.
drawPixels(ImageProcessor) - Method in class ij.gui.TextRoi
  Renders the text on the image.
drawPlot(Plot) - Method in class ij.gui.PlotWindow
  Draws a new plot in this window.
drawPolygon(Polygon) - Method in class ij.process.ImageProcessor
  Draws a polygon.
drawRect(int, int, int, int) - Method in class ij.process.ImageProcessor
  Draws a rectangle.
drawRoi(Roi) - Method in class ij.process.ImageProcessor
  Draws the specified ROI on this image using the stroke width, stroke color and fill color defined by roi.setStrokeWidth, roi.setStrokeColor() and roi.setFillColor().
drawRoiBrush(Graphics) - Method in class ij.gui.ShapeRoi
drawShapes(String, ArrayList) - Method in class ij.gui.Plot
  Adds a set of 'shapes' such as boxes and whiskers
drawSphere(double, int, int, int) - Method in class ij.ImageStack
  Experimental
drawString(String) - Method in class ij.process.ImageProcessor
  Draws a string at the current drawing location using the current fill/draw value.
drawString(String, int, int) - Method in class ij.process.ImageProcessor
  Draws a string at the specified location using the current fill/draw value.
drawString(String, int, int, Color) - Method in class ij.process.ImageProcessor
  Draws a string at the specified location with a filled background.
drawUnscaledColorBar(ImageProcessor, int, int, int, int) - Method in class ij.LookUpTable
drawVectors(double[], double[], double[], double[]) - Method in class ij.gui.Plot
  Adds a set of points that will be drawn as ARROWs.
drawVectors(ArrayList, ArrayList, ArrayList, ArrayList) - Method in class ij.gui.Plot
  Adds a set of vectors to the plot using double ArrayLists.
drop(DropTargetDropEvent) - Method in class ij.plugin.DragAndDrop
dropActionChanged(DropTargetDragEvent) - Method in class ij.plugin.DragAndDrop
DROPPER - Static variable in class ij.gui.Toolbar
dstHeight - Variable in class ij.gui.ImageCanvas
dstWidth - Variable in class ij.gui.ImageCanvas
DUMP - Static variable in interface ij.macro.MacroConstants
dumpProgram() - Method in class ij.macro.Program
dumpSymbolTable() - Method in class ij.macro.Program
duplicate() - Method in class ij.gui.Overlay
  Returns a clone of this Overlay.
duplicate() - Method in class ij.ImagePlus
  Returns a copy of this image or stack.
duplicate() - Method in class ij.ImageStack
  Duplicates this stack.
duplicate() - Method in class ij.process.ByteProcessor
  Returns a duplicate of this image.
duplicate() - Method in class ij.process.ColorProcessor
  Returns a duplicate of this image.
duplicate() - Method in class ij.process.FloatPolygon
duplicate() - Method in class ij.process.FloatProcessor
  Returns a duplicate of this image.
duplicate() - Method in class ij.process.ImageProcessor
  Returns a duplicate of this image.
duplicate() - Method in class ij.process.ShortProcessor
  Returns a duplicate of this image.
Duplicater - Class in ij.plugin.filter
  Deprecated.
  replaced by ij.plugin.Duplicator class
Duplicater() - Constructor for class ij.plugin.filter.Duplicater
  Deprecated.
duplicateStack(ImagePlus, String) - Method in class ij.plugin.filter.Duplicater
  Deprecated.
duplicateSubstack(ImagePlus, String, int, int) - Method in class ij.plugin.filter.Duplicater
  Deprecated.
Duplicator - Class in ij.plugin
  This plugin implements the Image/Duplicate command.
Duplicator() - Constructor for class ij.plugin.Duplicator

## E

east(ImageProcessor) - Method in class ij.plugin.filter.Shadows
Editor - Class in ij.plugin.frame
  This is a simple TextArea based editor for editing and compiling plugins.
Editor() - Constructor for class ij.plugin.frame.Editor
Editor(int, int, int, int) - Constructor for class ij.plugin.frame.Editor
Editor(String) - Constructor for class ij.plugin.frame.Editor
EDM - Class in ij.plugin.filter
  This plugin implements the Euclidean Distance Map (EDM), Watershed, Ultimate Eroded Points and Voronoi commands in the Process/Binary submenu.
EDM() - Constructor for class ij.plugin.filter.EDM
edPaste(String) - Method in class ij.macro.FunctionFinder
EIGHT_CONNECTED - Static variable in class ij.gui.Wand
  Wand operation type: trace outline of 8-connected pixels
ELLIPSE - Static variable in class ij.io.RoiDecoder
ELLIPSE - Static variable in interface ij.measure.Measurements
ELLIPSE_ROI - Static variable in class ij.gui.Toolbar
EllipseFitter - Class in ij.process
  This class fits an ellipse to an ROI.
EllipseFitter() - Constructor for class ij.process.EllipseFitter
EllipseRoi - Class in ij.gui
  This class implements the ellipse selection tool.
EllipseRoi(double, double, double, double, double) - Constructor for class ij.gui.EllipseRoi
EllipseRoi(int, int, ImagePlus) - Constructor for class ij.gui.EllipseRoi
ELLIPSES - Static variable in class ij.plugin.filter.ParticleAnalyzer
ELSE - Static variable in interface ij.macro.MacroConstants
EMBEDDED - Static variable in class ij.ImageJ
  Run embedded in another application.
enableDebugging() - Method in class ij.io.TiffDecoder
enableLivePlot(boolean) - Method in class ij.gui.PlotWindow
  Enables or disables live plotting.
enableSubPixelResolution() - Method in class ij.gui.PolygonRoi
enableSubPixelResolution() - Method in class ij.gui.Roi
enableYesNoCancel() - Method in class ij.gui.GenericDialog
  Make this a "Yes No Cancel" dialog.
enableYesNoCancel(String, String) - Method in class ij.gui.GenericDialog
  Make this a "Yes No Cancel" dialog with custom labels.
endPaste() - Method in class ij.gui.Roi
ENDS_WITH - Static variable in interface ij.macro.MacroConstants
enhancedLineTool - Static variable in class ij.Prefs
  Allow lines to be created with one click at start and another at the end
enhanceQuality(boolean) - Static method in class ij.plugin.JpegWriter
  Enhance quality of JPEGs by disabing chroma subsampling.
enlarge(Roi, double) - Static method in class ij.plugin.RoiEnlarger
enlarge(ImagePlus, int) - Static method in class ij.plugin.RoiEnlarger
enlarge255(Roi, double) - Static method in class ij.plugin.RoiEnlarger
EOF - Static variable in interface ij.macro.MacroConstants
EQ - Static variable in interface ij.macro.MacroConstants
equalize(ImagePlus) - Method in class ij.plugin.ContrastEnhancer
equalize(ImageProcessor) - Method in class ij.plugin.ContrastEnhancer
  Changes the tone curves of images.
equals(Calibration) - Method in class ij.measure.Calibration
  Compares two Calibration objects for equality.
equals(Object) - Method in class ij.gui.Roi
  Checks whether two rectangles are equal.
erf(double) - Static method in class ij.util.IJMath
ERF - Static variable in class ij.measure.CurveFitter
  Constants for the built-in fit functions
erode() - Method in class ij.process.ByteProcessor
erode() - Method in class ij.process.ColorProcessor
erode() - Method in class ij.process.FloatProcessor
  Not implemented.
erode() - Method in class ij.process.ImageProcessor
  Erodes the image or ROI using a 3x3 maximum filter.
erode() - Method in class ij.process.ShortProcessor
  Not implemented.
erode(int, int) - Method in class ij.process.ByteProcessor
error(String) - Static method in class ij.IJ
  Displays a message in a dialog box titled "ImageJ".
error(String, String) - Static method in class ij.IJ
  Displays a message in a dialog box with the specified title.
ERROR - Static variable in class ij.gui.PlotContentsDialog
  Types of dialog (ERROR suppresses the dialog after an invalid call of a constructor)
escapePressed() - Method in class ij.gui.HTMLDialog
escapePressed() - Method in class ij.gui.MessageDialog
escapePressed() - Static method in class ij.IJ
  Returns true if the `Esc` key was pressed since the last ImageJ command started to execute or since resetEscape() was called.
escPressed() - Method in class ij.gui.WaitForUserDialog
eval(String) - Static method in class ij.Macro
  Evaluates 'code' and returns the output, or any error, as a String (e.g., Macro.eval("2+2") returns "4").
eval(String) - Method in class ij.macro.Interpreter
  Evaluates 'code' and returns the output, or any error, as a String.
eval(String) - Method in class ij.plugin.JavaScriptEvaluator
EVAL - Static variable in interface ij.macro.MacroConstants
evalSpline(double) - Method in class ij.measure.SplineFitter
  Evalutes spline function at given point
evalSpline(float[], float[], int, double) - Method in class ij.measure.SplineFitter
evalSpline(int[], int[], int, double) - Method in class ij.measure.SplineFitter
  provides interpolated function value at position xp
evaluateScript(String) - Method in class ij.plugin.frame.Editor
EventListener - Class in ij.plugin
  This plugin implements the Plugins/Utilities/Monitor Events command.
EventListener() - Constructor for class ij.plugin.EventListener
eventOccurred(int) - Method in interface ij.IJEventListener
eventOccurred(int) - Method in class ij.plugin.EventListener
ExceptionHandler() - Constructor for class ij.ImageJ.ExceptionHandler
EXCLUDE_EDGE_PARTICLES - Static variable in class ij.plugin.filter.ParticleAnalyzer
  Do not measure particles touching edge of image.
excludedFileType(String) - Static method in class ij.plugin.FolderOpener
excludeEdgeParticles - Variable in class ij.plugin.filter.ParticleAnalyzer
EXEC - Static variable in interface ij.macro.MacroConstants
Executer - Class in ij
  Runs ImageJ menu commands in a separate thread.
Executer(String) - Constructor for class ij.Executer
  Create an Executer to run the specified menu command in this thread using the active image.
Executer(String, ImagePlus) - Constructor for class ij.Executer
  Create an Executer that runs the specified menu command in a separate thread using the specified image, or using the active image if 'imp' is null.
exit() - Static method in class ij.IJ
  Aborts any currently running JavaScript, or use IJ.error(string) to abort a JavaScript with a message.
EXIT - Static variable in interface ij.macro.MacroConstants
exitConstructingMode() - Method in class ij.gui.PolygonRoi
exitWhenQuitting(boolean) - Method in class ij.ImageJ
  ImageJ calls System.exit() when qutting when 'exitWhenQuitting' is true.
exp() - Method in class ij.process.FloatProcessor
exp() - Method in class ij.process.ImageProcessor
  Performs a exponential transform on the image or ROI.
exp() - Method in class ij.process.ShortProcessor
EXP - Static variable in interface ij.macro.MacroConstants
EXP_RECOVERY - Static variable in class ij.measure.Calibration
EXP_RECOVERY - Static variable in class ij.measure.CurveFitter
  Constants for the built-in fit functions
EXP_RECOVERY_NOOFFSET - Static variable in class ij.measure.CurveFitter
  Constants for the built-in fit functions
EXP_REGRESSION - Static variable in class ij.measure.CurveFitter
  Constants for the built-in fit functions
EXP_WITH_OFFSET - Static variable in class ij.measure.Calibration
EXP_WITH_OFFSET - Static variable in class ij.measure.CurveFitter
  Constants for the built-in fit functions
expandImage(ImageProcessor, int, int, int, int) - Method in class ij.plugin.CanvasResizer
expandStack(ImageStack, int, int, int, int) - Method in class ij.plugin.CanvasResizer
EXPONENTIAL - Static variable in class ij.measure.Calibration
EXPONENTIAL - Static variable in class ij.measure.CurveFitter
  Constants for the built-in fit functions
EXT - Static variable in interface ij.macro.MacroConstants
EXTENDED - Static variable in interface ij.gui.RoiListener
ExtendedPlugInFilter - Interface in ij.plugin.filter
  ImageJ plugins that process an image may implement this interface.
ExtensionDescriptor - Class in ij.macro
ExtensionDescriptor(String, int[], MacroExtension) - Constructor for class ij.macro.ExtensionDescriptor

## F

f(double) - Method in class ij.measure.CurveFitter
  Returns the formula value for parameters 'p' at 'x'.
f(double[], double) - Method in class ij.measure.CurveFitter
  Returns the formula value for parameters 'p' at 'x'.
f(int, double[], double) - Static method in class ij.measure.CurveFitter
  Returns value of built-in 'fitType' formula value for parameters "p" at "x"
f2hex(float) - Static method in class ij.util.Tools
  Converts a float to an 9 byte hex string starting with '#'.
FALSE - Static variable in interface ij.macro.MacroConstants
FAST_TRACE - Static variable in interface ij.macro.Debugger
FCOLOR - Static variable in class ij.Prefs
FERET - Static variable in interface ij.measure.Measurements
FERET - Static variable in class ij.measure.ResultsTable
FERET_ANGLE - Static variable in class ij.measure.ResultsTable
FERET_ARRAY_POINTOFFSET - Static variable in class ij.gui.Roi
FERET_ARRAYSIZE - Static variable in class ij.gui.Roi
FERET_X - Static variable in class ij.measure.ResultsTable
FERET_Y - Static variable in class ij.measure.ResultsTable
FFT - Class in ij.plugin
  This class implements the FFT, Inverse FFT and Redisplay Power Spectrum commands in the Process/FFT submenu.
FFT() - Constructor for class ij.plugin.FFT
FFTCustomFilter - Class in ij.plugin.filter
  This class implements the Process/FFT/Custom Filter command.
FFTCustomFilter() - Constructor for class ij.plugin.filter.FFTCustomFilter
FFTFilter - Class in ij.plugin.filter
  This class implements the Process/FFT/Bandpass Filter command.
FFTFilter() - Constructor for class ij.plugin.filter.FFTFilter
FFTMath - Class in ij.plugin
  The class implements the Process/FFT/Math command.
FFTMath() - Constructor for class ij.plugin.FFTMath
FHT - Class in ij.process
  This class contains a Java implementation of the Fast Hartley Transform.
FHT() - Constructor for class ij.process.FHT
FHT(ImageProcessor) - Constructor for class ij.process.FHT
  Constructs a FHT object from an ImageProcessor.
FHT(ImageProcessor, boolean) - Constructor for class ij.process.FHT
FILE - Static variable in interface ij.macro.MacroConstants
fileChanged() - Method in class ij.plugin.frame.Editor
fileFormat - Variable in class ij.io.FileInfo
FileInfo - Class in ij.io
  This class consists of public fields that describe an image file.
FileInfo() - Constructor for class ij.io.FileInfo
  Creates a FileInfo object with all of its fields set to their default value.
FileInfoVirtualStack - Class in ij.plugin
  This plugin opens a multi-page TIFF file, or a set of raw images, as a virtual stack.
FileInfoVirtualStack() - Constructor for class ij.plugin.FileInfoVirtualStack
FileInfoVirtualStack(FileInfo) - Constructor for class ij.plugin.FileInfoVirtualStack
FileInfoVirtualStack(FileInfo[]) - Constructor for class ij.plugin.FileInfoVirtualStack
FileInfoVirtualStack(FileInfo, boolean) - Constructor for class ij.plugin.FileInfoVirtualStack
fileName - Variable in class ij.io.FileInfo
fileName - Static variable in class ij.plugin.FFT
FileOpener - Class in ij.io
  Opens or reverts an image specified by a FileInfo object.
FileOpener(FileInfo) - Constructor for class ij.io.FileOpener
FileSaver - Class in ij.io
  Saves images in tiff, gif, jpeg, raw, zip and text format.
FileSaver(ImagePlus) - Constructor for class ij.io.FileSaver
  Constructs a FileSaver from an ImagePlus.
fileType - Variable in class ij.io.FileInfo
fill() - Method in class ij.process.ColorProcessor
  Fills the current rectangular ROI.
fill() - Method in class ij.process.FloatProcessor
  Fills the current rectangular ROI.
fill() - Method in class ij.process.ImageProcessor
  Fills the image or ROI bounding rectangle with the current fill/draw value.
fill() - Method in class ij.process.ShortProcessor
  Fills the current rectangular ROI.
fill(int, int) - Method in class ij.process.FloodFiller
  Does a 4-connected flood fill using the current fill/draw value, which is defined by ImageProcessor.setValue().
fill(Roi) - Method in class ij.process.ImageProcessor
  Fills the ROI with the current fill/draw value.
fill(ImagePlus, Color, Color) - Method in class ij.gui.Overlay
  Fills all the ROIs in this overlay with 'foreground' after clearing the the image to 'background' if it is not null.
fill(ImageProcessor) - Method in class ij.plugin.filter.Filler
  Deprecated.
  replaced by ImageProcessor.fill(Roi)
fill(ImageProcessor) - Method in class ij.process.ByteProcessor
  Sets pixels that are within roi and part of the mask to the foreground color.
fill(ImageProcessor) - Method in class ij.process.ColorProcessor
  Fills pixels that are within roi and part of the mask.
fill(ImageProcessor) - Method in class ij.process.FloatProcessor
  Fills pixels that are within roi and part of the mask.
fill(ImageProcessor) - Method in class ij.process.ImageProcessor
  Fills pixels that are within the ROI bounding rectangle and part of the mask (i.e.
fill(ImageProcessor) - Method in class ij.process.ShortProcessor
  Fills pixels that are within roi and part of the mask.
fill(ImageProcessor, Rectangle) - Method in class ij.process.PolygonFiller
  Fills the polygon using the ImageProcessor's current drawing color.
FILL - Static variable in interface ij.macro.MacroConstants
FILL_BLACK - Static variable in class ij.gui.NewImage
FILL_COLOR - Static variable in class ij.io.RoiDecoder
FILL_NOISE - Static variable in class ij.gui.NewImage
FILL_OVAL - Static variable in interface ij.macro.MacroConstants
FILL_RAMP - Static variable in class ij.gui.NewImage
FILL_RANDOM - Static variable in class ij.gui.NewImage
FILL_RECT - Static variable in interface ij.macro.MacroConstants
FILL_WHITE - Static variable in class ij.gui.NewImage
fill8(int, int) - Method in class ij.process.FloodFiller
  Does a 8-connected flood fill using the current fill/draw value, which is defined by ImageProcessor.setValue().
fillByteProcessorMask(ByteProcessor) - Method in class ij.process.PolygonFiller
  Fills the ByteProcessor with 255 inside the polygon
fillColor - Variable in class ij.gui.Roi
FILLED - Static variable in class ij.gui.Arrow
FILLED - Static variable in class ij.gui.Plot
  Fill area between line plot and x-axis at y=0.
Filler - Class in ij.plugin.filter
  This plugin implements ImageJ's Fill, Clear, Clear Outside and Draw commands.
Filler() - Constructor for class ij.plugin.filter.Filler
fillOutside(Roi) - Method in class ij.process.ImageProcessor
  Fills outside an Roi.
fillOval(int, int, int, int) - Method in class ij.process.ImageProcessor
  Fills an elliptical shape.
fillPolygon(Polygon) - Method in class ij.process.ImageProcessor
  Fills a polygon.
fillRect(int, int, int, int) - Method in class ij.process.ImageProcessor
  Fills a rectangle.
fillValueSet - Variable in class ij.process.ImageProcessor
fillValueSet() - Method in class ij.process.ImageProcessor
  Returns 'true' if the fill/draw value has been set.
filter(int) - Method in class ij.process.ByteProcessor
  Filters using a 3x3 neighborhood.
filter(int) - Method in class ij.process.ColorProcessor
  A 3x3 filter operation, where the argument (ImageProcessor.BLUR_MORE, FIND_EDGES, MEDIAN_FILTER, MIN or MAX) determines the filter type.
filter(int) - Method in class ij.process.FloatProcessor
  Filters using a 3x3 neighborhood.
filter(int) - Method in class ij.process.ImageProcessor
  A 3x3 filter operation, where the argument (BLUR_MORE, FIND_EDGES, MEDIAN_FILTER, MIN or MAX) determines the filter type.
filter(int) - Method in class ij.process.ShortProcessor
  Filters using a 3x3 neighborhood.
filter(ImagePlus, ImagePlus) - Static method in class ij.plugin.FFT
  Version of filter() that accepts an ImagePlus for the filter.
filter(ImagePlus, ImageProcessor) - Static method in class ij.plugin.FFT
  Does frequency domain fitering of the speciified image
filter(ImageStack, int, float, float, float) - Static method in class ij.plugin.Filters3D
FILTER - Static variable in class ij.Undo
  Undo using ImageProcessor.snapshot.
FILTER_MAX - Static variable in class ij.process.StackProcessor
FILTER_MAXLOCAL - Static variable in class ij.process.StackProcessor
FILTER_MEAN - Static variable in class ij.process.StackProcessor
FILTER_MEDIAN - Static variable in class ij.process.StackProcessor
FILTER_MIN - Static variable in class ij.process.StackProcessor
FILTER_VAR - Static variable in class ij.process.StackProcessor
filter3D(ImageStack, float, float, float, int, int, int) - Method in class ij.process.StackProcessor
  3D filter using threads
filterRGB(int, double) - Method in class ij.process.ColorProcessor
  Performs the specified filter on the red, green and blue planes of this image.
Filters - Class in ij.plugin.filter
  This plugin implements the Invert, Smooth, Sharpen, Find Edges, and Add Noise commands.
Filters() - Constructor for class ij.plugin.filter.Filters
FILTERS_MENU - Static variable in class ij.Menus
Filters3D - Class in ij.plugin
Filters3D() - Constructor for class ij.plugin.Filters3D
FINAL_PROCESSING - Static variable in interface ij.plugin.filter.PlugInFilter
  Set this flag if the setup method of the filter should be called again after the calls to the run(ip) have finished.
FIND_EDGES - Static variable in class ij.process.ImageProcessor
findAllMenuItems() - Method in class ij.plugin.CommandFinder
findEdges() - Method in class ij.process.ColorProcessor
findEdges() - Method in class ij.process.ImageProcessor
  Finds edges in the image or ROI using a Sobel operator.
findMaxima(double[], double, boolean) - Static method in class ij.plugin.filter.MaximumFinder
findMaxima(double[], double, int) - Static method in class ij.plugin.filter.MaximumFinder
  Calculates peak positions of 1D array N.Vischer, 06-mar-2017
findMaxima(ImageProcessor, double, boolean, double, int, boolean, boolean) - Method in class ij.plugin.filter.MaximumFinder
  Here the processing is done: Find the maxima of an image (does not find minima).
findMaxima(ImageProcessor, double, double, int, boolean, boolean) - Method in class ij.plugin.filter.MaximumFinder
  Finds the maxima of an image (does not find minima).
findMaxima(ImageProcessor, double, int, boolean) - Method in class ij.plugin.filter.MaximumFinder
  Find the maxima of an image.
findMinAndMax() - Method in class ij.process.FloatProcessor
  Calculates the minimum and maximum pixel value for the entire image.
findMinAndMax() - Method in class ij.process.IntProcessor
findMinAndMax() - Method in class ij.process.ShortProcessor
findMinAndMax() - Method in class ij.process.SignedShortProcessor
findMinima(double[], double, boolean) - Static method in class ij.plugin.filter.MaximumFinder
  Returns minimum positions of array xx, sorted with decreasing strength
findMinima(double[], double, int) - Static method in class ij.plugin.filter.MaximumFinder
findNthLowestNumber(float[], int, int) - Static method in class ij.plugin.filter.RankFilters
  Find the n-th lowest number in part of an array
fit(ImageProcessor, ImageStatistics) - Method in class ij.process.EllipseFitter
  Fits an ellipse to the current ROI.
FIT - Static variable in interface ij.macro.MacroConstants
fitList - Static variable in class ij.measure.CurveFitter
  Names of the built-in fit functions
FITS - Static variable in class ij.io.FileInfo
FITS - Static variable in class ij.io.Opener
FITS_Reader - Class in ij.plugin
  Opens and displays FITS images.
FITS_Reader() - Constructor for class ij.plugin.FITS_Reader
FITS_Writer - Class in ij.plugin
  This plugin saves a 16 or 32 bit image in FITS format.
FITS_Writer() - Constructor for class ij.plugin.FITS_Writer
fitSpline() - Method in class ij.gui.PolygonRoi
  Fits a spline, which becomes the new shape of this Roi
fitSpline(int) - Method in class ij.gui.PolygonRoi
  Fits a spline, which becomes the new shape of this Roi
fitSplineForStraightening() - Method in class ij.gui.PolygonRoi
  Creates a spline fitted polygon with (roughly) one pixel segment lengths and sets it as the Roi shape.
Fitter - Class in ij.plugin.frame
  ImageJ plugin that does curve fitting using the modified CurveFitter class.
Fitter() - Constructor for class ij.plugin.frame.Fitter
fitToWindow() - Method in class ij.gui.ImageCanvas
fitToWindow() - Method in class ij.gui.PlotCanvas
  Resizes the plot (unless frozen) to fit the window
fix(Scrollbar) - Static method in class ij.gui.GUI
  Lightens overly dark scrollbar background on Windows 8.
fixedDicomScaling - Static variable in class ij.Prefs
  Assume DICOM volumes use identical RescaleSlope and RescaleIntercept across all slices
fixedScale - Variable in class ij.process.ShortProcessor
fixLineEndings() - Method in class ij.plugin.frame.Editor
  Changes Windows (CRLF) line separators to line feeds (LF).
fixNewLines(String) - Static method in class ij.util.Tools
  Converts carriage returns to line feeds.
fixPath(String) - Static method in class ij.plugin.frame.Recorder
  Replaces '\' characters with '/'.
fixScrollbar(Scrollbar) - Static method in class ij.gui.GUI
  Works around an OpenJDK bug on Windows that causes the scrollbar thumb color and background color to be almost identical.
fixString(String) - Static method in class ij.plugin.frame.Recorder
  Replaces special characters in a String for creation of a quoted macro String.
flags - Variable in class ij.gui.ImageCanvas
flatten() - Method in class ij.ImagePlus
  Returns a "flattened" version of this image, or stack slice, in RGB format.
flattenScale - Variable in class ij.gui.Roi
flattenStack() - Method in class ij.ImagePlus
  Flattens all slices of this stack or HyperStack.
flattenTitle - Static variable in class ij.ImagePlus
  Title of image used by Flatten command
FLATTOP - Static variable in class ij.process.FHT
flipHorizontal() - Method in class ij.process.ImageProcessor
  Flips the image or ROI horizontally.
flipHorizontal() - Method in class ij.process.StackProcessor
flipImages(boolean) - Static method in class ij.plugin.FITS_Reader
flipStack(ImagePlus) - Method in class ij.plugin.StackReverser
flipVertical() - Method in class ij.process.ByteProcessor
flipVertical() - Method in class ij.process.ColorProcessor
flipVertical() - Method in class ij.process.FloatProcessor
flipVertical() - Method in class ij.process.ImageProcessor
  Flips the image or ROI vertically.
flipVertical() - Method in class ij.process.ShortProcessor
flipVertical() - Method in class ij.process.StackProcessor
flipXZ - Static variable in class ij.Prefs
  Rotate XZ orthogonal views 180 degrees
fList - Static variable in class ij.measure.CurveFitter
  Equations of the built-in fit functions
FLOAT - Static variable in class ij.plugin.filter.EDM
  Output type: new 32-bit image
FLOAT_PARAM - Static variable in class ij.io.RoiDecoder
FLOAT_STROKE_WIDTH - Static variable in class ij.io.RoiDecoder
FloatArray - Class in ij.util
  This class implements an expandable float array similar to an ArrayList or Vector but more efficient.
FloatArray() - Constructor for class ij.util.FloatArray
  Creates a new expandable array with an initial capacity of 100.
FloatArray(int) - Constructor for class ij.util.FloatArray
  Creates a new expandable array with specified initial capacity.
FloatBlitter - Class in ij.process
  This class does bit blitting of 32-bit floating-point images.
FloatBlitter(FloatProcessor) - Constructor for class ij.process.FloatBlitter
  Constructs a FloatBlitter from a FloatProcessor.
FloatPolygon - Class in ij.process
  Used by the Roi classes to return float coordinate arrays and to determine if a point is inside or outside of spline fitted selections.
FloatPolygon() - Constructor for class ij.process.FloatPolygon
  Constructs an empty FloatPolygon.
FloatPolygon(float[], float[]) - Constructor for class ij.process.FloatPolygon
  Constructs a FloatPolygon from x and y arrays.
FloatPolygon(float[], float[], int) - Constructor for class ij.process.FloatPolygon
  Constructs a FloatPolygon from x and y arrays.
FloatProcessor - Class in ij.process
  This is an 32-bit floating-point image and methods that operate on that image.
FloatProcessor(float[][]) - Constructor for class ij.process.FloatProcessor
  Creates a FloatProcessor from a 2D float array using the default LUT.
FloatProcessor(int[][]) - Constructor for class ij.process.FloatProcessor
  Creates a FloatProcessor from a 2D int array.
FloatProcessor(int, int) - Constructor for class ij.process.FloatProcessor
  Creates a blank FloatProcessor using the default grayscale LUT that displays zero as black.
FloatProcessor(int, int, double[]) - Constructor for class ij.process.FloatProcessor
  Creates a FloatProcessor from a double array using the default grayscale LUT.
FloatProcessor(int, int, float[]) - Constructor for class ij.process.FloatProcessor
  Creates a new FloatProcessor using the specified pixel array.
FloatProcessor(int, int, float[], ColorModel) - Constructor for class ij.process.FloatProcessor
  Creates a new FloatProcessor using the specified pixel array and ColorModel.
FloatProcessor(int, int, int[]) - Constructor for class ij.process.FloatProcessor
  Creates a FloatProcessor from an int array using the default grayscale LUT.
FloatStatistics - Class in ij.process
  32-bit (float) image statistics, including histogram.
FloatStatistics(ImageProcessor) - Constructor for class ij.process.FloatStatistics
  Constructs an ImageStatistics object from a FloatProcessor using the standard measurement options (area, mean, mode, min and max).
FloatStatistics(ImageProcessor, int, Calibration) - Constructor for class ij.process.FloatStatistics
  Constructs a FloatStatistics object from a FloatProcessor using the specified measurement options.
FLOOD_FILL - Static variable in interface ij.macro.MacroConstants
floodFill - Variable in class ij.plugin.filter.ParticleAnalyzer
FloodFiller - Class in ij.process
  This class, which does flood filling, is used by the floodFill() macro function and by the particle analyzer The Wikipedia at "http://en.wikipedia.org/wiki/Flood_fill" has a good description of the algorithm used here as well as examples in C and Java.
FloodFiller(ImageProcessor) - Constructor for class ij.process.FloodFiller
FLOOR - Static variable in interface ij.macro.MacroConstants
flush() - Method in class ij.ImagePlus
  Sets the ImageProcessor, Roi, AWT Image and stack image arrays to null.
flush() - Method in class ij.io.LogStream
fMacro - Static variable in class ij.measure.CurveFitter
  ImageJ Macro language code for the built-in functions
fmGraphics - Variable in class ij.process.ImageProcessor
fmImage - Variable in class ij.process.ImageProcessor
focusGained(FocusEvent) - Method in class ij.gui.GenericDialog
focusGained(FocusEvent) - Method in class ij.gui.ImageWindow
focusGained(FocusEvent) - Method in class ij.plugin.frame.ColorThresholder
focusGained(FocusEvent) - Method in class ij.plugin.frame.PlugInDialog
focusGained(FocusEvent) - Method in class ij.plugin.frame.PlugInFrame
focusGained(FocusEvent) - Method in class ij.plugin.Orthogonal_Views
focusGained(FocusEvent) - Method in class ij.plugin.Scaler
focusGained(FocusEvent) - Method in class ij.text.TextWindow
focusLost(FocusEvent) - Method in class ij.gui.GenericDialog
focusLost(FocusEvent) - Method in class ij.gui.ImageWindow
focusLost(FocusEvent) - Method in class ij.plugin.frame.ColorThresholder
focusLost(FocusEvent) - Method in class ij.plugin.frame.PlugInDialog
focusLost(FocusEvent) - Method in class ij.plugin.frame.PlugInFrame
focusLost(FocusEvent) - Method in class ij.plugin.frame.ThresholdAdjuster
focusLost(FocusEvent) - Method in class ij.plugin.Orthogonal_Views
focusLost(FocusEvent) - Method in class ij.plugin.Scaler
focusLost(FocusEvent) - Method in class ij.text.TextWindow
FolderOpener - Class in ij.plugin
  Implements the File/Import/Image Sequence command, which opens a folder of images as a stack.
FolderOpener() - Constructor for class ij.plugin.FolderOpener
font - Variable in class ij.process.ImageProcessor
font10 - Static variable in class ij.IJ
  SansSerif, plain, 10-point font
font12 - Static variable in class ij.IJ
  SansSerif, plain, 12-point font
font14 - Static variable in class ij.IJ
  SansSerif, plain, 14-point font
fontMetrics - Variable in class ij.process.ImageProcessor
fontSize - Static variable in class ij.gui.PlotWindow
  The plot text size, can be overridden by Plot.setFont, Plot.setFontSize, Plot.setXLabelFont etc.
FontUtil - Class in ij.util
  This class contains static utility methods for replacing fonts that are not available on the current system.
FontUtil() - Constructor for class ij.util.FontUtil
FOR - Static variable in interface ij.macro.MacroConstants
FOREGROUND_COLOR_CHANGED - Static variable in interface ij.IJEventListener
forward(ImagePlus) - Static method in class ij.plugin.FFT
  Performs a forward FHT transform.
FOUR_CONNECTED - Static variable in class ij.gui.Wand
  Wand operation type: trace outline of 4-connected pixels
FOUR_CONNECTED - Static variable in class ij.plugin.filter.ParticleAnalyzer
  Use 4-connected particle tracing.
fourier1D(float[], int) - Method in class ij.process.FHT
  Calculates the Fourier amplitudes of an array, based on a 1D Fast Hartley Transform.
fps - Variable in class ij.measure.Calibration
  Frame rate in frames per second
FPS - Static variable in class ij.Prefs
FractalBoxCounter - Class in ij.plugin.filter
  Calculate the so-called "capacity" fractal dimension.
FractalBoxCounter() - Constructor for class ij.plugin.filter.FractalBoxCounter
frame - Variable in class ij.gui.HistogramWindow
FRAME - Static variable in class ij.measure.ResultsTable
frameInterval - Variable in class ij.io.FileInfo
frameInterval - Variable in class ij.measure.Calibration
  Frame interval in 'timeUnit's
FreehandRoi - Class in ij.gui
  Freehand region of interest or freehand line of interest
FreehandRoi(int, int, ImagePlus) - Constructor for class ij.gui.FreehandRoi
FREELINE - Static variable in class ij.gui.Roi
FREELINE - Static variable in class ij.gui.Toolbar
freeMemory() - Static method in class ij.IJ
  Returns a string something like "64K of 256MB (25%)" that shows how much of the available memory is in use.
FREEROI - Static variable in class ij.gui.Roi
FREEROI - Static variable in class ij.gui.Toolbar
freeze() - Static method in class ij.gui.PlotWindow
  Freezes the active plot window, so the image does not get redrawn for zooming, setting the range, etc.
FROM_CHAR_CODE - Static variable in interface ij.macro.MacroConstants
fullRange16bitInversions - Static variable in class ij.Prefs
  Use full range for 16-bit inversions
FUNCTION - Static variable in interface ij.macro.MacroConstants
FunctionFinder - Class in ij.macro
  This class implements the text editor's Macros/Find Functions command.
FunctionFinder() - Constructor for class ij.macro.FunctionFinder
FunctionFinder(Editor) - Constructor for class ij.macro.FunctionFinder
functionIDs - Static variable in interface ij.macro.MacroConstants
functions - Static variable in interface ij.macro.MacroConstants
Functions - Class in ij.macro
  This class implements the built-in macro functions.

## G

gamma(double) - Method in class ij.process.FloatProcessor
gamma(double) - Method in class ij.process.ImageProcessor
  Performs gamma correction of the image or ROI.
gamma(double) - Method in class ij.process.ShortProcessor
GAMMA_VARIATE - Static variable in class ij.measure.Calibration
GAMMA_VARIATE - Static variable in class ij.measure.CurveFitter
  Constants for the built-in fit functions
gapBetweenImages - Variable in class ij.io.FileInfo
GAUSSIAN - Static variable in class ij.measure.Calibration
GAUSSIAN - Static variable in class ij.measure.CurveFitter
  Constants for the built-in fit functions
GAUSSIAN_NOOFFSET - Static variable in class ij.measure.CurveFitter
  Constants for the built-in fit functions
GaussianBlur - Class in ij.plugin.filter
  This plug-in filter uses convolution with a Gaussian function for smoothing.
GaussianBlur() - Constructor for class ij.plugin.filter.GaussianBlur
GaussianBlur3D - Class in ij.plugin
GaussianBlur3D() - Constructor for class ij.plugin.GaussianBlur3D
GelAnalyzer - Class in ij.plugin
  This plugin generates gel profile plots that can be analyzed using the wand tool.
GelAnalyzer() - Constructor for class ij.plugin.GelAnalyzer
GenericDialog - Class in ij.gui
  This class is a customizable modal dialog box.
GenericDialog(String) - Constructor for class ij.gui.GenericDialog
  Creates a new GenericDialog with the specified title.
GenericDialog(String, Frame) - Constructor for class ij.gui.GenericDialog
  Creates a new GenericDialog using the specified title and parent frame.
get(int) - Method in class ij.gui.Overlay
  Returns the ROI with the specified index or null if the index is invalid.
get(int) - Method in class ij.process.ByteProcessor
get(int) - Method in class ij.process.ColorProcessor
get(int) - Method in class ij.process.FloatProcessor
get(int) - Method in class ij.process.ImageProcessor
get(int) - Method in class ij.process.ShortProcessor
get(int) - Method in class ij.util.FloatArray
  Returns the element at the specified position in this FloatArray.
get(int, int) - Method in class ij.process.ByteProcessor
get(int, int) - Method in class ij.process.ColorProcessor
get(int, int) - Method in class ij.process.FloatProcessor
get(int, int) - Method in class ij.process.ImageProcessor
  This is a faster version of getPixel() that does not do bounds checking.
get(int, int) - Method in class ij.process.ShortProcessor
get(int, int) - Method in class ij.process.SignedShortProcessor
get(String) - Method in class ij.gui.Overlay
  Returns the ROI with the specified name or null if not found.
get(String, boolean) - Static method in class ij.Prefs
  Uses the keyword `key` to retrieve a boolean from the preferences file.
get(String, double) - Static method in class ij.Prefs
  Uses the keyword `key` to retrieve a number from the preferences file.
get(String, String) - Static method in class ij.Prefs
  Uses the keyword `key` to retrieve a string from the preferences file.
GET_ARGUMENT - Static variable in interface ij.macro.MacroConstants
GET_BOOLEAN - Static variable in interface ij.macro.MacroConstants
GET_BOUNDING_RECT - Static variable in interface ij.macro.MacroConstants
GET_BOUNDS - Static variable in interface ij.macro.MacroConstants
GET_COORDINATES - Static variable in interface ij.macro.MacroConstants
GET_COUNT - Static variable in interface ij.macro.MacroConstants
GET_CURSOR_LOC - Static variable in interface ij.macro.MacroConstants
GET_DATE_AND_TIME - Static variable in interface ij.macro.MacroConstants
GET_DIMENSIONS - Static variable in interface ij.macro.MacroConstants
GET_DIR - Static variable in interface ij.macro.MacroConstants
GET_DIRECTORY - Static variable in interface ij.macro.MacroConstants
GET_DISPLAYED_AREA - Static variable in interface ij.macro.MacroConstants
GET_FILE_LIST - Static variable in interface ij.macro.MacroConstants
GET_FONT_LIST - Static variable in interface ij.macro.MacroConstants
GET_HEIGHT - Static variable in interface ij.macro.MacroConstants
GET_HISTOGRAM - Static variable in interface ij.macro.MacroConstants
GET_ID - Static variable in interface ij.macro.MacroConstants
GET_IMAGE_INFO - Static variable in interface ij.macro.MacroConstants
GET_INFO - Static variable in interface ij.macro.MacroConstants
GET_LINE - Static variable in interface ij.macro.MacroConstants
GET_LIST - Static variable in interface ij.macro.MacroConstants
GET_LOCATION_AND_SIZE - Static variable in interface ij.macro.MacroConstants
GET_LUT - Static variable in interface ij.macro.MacroConstants
GET_METADATA - Static variable in interface ij.macro.MacroConstants
GET_MIN_AND_MAX - Static variable in interface ij.macro.MacroConstants
GET_NUMBER - Static variable in interface ij.macro.MacroConstants
GET_PIXEL - Static variable in interface ij.macro.MacroConstants
GET_PIXEL_SIZE - Static variable in interface ij.macro.MacroConstants
GET_PROFILE - Static variable in interface ij.macro.MacroConstants
GET_RAW_STATISTICS - Static variable in interface ij.macro.MacroConstants
GET_RESULT - Static variable in interface ij.macro.MacroConstants
GET_RESULT_LABEL - Static variable in interface ij.macro.MacroConstants
GET_RESULT_STRING - Static variable in interface ij.macro.MacroConstants
GET_SLICE_NUMBER - Static variable in interface ij.macro.MacroConstants
GET_STATISTICS - Static variable in interface ij.macro.MacroConstants
GET_STRING - Static variable in interface ij.macro.MacroConstants
GET_STRING_WIDTH - Static variable in interface ij.macro.MacroConstants
GET_THRESHOLD - Static variable in interface ij.macro.MacroConstants
GET_TIME - Static variable in interface ij.macro.MacroConstants
GET_TITLE - Static variable in interface ij.macro.MacroConstants
GET_VALUE - Static variable in interface ij.macro.MacroConstants
GET_VERSION - Static variable in interface ij.macro.MacroConstants
GET_VOXEL_SIZE - Static variable in interface ij.macro.MacroConstants
GET_WIDTH - Static variable in interface ij.macro.MacroConstants
GET_ZOOM - Static variable in interface ij.macro.MacroConstants
get16BitBufferedImage() - Method in class ij.process.ShortProcessor
  Returns a copy of this image as a TYPE_USHORT_GRAY BufferedImage.
get16bitRangeIndex() - Static method in class ij.plugin.frame.ContrastAdjuster
getActiveChannels() - Method in class ij.CompositeImage
getActiveTable() - Static method in class ij.measure.ResultsTable
  Returns the active (front most) displayed ResultsTable.
getActiveTable() - Static method in class ij.WindowManager
  Returns the Window containing the active table, or null.
getActiveWindow() - Static method in class ij.WindowManager
  Returns the front most window or null.
getAdditionalFunctions() - Static method in class ij.macro.Interpreter
getAllNonImageWindows() - Static method in class ij.WindowManager
  Returns an array containing a list of the non-image Frames and Dialogs.
getAllStatistics() - Method in class ij.ImagePlus
  This method returns complete calibrated statistics for this image or ROI (with "Limit to threshold"), but it is up to 70 times slower than getStatistics().
getAngle() - Method in class ij.gui.Line
getAngle() - Method in class ij.gui.PolygonRoi
  Returns the angle in degrees between the first two segments of this polyline.
getAngle() - Method in class ij.gui.Roi
  Overridden by PolygonRoi (angle between first two points), TextRoi (text angle) and Line (line angle).
getAngle() - Method in class ij.gui.TextRoi
getAngle() - Static method in class ij.plugin.filter.Rotator
  Returns the current angle.
getAngle(int, int, int, int) - Method in class ij.gui.Roi
  Returns the angle in degrees between the specified line and a horizontal line.
getAnimate() - Method in class ij.gui.StackWindow
getAntiAlias() - Method in class ij.gui.Roi
getAntialiased() - Method in class ij.gui.TextRoi
  Returns the state of the 'antiAlias' instance variable.
getApplet() - Static method in class ij.IJ
  Returns the Applet that created this ImageJ or null if running as an application.
getArgs() - Static method in class ij.ImageJ
  Returns the command line arguments passed to ImageJ.
getAutoThreshold() - Method in class ij.process.ImageProcessor
  Returns a pixel value (threshold) that can be used to divide the image into objects and background.
getAutoThreshold(int[]) - Method in class ij.process.ImageProcessor
  This is a version of getAutoThreshold() that uses a histogram passed as an argument.
getBackgroundColor() - Static method in class ij.gui.Toolbar
getBackgroundValue() - Static method in class ij.gui.Toolbar
getBackgroundValue() - Method in class ij.process.ByteProcessor
  Returns the background fill value.
getBackgroundValue() - Method in class ij.process.ColorProcessor
  Returns the background fill value.
getBackgroundValue() - Method in class ij.process.FloatProcessor
getBackgroundValue() - Method in class ij.process.ImageProcessor
  Returns the background fill value.
getBackgroundValue() - Method in class ij.process.ShortProcessor
getBatchModeImage(int) - Static method in class ij.macro.Interpreter
getBatchModeImageCount() - Static method in class ij.macro.Interpreter
getBatchModeImageIDs() - Static method in class ij.macro.Interpreter
getBatchModeRoiManager() - Static method in class ij.macro.Interpreter
  Returns the batch mode RoiManager instance.
getBestIndex(Color) - Method in class ij.process.ColorProcessor
  Always returns 0 since RGB images do not use LUTs.
getBestIndex(Color) - Method in class ij.process.ImageProcessor
  Returns the LUT index that's the best match for this color.
getBicubicInterpolatedPixel(double, double, ImageProcessor) - Method in class ij.process.FloatProcessor
  This method is from Chapter 16 of "Digital Image Processing: An Algorithmic Introduction Using Java" by Burger and Burge (http://www.imagingbook.com/).
getBicubicInterpolatedPixel(double, double, ImageProcessor) - Method in class ij.process.ImageProcessor
  This method is from Chapter 16 of "Digital Image Processing: An Algorithmic Introduction Using Java" by Burger and Burge (http://www.imagingbook.com/).
getBitDepth() - Method in class ij.gui.PlotVirtualStack
  Returns either 24 (RGB) or 8 (grayscale).
getBitDepth() - Method in class ij.ImagePlus
  Returns the bit depth, 8, 16, 24 (RGB) or 32, or 0 if the bit depth is unknown.
getBitDepth() - Method in class ij.ImageStack
  Returns the bit depth (8=byte, 16=short, 24=RGB, 32=float).
getBitDepth() - Method in class ij.process.ByteProcessor
getBitDepth() - Method in class ij.process.ColorProcessor
getBitDepth() - Method in class ij.process.FloatProcessor
getBitDepth() - Method in class ij.process.ImageProcessor
  Returns the bit depth, 8, 16, 24 (RGB) or 32.
getBitDepth() - Method in class ij.process.ShortProcessor
getBitDepth() - Method in class ij.VirtualStack
  Returns the bit depth (8, 16, 24 or 32), or 0 if the bit depth is not known.
getBits(int) - Method in class ij.io.BitBuffer
getBlockIncrement() - Method in class ij.gui.ScrollbarWithLabel
getBlue(String) - Static method in class ij.plugin.Colors
getBlues() - Method in class ij.LookUpTable
getBoolean(String, boolean) - Static method in class ij.Prefs
  Retrieves a boolean from IJ_Props or IJ_Prefs.txt.
getBoundingRect() - Method in class ij.gui.Roi
  Deprecated.
  replaced by getBounds()
getBounds() - Method in class ij.gui.Arrow
  Return the bounding rectangle of this arrow.
getBounds() - Method in class ij.gui.Roi
  Returns this selection's bounding rectangle.
getBounds() - Method in class ij.process.FloatPolygon
getBrightness() - Method in class ij.process.ColorProcessor
  Returns brightness as a FloatProcessor.
getBrushSize() - Static method in class ij.gui.Toolbar
  Returns the size of the selection brush tool, or 0 if the brush tool is not enabled.
getBufferedImage() - Method in class ij.ImagePlus
  Returns a copy of this image as an 8-bit or RGB BufferedImage.
getBufferedImage() - Method in class ij.process.ByteProcessor
  Returns this image as a BufferedImage.
getBufferedImage() - Method in class ij.process.FloatProcessor
  Returns this image as an 8-bit BufferedImage.
getBufferedImage() - Method in class ij.process.ImageProcessor
  Returns this image as a BufferedImage.
getBufferedImage() - Method in class ij.process.IntProcessor
  Returns this image as an 8-bit BufferedImage .
getBufferedImage() - Method in class ij.process.ShortProcessor
  Returns this image as an 8-bit BufferedImage .
getButton() - Method in class ij.gui.WaitForUserDialog
  Returns a reference to the 'OK' button
getButtons() - Method in class ij.gui.GenericDialog
  Returns references to the "OK" ("Yes"), "Cancel", "No", and "Help" buttons as an array of length 4.
getButtonSize() - Static method in class ij.gui.Toolbar
  Returns the button width (button spacing).
getBytes() - Method in class ij.process.LUT
getBytesPerPixel() - Method in class ij.ImagePlus
  Returns the number of bytes per pixel.
getBytesPerPixel() - Method in class ij.io.FileInfo
  Returns the number of bytes used per pixel.
getC() - Method in class ij.ImagePlus
  Returns the current hyperstack channel position.
getCachedFont() - Static method in class ij.Menus
getCalibration() - Method in class ij.ImagePlus
  Returns this image's calibration.
getCalibrationTable() - Method in class ij.process.ImageProcessor
  Returns the calibration table or null.
getCanvas() - Method in class ij.gui.ImageWindow
getCanvas() - Method in class ij.ImagePlus
  Returns the ImageCanvas being used to display this image, or null.
getCaseSensitive() - Method in class ij.util.WildcardMatch
  Returns the current state of case sensitivity.
getChannel() - Method in class ij.ImagePlus
getChannel(int) - Method in class ij.process.ColorProcessor
  Returns the specified plane (1=red, 2=green, 3=blue, 4=alpha) as a byte array.
getChannel(int, ByteProcessor) - Method in class ij.process.ColorProcessor
  Returns the specified plane (1=red, 2=green, 3=blue, 4=alpha) as a ByteProcessor.
getChannel(ImagePlus, int) - Static method in class ij.plugin.ChannelSplitter
  Returns, as an ImageStack, the specified channel, where 'c' must be greater than zero and less than or equal to the number of channels in the image.
getChannelColor() - Method in class ij.CompositeImage
  Returns the color used to display the image subtitle and "Binvalid input: '&C'" histogram.
getChannelLut() - Method in class ij.CompositeImage
getChannelLut(int) - Method in class ij.CompositeImage
getChannelProcessor() - Method in class ij.CompositeImage
getChannelProcessor() - Method in class ij.ImagePlus
  Returns a reference to the current ImageProcessor.
getCheckboxes() - Method in class ij.gui.GenericDialog
  Returns the Vector containing the Checkboxes.
getChoices() - Method in class ij.gui.GenericDialog
  Returns the Vector containing the Choices.
getClassLoader() - Static method in class ij.IJ
  Returns the class loader ImageJ uses to run plugins or the system class loader if Menus.getPlugInsPath() returns null.
getClipboard() - Static method in class ij.ImagePlus
  Returns the internal clipboard or null if the internal clipboard is empty.
getClosestPoint(double, double, FloatPolygon) - Method in class ij.gui.PointRoi
getClosestPoint(double, double, FloatPolygon) - Method in class ij.gui.PolygonRoi
getCode() - Method in class ij.io.FileInfo
  Returns JavaScript code that can be used to recreate this FileInfo.
getCode() - Method in class ij.macro.Program
getCoefficients() - Method in class ij.measure.Calibration
  Returns the calibration function coefficients.
getColor() - Method in class ij.gui.ColorChooser
  Displays a color selection dialog and returns the color selected by the user.
getColor() - Static method in class ij.gui.Roi
  Returns the default (global) color used for drawing ROI outlines.
getColor() - Method in class ij.gui.Toolbar
  Deprecated.
  replaced by getForegroundColor()
getColor(int, int) - Method in class ij.process.ColorProcessor
getColor(String, Color) - Static method in class ij.plugin.Colors
  For named colors, converts the name String to the corresponding color.
getColor(String, Color) - Static method in class ij.Prefs
  Finds a color in IJ_Props or IJ_Prefs.txt.
getColorModel() - Method in class ij.ImageStack
  Returns this stack's color model.
getColorModel() - Method in class ij.LookUpTable
getColorModel() - Method in class ij.process.ImageProcessor
  Returns this processor's color model.
getColorModel() - Method in class ij.process.LUT
getColorName(Color, String) - Static method in class ij.plugin.Colors
  For named colors, returns the name, or 'defaultName' if not a named color.
getColors(String...) - Static method in class ij.plugin.Colors
  Returns an array of the color Strings in the argument(s) and the 13 predefined color names "Red", "Green", ...
getColumn(int) - Method in class ij.measure.ResultsTable
  Returns a copy of the given column as a float array, or null if the column is empty.
getColumn(int, int, float[], int) - Method in class ij.process.ImageProcessor
  Returns the pixel values down the column starting at (x,y).
getColumn(int, int, int[], int) - Method in class ij.process.ImageProcessor
  Returns the pixel values down the column starting at (x,y).
getColumn(String) - Method in class ij.measure.ResultsTable
  Returns a copy of the given column as a double array, or null if the column is not found.
getColumnAsDoubles(int) - Method in class ij.measure.ResultsTable
  Returns a copy of the given column as a double array, or null if the column is empty.
getColumnAsStrings(String) - Method in class ij.measure.ResultsTable
  Returns a copy of the given column as a String array, or null if the column is not found.
getColumnAsVariables(String) - Method in class ij.measure.ResultsTable
  Implements the Table.getColumn() macro function.
getColumnAverageProfile(Rectangle, ImageProcessor) - Static method in class ij.gui.ProfilePlot
getColumnHeading(int) - Method in class ij.measure.ResultsTable
  Returns the heading of the specified column or null if the column is empty.
getColumnHeadings() - Method in class ij.measure.ResultsTable
  Returns a tab or comma delimited string containing the column headings.
getColumnHeadings() - Method in class ij.text.TextPanel
  Returns the column headings as a tab-delimited string.
getColumnIndex(String) - Method in class ij.measure.ResultsTable
  Returns the index of the first column with the given heading.
getCommand() - Static method in class ij.Executer
  Returns the last command executed.
getCommand() - Static method in class ij.plugin.frame.Recorder
  Returns the name of the command currently being recorded, or null.
getCommandName() - Static method in class ij.ImageJ
getCommandOptions() - Static method in class ij.plugin.frame.Recorder
  Used by GenericDialog to determine if any options have been recorded.
getCommands() - Static method in class ij.Menus
  Returns the hashtable that associates commands with plugins.
getCompletedMinimizations() - Method in class ij.measure.Minimizer
  Get number of minimizations completed (i.e.
getComplexTransform() - Method in class ij.process.FHT
  Converts this FHT to a complex Fourier transform and returns it as a two slice stack.
getCompositeMode() - Method in class ij.ImagePlus
  Returns the display mode (IJ.COMPOSITE, IJ.COLOR or IJ.GRAYSCALE) if this is a CompositeImage, otherwise returns -1.
getContainedFloatPoints() - Method in class ij.gui.PointRoi
  Returns the points as a FloatPolygon.
getContainedFloatPoints() - Method in class ij.gui.Roi
  Returns the coordinates of the pixels inside this ROI as a FloatPolygon.
getContainedPoints() - Method in class ij.gui.PointRoi
  Returns the points as an array of Points.
getContainedPoints() - Method in class ij.gui.Roi
  Returns the coordinates of the pixels inside this ROI as an array of Points.
getContourCentroid() - Method in class ij.gui.Roi
getControlPanelProperties() - Static method in class ij.Prefs
getConvexHull() - Method in class ij.gui.Roi
  Returns the convex hull of this Roi as a Polygon with integer coordinates by rounding the floating-point values.
getConvexHull() - Method in class ij.process.FloatPolygon
  Uses the gift wrap algorithm to find the convex hull of all points in this FloatPolygon and returns it as a new FloatPolygon.
getCopy() - Method in class ij.process.FHT
  Returns a clone of this FHT.
getCornerDiameter() - Method in class ij.gui.Roi
  Returns the rounded rectangle corner diameter (pixels).
getCount() - Method in class ij.plugin.frame.RoiManager
  Returns the ROI count.
getCount(int) - Method in class ij.gui.PointRoi
  Returns the count associated with the specified counter index.
getCounter() - Method in class ij.gui.PointRoi
  Returns the index of the current counter.
getCounter() - Method in class ij.measure.ResultsTable
  Returns the current value of the measurement counter.
getCounter() - Static method in class ij.plugin.filter.Analyzer
  Returns the current measurement count.
getCounter(int) - Method in class ij.gui.PointRoi
  Returns the counter assocated with the specified point.
getCounterChoices() - Static method in class ij.gui.PointRoi
getCounterInfo() - Method in class ij.gui.PointRoi
getCounters() - Method in class ij.gui.PointRoi
  Returns an array containing for each point: The counter number (0-100) in the lower 8 bits, and the slice number (or 0, if the point appears on all slices) in the higher 24 bits.
getCPosition() - Method in class ij.gui.Roi
  Returns the channel position of this ROI, or zero if this ROI is not associated with a particular channel.
getCrossLoc() - Method in class ij.plugin.Orthogonal_Views
getCTable() - Method in class ij.measure.Calibration
  Returns the calibration table.
getCurrentColorModel() - Method in class ij.process.ImageProcessor
  Returns the current color model, which may have been modified by setMinAndMax() or setThreshold().
getCurrentErrStream() - Static method in class ij.io.LogStream
  Returns the redirection stream for `System.err` if it exists.
getCurrentFont() - Method in class ij.gui.Plot
  Returns the font currently used (e.g.
getCurrentFont() - Method in class ij.gui.TextRoi
  Returns the current font.
getCurrentImage() - Static method in class ij.WindowManager
  Returns a reference to the active image or null if there isn't one.
getCurrentOutStream() - Static method in class ij.io.LogStream
  Returns the redirection stream for `System.out` if it exists.
getCurrentPasteMode() - Static method in class ij.gui.Roi
  Returns the current paste transfer mode.
getCurrentSlice() - Method in class ij.ImagePlus
  Returns the current stack index (one-based) or 1 if this is a single image.
getCurrentWindow() - Static method in class ij.WindowManager
  Returns the active ImageWindow.
getCursorLoc() - Method in class ij.gui.ImageCanvas
  Returns the current cursor location in image coordinates.
getCustomPrefsPath() - Static method in class ij.Prefs
  Returns the custom preferences (IJ_Prefs.txt) file path.
getCustomPropsPath() - Static method in class ij.Prefs
  Returns the custom properties (IJ_Props.txt) file path.
getCustomRoi() - Method in class ij.gui.ImageCanvas
getCValue(double) - Method in class ij.measure.Calibration
  Converts a raw pixel value to a density calibrated value.
getCValue(int) - Method in class ij.measure.Calibration
  Converts a raw pixel value to a density calibrated value.
getDataObjectArrays(int) - Method in class ij.gui.Plot
  Get the data of the n-th Plot Object containing xy data in the sequence they were added (Other Plot Objects such as labels, arrows, lines, shapes and hidden PlotObjects are not counted).
getDataObjectDesignations() - Method in class ij.gui.Plot
  Gets an array with human-readable designations of the PlotObjects containing xy data in the sequence they were added.
getDebugger() - Method in class ij.macro.Interpreter
getDebugInfo() - Method in class ij.gui.PolygonRoi
getDebugInfo() - Method in class ij.gui.Roi
getDecimalPlaces(double) - Static method in class ij.util.Tools
  Returns the number of decimal places needed to display a number, or -2 if exponential notation should be used.
getDecimalPlaces(double, double) - Static method in class ij.util.Tools
  Returns the number of decimal places needed to display two numbers, or -2 if exponential notation should be used.
getDefault16bitRange() - Static method in class ij.ImagePlus
  Returns the default 16-bit display range, 0 (auto-scaling), 8, 10, 12, 14, 15 or 16.
getDefaultColorModel() - Method in class ij.process.ImageProcessor
  Returns the default grayscale IndexColorModel.
getDefaultCrossColor() - Static method in class ij.gui.PointRoi
  Deprecated
getDefaultDirectory() - Static method in class ij.io.OpenDialog
  Returns the default directory as a string ending in the separator character ("/" or "\"), or a null string.
getDefaultDirectory() - Static method in class ij.Prefs
  Returns the default directory, if any, or null.
getDefaultDoubleHeaded() - Static method in class ij.gui.Arrow
getDefaultFillColor() - Static method in class ij.gui.Roi
getDefaultFlags() - Static method in class ij.gui.Plot
  The default flags, taking PlotWindow.noGridLines, PlotWindow.noTicks into account
getDefaultFont() - Method in class ij.gui.Plot
  Returns the default font for the plot
getDefaultFontName() - Static method in class ij.gui.TextRoi
  Returns the name of the default font.
getDefaultFontSize() - Static method in class ij.gui.PlotWindow
getDefaultFontSize() - Static method in class ij.gui.TextRoi
  Returns the default font size.
getDefaultFontStyle() - Static method in class ij.gui.TextRoi
  Returns the default font style.
getDefaultGroup() - Static method in class ij.gui.Roi
  Returns the group value assigned to newly created ROIs.
getDefaultHandleSize() - Static method in class ij.gui.Roi
  Returns the default handle size.
getDefaultHeading(int) - Static method in class ij.measure.ResultsTable
getDefaultHeadings() - Static method in class ij.measure.ResultsTable
  Returns the default headings ("Area","Mean","StdDev", etc.).
getDefaultHeadSize() - Static method in class ij.gui.Arrow
getDefaultMarkerSize() - Static method in class ij.gui.PointRoi
  Deprecated.
getDefaultOutline() - Static method in class ij.gui.Arrow
getDefaultSize() - Static method in class ij.gui.PointRoi
  Returns the default point size 0-6 (Tiny-XXXL).
getDefaultStrokeColor() - Static method in class ij.plugin.RectToolOptions
getDefaultStrokeWidth() - Static method in class ij.gui.Roi
  Returns the default stroke width.
getDefaultStrokeWidth() - Static method in class ij.plugin.RectToolOptions
getDefaultStyle() - Static method in class ij.gui.Arrow
getDefaultType() - Static method in class ij.gui.PointRoi
getDefaultWidth() - Static method in class ij.gui.Arrow
getDescriptionString() - Method in class ij.io.FileSaver
  Returns a string containing information about the specified image.
getDimensions() - Method in class ij.ImagePlus
  Returns the dimensions of this image (width, height, nChannels, nSlices, nFrames) as a 5 element int array.
getDimensions(boolean) - Method in class ij.ImagePlus
getDir(String) - Static method in class ij.IJ
  Alias for getDirectory().
getDir(String) - Method in class ij.io.Opener
getDir(String) - Static method in class ij.Macro
getDirectory() - Method in class ij.io.DirectoryChooser
  Returns the directory selected by the user.
getDirectory() - Method in class ij.io.OpenDialog
  Returns the selected directory.
getDirectory() - Method in class ij.io.SaveDialog
  Returns the selected directory.
getDirectory() - Method in class ij.macro.Functions
getDirectory() - Method in class ij.plugin.FileInfoVirtualStack
getDirectory() - Method in class ij.VirtualStack
  Returns the path to the directory containing the images.
getDirectory(String) - Static method in class ij.IJ
  Returns the path to the specified directory if `title` is "home" ("user.home"), "downloads", "startup", "imagej" (ImageJ directory), "plugins", "macros", "luts", "temp", "current", "default", "image" (directory active image was loaded from), "file" (directory most recently used to open or save a file), "cwd" (current working directory) or "preferences" (location of "IJ_Prefs.txt" file), otherwise displays a dialog and returns the path to the directory selected by the user.
getDisplayList() - Method in class ij.gui.ImageCanvas
  Deprecated.
  replaced by ImagePlus.getOverlay()
getDisplayMode() - Method in class ij.ImagePlus
  Returns the display mode (IJ.COMPOSITE, IJ.COLOR or IJ.GRAYSCALE) if this is a composite color image, or 0 if it not.
getDisplayRangeMax() - Method in class ij.CompositeImage
getDisplayRangeMax() - Method in class ij.ImagePlus
  Returns the display range maximum of the current channel.
getDisplayRangeMin() - Method in class ij.CompositeImage
getDisplayRangeMin() - Method in class ij.ImagePlus
  Returns the display range minimum of the current channel.
getDoScaling() - Static method in class ij.process.ImageConverter
  Returns true if scaling is enabled.
getDouble(String, double) - Static method in class ij.Prefs
  Retrieves a number from IJ_Props or IJ_Prefs.txt.
getDoubleFromArrayList(ArrayList) - Method in class ij.gui.Plot
getDoubleHeaded() - Method in class ij.gui.Arrow
getDrawBackgrounds() - Method in class ij.gui.Overlay
getDrawingFrame() - Method in class ij.gui.Plot
  Returns the rectangle where the data are plotted.
getDrawLabels() - Method in class ij.gui.Overlay
getDrawLabels() - Method in class ij.plugin.frame.RoiManager
getDrawNames() - Method in class ij.gui.Overlay
getDrawOffset() - Method in class ij.gui.Roi
  Deprecated.
  Drawoffset is not used any more.
getDrawStringMode() - Method in class ij.gui.TextRoi
getEditor() - Method in class ij.plugin.NewPlugin
  Returns the Editor the newly created macro or plugin was opened in.
getErrorMessage() - Method in class ij.gui.GenericDialog
  Returns an error message if getNextNumber was unable to convert a string into a number, otherwise, returns null.
getErrorMessage() - Static method in class ij.IJ
  Returns the last error message written by IJ.error() or null if there was no error since the last time this method was called.
getErrorMessage() - Method in class ij.macro.Interpreter
getErrorMessage() - Static method in class ij.plugin.frame.RoiManager
  Returns the most recent I/O error message, or null if there was no error.
getErrorText() - Method in class ij.plugin.AVI_Reader
  Returns a description of the error reading the file with `makeStack` or null if no error
getEscapeChar() - Method in class ij.util.WildcardMatch
  Returns the character used to escape the wildcard functionality of a wildcard character.
getExamplesMenu(ActionListener) - Static method in class ij.Menus
getExifData(ImagePlus) - Method in class ij.plugin.ImageInfo
getExtensionFunctions() - Method in interface ij.macro.MacroExtension
getf(int) - Method in class ij.process.ByteProcessor
getf(int) - Method in class ij.process.ColorProcessor
getf(int) - Method in class ij.process.FloatProcessor
getf(int) - Method in class ij.process.ImageProcessor
getf(int) - Method in class ij.process.ShortProcessor
getf(int, int) - Method in class ij.process.ByteProcessor
getf(int, int) - Method in class ij.process.ColorProcessor
getf(int, int) - Method in class ij.process.FloatProcessor
getf(int, int) - Method in class ij.process.ImageProcessor
  Returns the value of the pixel at (x,y) as a float.
getf(int, int) - Method in class ij.process.ShortProcessor
getFeretsDiameter() - Method in class ij.gui.Roi
  Returns Feret's diameter, the greatest distance between any two points along the ROI boundary.
getFeretValues() - Method in class ij.gui.EllipseRoi
getFeretValues() - Method in class ij.gui.OvalRoi
  Feret (caliper width) values, see ij.gui.Roi.getFeretValues().
getFeretValues() - Method in class ij.gui.Roi
  Returns an array with the following values:
  [0] "Feret" (maximum caliper width)
  [1] "FeretAngle" (angle of diameter with maximum caliper width, between 0 and 180 deg)
  [2] "MinFeret" (minimum caliper width)
  [3][4] , "FeretX" and "FeretY", the X and Y coordinates of the starting point (leftmost point) of the maximum-caliper-width diameter.
getFileFormat(String) - Static method in class ij.io.Opener
getFileInfo() - Method in class ij.ImagePlus
  Returns a FileInfo object containing information, including the pixel array, needed to save this image.
getFileInfo() - Method in class ij.io.ImportDialog
  Displays the dialog and returns a FileInfo object that can be used to open the image.
getFileName() - Method in class ij.io.OpenDialog
  Returns the selected file name.
getFileName() - Method in class ij.io.SaveDialog
  Returns the selected file name.
getFileName() - Static method in class ij.plugin.MacroInstaller
getFileName(int) - Method in class ij.plugin.FileInfoVirtualStack
getFileName(int) - Method in class ij.VirtualStack
  Returns the file name of the specified slice, where 1<=n<=nslices.
getFilePath() - Method in class ij.io.FileInfo
  Returns the file path.
getFilePath() - Static method in class ij.plugin.Macro_Runner
  Returns the file path of the most recently loaded macro or script.
getFilePath(String) - Static method in class ij.IJ
  Displays an open file dialog and returns the path to the choosen file, or returns null if the dialog is canceled.
getFilePointer() - Method in class ij.io.RandomAccessStream
getFileSeparator() - Static method in class ij.Prefs
  Returns the file.separator system property.
getFileType(String) - Method in class ij.io.Opener
  Attempts to determine the image file type by looking for 'magic numbers' and the file name extension.
getFillColor() - Method in class ij.gui.Roi
  Returns the fill color used to display this ROI, or null if it is displayed transparently.
getFilteredList(String[], String, String) - Static method in class ij.plugin.FolderOpener
getFit() - Method in class ij.measure.CurveFitter
  returns the code of the fit type of the fit performed
getFitCode(String) - Static method in class ij.measure.CurveFitter
  Returns the code for a fit with given name as defined in fitList, or -1 if not found
getFitGoodness() - Method in class ij.measure.CurveFitter
  Get a measure of "goodness of fit" where 1.0 is best.
getFixedMax() - Static method in class ij.gui.ProfilePlot
  Returns the profile plot y-axis max.
getFixedMin() - Static method in class ij.gui.ProfilePlot
  Returns the profile plot y-axis min.
getFlags() - Method in class ij.gui.Plot
  Returns the flags that control the axes
getFloatAngle(double, double, double, double) - Method in class ij.gui.Roi
  Returns the angle in degrees between the specified line and a horizontal line.
getFloatArray() - Method in class ij.process.ImageProcessor
  Returns a copy of the pixel data as a 2D float array with dimensions [x=0..width-1][y=0..height-1].
getFloatBounds() - Method in class ij.gui.Roi
  Returns this selection's bounding rectangle (with subpixel accuracy).
getFloatBounds() - Method in class ij.process.FloatPolygon
getFloatConvexHull() - Method in class ij.gui.Roi
  Returns the convex hull of this Roi as a FloatPolygon.
getFloatConvexHull() - Method in class ij.gui.ShapeRoi
getFloatHeight() - Method in class ij.gui.Roi
getFloatPoints() - Method in class ij.gui.Line
  Returns, as a FloatPolygon, the two points that define this line.
getFloatPolygon() - Method in class ij.gui.Line
  If the width of this line is less than or equal to one, returns the starting and ending coordinates as a 2-point FloatPolygon, or, if the width is greater than one, returns an outline of the line as a 4-point FloatPolygon.
getFloatPolygon() - Method in class ij.gui.OvalRoi
  Returns this OvalRoi as a FloatPolygon approximating the ellipse.
getFloatPolygon() - Method in class ij.gui.PolygonRoi
  Returns this polygon or polyline as float arrays in image pixel coordinates.
getFloatPolygon() - Method in class ij.gui.Roi
  Returns the outline of this selection as a FloatPolygon
getFloatPolygon() - Method in class ij.gui.ShapeRoi
  Returns all vertex points of the shape as approximated by polygons, in image pixel coordinates
getFloatPolygon(double) - Method in class ij.gui.Line
  Obsolete
getFloatPolygon(double, boolean, boolean, boolean) - Method in class ij.gui.ShapeRoi
  Returns a FloatPolygon with all vertices of the flattened shape, i.e., the shape approximated by straight line segments.
getFloatPolygon(Shape, double, boolean, boolean, boolean) - Method in class ij.gui.ShapeRoi
getFloatPolygon(String) - Method in class ij.gui.Roi
  Returns the outline in image pixel coordinates, where options may include "close" to add a point to close the outline if this is an area roi and the outline is not closed yet.
getFloatPolygon(String) - Method in class ij.gui.ShapeRoi
  Returns all vertex points of the shape as approximated by polygons, where options may include "close" to add points to close each subpath, and "separate" to insert NaN values between subpaths (= individual polygons)
getFloatPolygon4() - Method in class ij.gui.OvalRoi
  Returns this OvalRoi as a 4 point FloatPolygon (x,y,w,h).
getFloatWidth() - Method in class ij.gui.Roi
getFont() - Static method in class ij.gui.TextRoi
  Deprecated.
  Replaced by getDefaultFontName
getFont() - Static method in class ij.Menus
getFont() - Method in class ij.process.ImageProcessor
  Returns the current font.
getFont(boolean) - Static method in class ij.Menus
getFont(char) - Method in class ij.gui.Plot
  Gets the font for xLabel ('x'), yLabel('y'), numbers ('f' for 'frame') or the legend ('l').
getFont(String, int, float) - Static method in class ij.util.FontUtil
  Returns a font with the given family name or, if not available, a similar font, e.g.
getFontMetrics() - Method in class ij.process.ImageProcessor
  Returns the current FontMetrics.
getFontSize() - Static method in class ij.Menus
  Returns the size (in points) used for the fonts in ImageJ menus.
getFontSize() - Method in class ij.plugin.frame.Editor
getForegroundColor() - Static method in class ij.gui.Toolbar
getForegroundValue() - Static method in class ij.gui.Toolbar
getForegroundValue() - Method in class ij.process.ByteProcessor
  Returns the foreground fill/draw value.
getForegroundValue() - Method in class ij.process.ColorProcessor
  Returns the foreground fill/draw value.
getForegroundValue() - Method in class ij.process.FloatProcessor
  Returns the foreground fill/draw value.
getForegroundValue() - Method in class ij.process.ImageProcessor
  Returns the default fill/draw value.
getForegroundValue() - Method in class ij.process.ShortProcessor
  Returns the foreground fill/draw value.
getFormula() - Method in class ij.measure.CurveFitter
  returns a String with the formula of the fit function used
getFrame() - Method in class ij.ImagePlus
getFrame(String) - Static method in class ij.WindowManager
  Obsolete; replaced by getWindow().
getFrameRate() - Static method in class ij.plugin.Animator
  Returns the current animation speed in frames per second.
getFreeColumn(String) - Method in class ij.measure.ResultsTable
  Sets the heading of the the first available column and returns that column's index.
getFrontWindow() - Static method in class ij.WindowManager
  Obsolete; replaced by getActiveWindow.
getFullVersion() - Static method in class ij.IJ
  Returns the ImageJ version and build number as a String, for example "1.46n05", or 1.46n99 if there is no build number.
getFunction() - Method in class ij.measure.Calibration
  Returns the calibration function ID.
getFunctionValue() - Method in class ij.measure.Minimizer
  Get the value of the minimum, i.e.
getGap() - Method in class ij.io.FileInfo
  Returns the gap between images as a long.
getGelImage() - Static method in class ij.plugin.GelAnalyzer
getGlobalCalibration() - Method in class ij.ImagePlus
  Returns the system-wide calibration, or null.
getGlobalJustification() - Static method in class ij.gui.TextRoi
  Returns the default text tool justification (LEFT, CENTER or RIGHT).
getGlobals() - Method in class ij.macro.Program
getGreen(String) - Static method in class ij.plugin.Colors
getGreens() - Method in class ij.LookUpTable
getGroup() - Method in class ij.gui.Roi
  Returns the group attribute of this ROI.
getGroupName(int) - Static method in class ij.gui.Roi
  Returns the group name associtated with the specified group.
getGroupNames() - Static method in class ij.gui.Roi
  Returns the group names as a comma-delimeted string.
getGuiScale() - Static method in class ij.Prefs
  Returns the GenericDialog and Command Finder text scale.
getHandleSize() - Method in class ij.gui.Roi
  Returns the current handle size.
getHash(String, boolean, String) - Static method in class ij.util.Tools
  Returns the checksum of a string or file, or "0" if no success.
getHashCode() - Method in class ij.gui.Roi
  Returns a hashcode for this Roi that typically changes if it is moved, even though it is still the same object.
getHeader(ImagePlus) - Static method in class ij.plugin.FITS_Writer
  Extracts the original FITS header from the Properties object of the ImagePlus image (or from the current slice label in the case of an ImageStack) and returns it as an array of String objects representing each card.
getHeadings() - Method in class ij.measure.ResultsTable
  Returns the column headings as an array of Strings.
getHeadingsAsVariableNames() - Method in class ij.measure.ResultsTable
  Returns the column headings; headings not suitable as variable names are converted to valid variable names by replacing non-fitting characters with underscores and adding underscores.
getHeadSize() - Method in class ij.gui.Arrow
getHeight() - Method in class ij.ImagePlus
  Returns the height of this image in pixels.
getHeight() - Method in class ij.ImageStack
getHeight() - Method in class ij.plugin.AVI_Reader
  Returns the image height of the virtual stack
getHeight() - Method in class ij.plugin.FileInfoVirtualStack
getHeight() - Method in class ij.plugin.ListVirtualStack
getHeight() - Method in class ij.process.ImageProcessor
  Returns the height of this image in pixels.
getHideOverlay() - Method in class ij.ImagePlus
getHigherZoomLevel(double) - Static method in class ij.gui.ImageCanvas
getHistogram() - Method in class ij.gui.HistogramPlot
getHistogram() - Method in class ij.gui.HistogramWindow
getHistogram() - Method in class ij.process.ByteProcessor
getHistogram() - Method in class ij.process.ColorProcessor
getHistogram() - Method in class ij.process.FloatProcessor
  Returns a 256 bin histogram of the current ROI or of the entire image if there is no ROI.
getHistogram() - Method in class ij.process.ImageProcessor
  Returns the histogram of the image or ROI.
getHistogram() - Method in class ij.process.ImageStatistics
  Returns the histogram as an array of longs.
getHistogram() - Method in class ij.process.ShortProcessor
  Returns 65,536 bin histogram of the current ROI, which can be non-rectangular.
getHistogram(int) - Method in class ij.process.ImageProcessor
  Returns the histogram of the image or ROI, using the specified number of bins.
getHistogram(ImageProcessor) - Method in class ij.process.ByteProcessor
getHistogram(ImageProcessor) - Method in class ij.process.ColorProcessor
getHistogramMax() - Method in class ij.process.ImageProcessor
  Returns the maximum histogram value used for histograms of float images.
getHistogramMin() - Method in class ij.process.ImageProcessor
  Returns the minimum histogram value used for histograms of float images.
getHistogramSize() - Method in class ij.process.ImageProcessor
  Returns the number of float image histogram bins.
getHomeDir() - Static method in class ij.Prefs
  Obsolete, replaced by getImageJDir(), which, unlike this method, returns a path that ends with File.separator.
getHSB(byte[], byte[], byte[]) - Method in class ij.process.ColorProcessor
  Returns hue, saturation and brightness in 3 byte arrays.
getHSB(float[], float[], float[]) - Method in class ij.process.ColorProcessor
  Returns hue, saturation and brightness in 3 float arrays.
getHSB32Stack() - Method in class ij.process.ColorProcessor
  Returns an ImageStack with three 32-bit slices, representing hue, saturation and brightness
getHSBStack() - Method in class ij.process.ColorProcessor
  Returns an ImageStack with three 8-bit slices, representing hue, saturation and brightness
getID() - Method in class ij.ImagePlus
  Returns this image's unique numeric ID.
getIDList() - Static method in class ij.WindowManager
  Returns a list of the IDs of open images.
getImage() - Method in class ij.CompositeImage
getImage() - Method in class ij.gui.ImageCanvas
  Returns the ImagePlus object that is associated with this ImageCanvas.
getImage() - Method in class ij.gui.Roi
  Returns the ImagePlus associated with this ROI, or null.
getImage() - Static method in class ij.IJ
  Returns a reference to the active image, or displays an error message and aborts the plugin or macro if no images are open.
getImage() - Method in class ij.ImagePlus
  Returns this image as a AWT image.
getImage() - Static method in class ij.plugin.Orthogonal_Views
getImage(int) - Static method in class ij.WindowManager
  For IDs less than zero, returns the ImagePlus with the specified ID.
getImage(Interpreter) - Static method in class ij.IJ
  The macro interpreter uses this method to call getImage().
getImage(String) - Static method in class ij.WindowManager
  Returns the first image that has the specified title or null if it is not found.
getImageArray() - Method in class ij.ImageStack
  Returns the stack as an array of 1D pixel arrays.
getImageArray() - Method in class ij.VirtualStack
  Returns null.
getImageCount() - Static method in class ij.WindowManager
  Returns the number of open images.
getImageFromVector(int) - Method in class ij.plugin.frame.SyncWindows
  Get ImagePlus from Windows-Vector vwins.
getImageID() - Method in class ij.gui.Roi
  Returns the ID of the image associated with this ROI.
getImageID() - Static method in class ij.plugin.Orthogonal_Views
getImageIDs() - Static method in class ij.plugin.Orthogonal_Views
  Returns the IDs of the XY, YZ and XZ images as an int array.
getImageInfo(ImagePlus) - Method in class ij.plugin.ImageInfo
getImageInfo(ImagePlus, ImageProcessor) - Method in class ij.plugin.filter.Info
  Deprecated.
getImageJDir() - Static method in class ij.Prefs
  Returns the path, ending in File.separator, to the ImageJ directory.
getImageJMenu(String) - Static method in class ij.Menus
  Returns the specified ImageJ menu (e.g., "File>New") or null if it is not found.
getImagePlus() - Method in class ij.gui.ImageWindow
getImagePlus() - Method in class ij.gui.Plot
  Returns the plot as an ImagePlus.
getImagePlus() - Method in class ij.plugin.AVI_Reader
  Returns the ImagePlus opened by run().
getImageProperties() - Method in class ij.ImagePlus
getImageSize(ImagePlus) - Static method in class ij.gui.ImageWindow
getImageStack() - Method in class ij.ImagePlus
  Returns the base image stack.
getImageStackSize() - Method in class ij.ImagePlus
  If this is a stack, returns the actual number of images in the stack, else returns 1.
getImagesURL() - Static method in class ij.Prefs
  Returns the URL of the directory that contains the ImageJ sample images.
getImageTitleFromVector(int) - Method in class ij.plugin.frame.SyncWindows
  Get the title of image n from Windows-Vector vwins.
getImageTitles() - Static method in class ij.WindowManager
  Returns a list of the titles of all open images.
getImports() - Method in class ij.plugin.PlugInInterpreter
  Returns the import statements that are added to the script.
getIndex(String) - Method in class ij.gui.Overlay
  Returns the index of the ROI with the specified name, or -1 if not found.
getIndex(String) - Method in class ij.plugin.frame.RoiManager
  Returns the index of the first ROI with the specified name, or -1 if no ROI has that name.
getIndexes() - Method in class ij.plugin.frame.RoiManager
  Returns an array of the selected indexes or all indexes if none are selected.
getIndexesAsString() - Static method in class ij.plugin.frame.RoiManager
  This is a macro-callable version of getSelectedIndexes().
getIndexOfImage(ImagePlus) - Method in class ij.plugin.frame.SyncWindows
  Get index of "image" in vector of synchronized windows, if image is in vector.
getIndexSampleModel() - Method in class ij.process.ImageProcessor
getInfo() - Method in class ij.ImageJ
getInfo(String) - Method in class ij.plugin.DICOM
  Returns the DICOM tags of the specified file as a string.
getInfoProperty() - Method in class ij.ImagePlus
  Returns the "Info" property string, or null if it is not found.
getInitialMagnification() - Method in class ij.gui.ImageWindow
getInsets() - Method in class ij.gui.GenericDialog
getInsets() - Method in class ij.gui.ImageWindow
getInsets() - Method in class ij.plugin.frame.SyncWindows
getInsets(boolean) - Method in class ij.gui.ImageWindow
  Override Container getInsets() to make room for some text above the image.
getInstance() - Static method in class ij.gui.GenericDialog
getInstance() - Static method in class ij.gui.Toolbar
  Returns a reference to the ImageJ toolbar.
getInstance() - Static method in class ij.IJ
  Returns a reference to the "ImageJ" frame.
getInstance() - Static method in class ij.macro.Interpreter
getInstance() - Static method in class ij.plugin.frame.Channels
  Obsolete; always returns null.
getInstance() - Static method in class ij.plugin.frame.Editor
getInstance() - Static method in class ij.plugin.frame.Recorder
getInstance() - Static method in class ij.plugin.frame.RoiManager
  Returns a reference to the ROI Manager, or null if it is not open and a batch mode macro is not running.
getInstance() - Static method in class ij.plugin.frame.SyncWindows
getInstance() - Static method in class ij.plugin.Orthogonal_Views
getInstance2() - Static method in class ij.plugin.frame.RoiManager
  Returns a reference to the ROI Manager window or to the macro batch mode RoiManager, or null if neither exists.
getInt(String, int) - Static method in class ij.Prefs
  Retrieves a number from IJ_Props or IJ_Prefs.txt.
getInt(Properties, String) - Static method in class ij.OtherInstance
getIntArray() - Method in class ij.process.ImageProcessor
  Returns a copy of the pixel data as a 2D int array with dimensions [x=0..width-1][y=0..height-1].
getInterpolate() - Method in class ij.process.ImageProcessor
  Returns the value of the interpolate field.
getInterpolatedPixel(double, double) - Method in class ij.process.ByteProcessor
  Uses the current interpolation method (BILINEAR or BICUBIC) to calculate the pixel value at real coordinates (x,y).
getInterpolatedPixel(double, double) - Method in class ij.process.ColorProcessor
  Calls getPixelValue(x,y).
getInterpolatedPixel(double, double) - Method in class ij.process.FloatProcessor
  Uses the current interpolation method (BILINEAR or BICUBIC) to calculate the pixel value at real coordinates (x,y).
getInterpolatedPixel(double, double) - Method in class ij.process.ImageProcessor
  Uses the current interpolation method (bilinear or bicubic) to find the pixel value at real coordinates (x,y).
getInterpolatedPixel(double, double) - Method in class ij.process.ShortProcessor
  Uses the current interpolation method (BILINEAR or BICUBIC) to calculate the pixel value at real coordinates (x,y).
getInterpolatedPolygon() - Method in class ij.gui.Roi
  Returns, as a FloatPolygon, an interpolated version of this selection that has points spaced 1.0 pixel apart.
getInterpolatedPolygon(double, boolean) - Method in class ij.gui.PolygonRoi
getInterpolatedPolygon(double, boolean) - Method in class ij.gui.Roi
  Returns, as a FloatPolygon, an interpolated version of this selection with points spaced 'interval' pixels apart.
getInterpolatedPolygon(FloatPolygon, double, boolean) - Method in class ij.gui.Roi
  Returns, as a FloatPolygon, an interpolated version of this selection with points spaced abs('interval') pixels apart.
getInterpolatedRGBPixel(double, double) - Method in class ij.process.ColorProcessor
  Uses bilinear interpolation to find the pixel value at real coordinates (x,y).
getInterpolatedValue(double, double) - Method in class ij.process.ImageProcessor
  Uses bilinear interpolation to find the pixel value at real coordinates (x,y).
getInterpolationMethod() - Method in class ij.process.ImageProcessor
  Returns the current interpolation method (NONE, BILINEAR or BICUBIC).
getInterpolationMethods() - Static method in class ij.process.ImageProcessor
getInverse(ImagePlus) - Method in class ij.gui.Roi
  Returns the inverted roi, or null if this is not an area roi or cannot be converted to a ShapeRoi.
getInvertY() - Method in class ij.measure.Calibration
  Returns the 'invertY' flag.
getIterations() - Method in class ij.measure.CurveFitter
  Get number of iterations performed.
getIterations() - Method in class ij.measure.Minimizer
  Get number of iterations performed (includes all restarts).
getJarFileForMenuEntry(String) - Static method in class ij.Menus
getJpegQuality() - Static method in class ij.io.FileSaver
  Returns the current JPEG quality setting (0-100).
getJSPrefix(String) - Static method in class ij.plugin.frame.Editor
getJustification() - Method in class ij.gui.TextRoi
  Returns the value of the 'justification' instance variable (LEFT, CENTER or RIGHT).
getLab(ImageProcessor, byte[], byte[], byte[]) - Static method in class ij.plugin.frame.ColorThresholder
  Returns Lab in 3 byte arrays.
getLabel() - Method in class ij.gui.GenericDialog
  Returns a reference to the label of the most recently added numeric field, string field, choice or slider.
getLabel(char) - Method in class ij.gui.Plot
  Gets the label String of the xLabel ('x'), yLabel('y') or the legend ('l').
getLabel(int) - Method in class ij.measure.ResultsTable
  Returns the label of the specified row.
getLabelColor() - Method in class ij.gui.Overlay
getLabelFont() - Method in class ij.gui.Overlay
getLast() - Method in class ij.util.FloatArray
  Returns the last element of this FloatArray.
getLastBatchModeImage() - Static method in class ij.macro.Interpreter
getLastColumn() - Method in class ij.measure.ResultsTable
  Returns the index of the last used column, or -1 if no columns are used.
getLastCounter() - Method in class ij.gui.PointRoi
  Returns the index of the last counter.
getLastDirectory() - Static method in class ij.io.OpenDialog
  Returns the path to the directory that contains the last file opened or saved, or null if a file has not been opened or saved.
getLastFileInfo() - Static method in class ij.io.ImportDialog
  Returns the FileInfo object used to import the last raw image, or null if a raw image has not been imported.
getLastName() - Static method in class ij.io.OpenDialog
  Returns the name of the last file opened by the user using a file open or file save dialog, or using drag and drop.
getLength() - Method in class ij.gui.EllipseRoi
  Returns the perimeter of this ellipse.
getLength() - Method in class ij.gui.Line
  Returns the length of this line.
getLength() - Method in class ij.gui.OvalRoi
  Returns the perimeter length using Ramanujan's approximation for the circumference of an ellipse
getLength() - Method in class ij.gui.PolygonRoi
  Returns the perimeter (for ROIs) or length (for lines).
getLength() - Method in class ij.gui.Roi
  Returns the perimeter length.
getLength() - Method in class ij.gui.ShapeRoi
  Returns the perimeter of this ShapeRoi.
getLength(boolean) - Method in class ij.process.FloatPolygon
getLimits() - Method in class ij.gui.Plot
  Returns the current limits as an array xMin, xMax, yMin, yMax.
getLine(double, double, double, double) - Method in class ij.process.ImageProcessor
  Returns an array containing the pixel values along the line starting at (x1,y1) and ending at (x2,y2).
getLine(int) - Method in class ij.text.TextPanel
  Returns the specified line as a string.
getLineCount() - Method in class ij.text.TextPanel
  Returns the number of lines of text in this TextPanel.
getLineNumber() - Method in class ij.macro.Interpreter
getLineWidth() - Method in class ij.process.ImageProcessor
  Returns the current line width.
getList() - Method in class ij.plugin.frame.RoiManager
  Deprecated.
getListenerCount() - Static method in class ij.Executer
getListeners() - Static method in class ij.gui.Roi
getListeners() - Static method in class ij.ImagePlus
getLoadRate(double, ImagePlus) - Static method in class ij.io.Opener
getLocalCalibration() - Method in class ij.ImagePlus
  Returns this image's local calibration, ignoring the "Global" calibration flag.
getLocation(String) - Static method in class ij.Prefs
  Uses the keyword `key` to retrieve a location from the preferences file.
getLocationAsString(int, int) - Method in class ij.ImagePlus
  Converts the current cursor location to a string.
getLog() - Static method in class ij.IJ
  Returns the contents of the Log window or null if the Log window is not open.
getLongFilePointer() - Method in class ij.io.RandomAccessStream
getLookAndFeel() - Static method in class ij.util.Java2
  Returns the current Swing look and feel or null.
getLowerZoomLevel(double) - Static method in class ij.gui.ImageCanvas
getLut() - Method in class ij.process.ImageProcessor
getLut(String) - Static method in class ij.plugin.LutLoader
  Returns the LUT 'name' as an IndexColorModel, where 'name' can be any entry in the Image/Lookup Tables menu.
getLuts() - Method in class ij.CompositeImage
getLuts() - Static method in class ij.IJ
  Returns, as an array of strings, a list of the LUTs in the Image/Lookup Tables menu.
getLuts() - Method in class ij.ImagePlus
  Returns an array containing the lookup tables used by this image, one per channel, or an empty array if this is an RGB image.
getLutUpdateMode() - Method in class ij.process.ImageProcessor
  Returns the LUT update mode, which can be RED_LUT, BLACK_AND_WHITE_LUT, OVER_UNDER_LUT or NO_LUT_UPDATE.
getMacroCode() - Method in class ij.measure.CurveFitter
  Returns macro code of the form "y = ...x" for the fit function used.
getMacroCode(String, ImagePlus) - Method in class ij.gui.TextRoi
  Used by the Recorder for recording the text tool.
getMacroCount() - Method in class ij.Menus
getMacroCount() - Method in class ij.plugin.MacroInstaller
getMacroCount() - Method in class ij.plugin.tool.MacroToolRunner
getMacroProgram() - Method in class ij.plugin.tool.MacroToolRunner
getMacroProgram() - Method in class ij.plugin.tool.PlugInTool
getMacroShortcuts() - Static method in class ij.Menus
  Returns the hashtable that associates keyboard shortcuts with macros.
getMacrosMenu() - Static method in class ij.Menus
getMacrosPath() - Static method in class ij.Menus
  Returns the path to the macros directory or null if the macros directory was not found.
getMagnification() - Method in class ij.gui.ImageCanvas
getMagnification() - Method in class ij.gui.Roi
getMapSize() - Method in class ij.LookUpTable
getMask() - Method in class ij.gui.Arrow
getMask() - Method in class ij.gui.OvalRoi
getMask() - Method in class ij.gui.PointRoi
getMask() - Method in class ij.gui.PolygonRoi
getMask() - Method in class ij.gui.Roi
  Always returns null for rectangular Roi's
getMask() - Method in class ij.gui.ShapeRoi
  Returns this ROI's mask pixels as a ByteProcessor with pixels "in" the mask set to white (255) and pixels "outside" the mask set to black (0).
getMask() - Method in class ij.ImagePlus
  For images with irregular ROIs, returns a byte mask, otherwise, returns null.
getMask() - Method in class ij.process.ImageProcessor
  For images with irregular ROIs, returns a mask, otherwise, returns null.
getMask(int, int) - Method in class ij.process.PolygonFiller
  Returns a byte mask containing a filled version of the polygon.
getMaskArray() - Method in class ij.process.ImageProcessor
  Returns a reference to the mask pixel array, or null if there is no mask.
getMatchingCoords(ImageCanvas, ImageCanvas, int, int) - Method in class ij.plugin.frame.SyncWindows
  Get Screen Coordinates for ImageCanvas ic matching the OffScreen Coordinates of the current ImageCanvas.
getMax() - Method in class ij.gui.ProfilePlot
  Returns the calculated maximum value.
getMax() - Method in class ij.process.ByteProcessor
  Returns the largest displayed pixel value.
getMax() - Method in class ij.process.ColorProcessor
  Returns the largest displayed pixel value.
getMax() - Method in class ij.process.FloatProcessor
  Returns the largest displayed pixel value.
getMax() - Method in class ij.process.ImageProcessor
  Returns the maximum displayed pixel value.
getMax() - Method in class ij.process.ShortProcessor
  Returns the largest displayed pixel value.
getMax(double[]) - Static method in class ij.measure.CurveFitter
  Gets index of highest value in an array.
getMaxima(ImageProcessor, double, boolean) - Method in class ij.plugin.filter.MaximumFinder
  Finds the image maxima and returns them as a Polygon, where poly.npoints is the number of maxima.
getMaxima(ImageProcessor, double, boolean, boolean) - Method in class ij.plugin.filter.MaximumFinder
  Finds the image maxima and returns them as a Polygon, where poly.npoints is the number of maxima.
getMaximum() - Method in class ij.gui.ScrollbarWithLabel
getMaximum() - Method in class ij.util.ArrayUtil
  The maximum value
getMaximumBounds() - Method in class ij.gui.ImageWindow
getMaxIterations() - Method in class ij.measure.CurveFitter
  Get maximum number of iterations allowed (sum of iteration count for all restarts)
getMaxIterations() - Method in class ij.measure.Minimizer
  Get maximum number of iterations allowed.
getMaxRestarts() - Method in class ij.measure.Minimizer
  Get maximum number of minimization restarts to do
getMaxThreshold() - Method in class ij.process.ImageProcessor
  Returns the upper threshold level.
getMaxWindowBounds() - Static method in class ij.gui.GUI
getMaxWindowBounds(Component) - Static method in class ij.gui.GUI
getMaxWindowBounds(Point) - Static method in class ij.gui.GUI
getMean() - Method in class ij.util.ArrayUtil
  Average value
getMeasurements() - Static method in class ij.plugin.filter.Analyzer
getMemorySetting() - Method in class ij.plugin.Memory
getMenuBar() - Static method in class ij.Menus
getMenus() - Method in class ij.macro.Program
getMessage() - Method in class ij.gui.GenericDialog
  Returns a reference to the Label or MultiLineLabel created by the last addMessage() call.
getMethod() - Static method in class ij.plugin.frame.ThresholdAdjuster
  Returns the current thresholding method ("Default", "Huang", etc).
getMethods() - Static method in class ij.process.AutoThresholder
getMin() - Method in class ij.gui.ProfilePlot
  Returns the calculated minimum value.
getMin() - Method in class ij.process.ByteProcessor
  Returns the smallest displayed pixel value.
getMin() - Method in class ij.process.ColorProcessor
  Returns the smallest displayed pixel value.
getMin() - Method in class ij.process.FloatProcessor
  Returns the smallest displayed pixel value.
getMin() - Method in class ij.process.ImageProcessor
  Returns the minimum displayed pixel value.
getMin() - Method in class ij.process.ShortProcessor
  Returns the smallest displayed pixel value.
getMinimizer() - Method in class ij.measure.CurveFitter
  Returns a reference to the Minimizer used, for accessing Minimizer methods directly.
getMinimum() - Method in class ij.gui.ScrollbarWithLabel
getMinimum() - Method in class ij.util.ArrayUtil
  The minimum value
getMinimumSize() - Method in class ij.gui.ImagePanel
getMinimumSize() - Method in class ij.gui.MultiLineLabel
getMinimumSize() - Method in class ij.gui.Plot
  The minimum plot size including borders, in pixels (at scale=1)
getMinimumSize() - Method in class ij.gui.ScrollbarWithLabel
getMinimumSize() - Method in class ij.gui.Toolbar
getMinimumSize() - Method in class ij.gui.TrimmedButton
getMinMax(double[]) - Static method in class ij.util.Tools
  Determines the minimum and maximum value in the array `a` and returns them as 2-element array {minimum, maximum}.
getMinMax(float[]) - Static method in class ij.util.Tools
  Determines the minimum and maximum value in the array `a` and returns them as 2-element array {minimum, maximum}.
getMinThreshold() - Method in class ij.process.ImageProcessor
  Returns the lower threshold level.
getMode() - Method in class ij.CompositeImage
getMode() - Static method in class ij.plugin.frame.ThresholdAdjuster
  Returns the current mode ("Red","Binvalid input: '&W'" or"Over/Under").
getMode() - Static method in class ij.plugin.WandToolOptions
getModeAsString() - Method in class ij.CompositeImage
getModifiers() - Method in class ij.gui.ImageCanvas
  Returns the mouse event modifiers.
getMultipleWildcardChar() - Method in class ij.util.WildcardMatch
  Returns the character used to specify any amount of characters.
getMultiPointMode() - Static method in class ij.gui.Toolbar
  Returns 'true' if the multi-point tool is enabled.
getName() - Method in class ij.gui.Roi
  Returns the name of this ROI, or null.
getName() - Method in class ij.measure.CurveFitter
  returns the name of the fit function of the fit performed
getName() - Method in class ij.plugin.PlugInInterpreter
  Returns the name of this PlugInInterpreter.
getName() - Method in class ij.plugin.TextReader
  Returns the file name.
getName(int) - Method in class ij.plugin.frame.RoiManager
  Returns the name of the ROI with the specified index, or null if the index is out of range.
getName(String) - Method in class ij.io.Opener
getName(String) - Static method in class ij.Macro
getName(String) - Static method in class ij.plugin.frame.RoiManager
  Returns the name of the ROI with the specified index.
getNbCpus() - Static method in class ij.util.ThreadUtil
getNChannels() - Method in class ij.ImagePlus
  Returns the number of channels.
getNChannels() - Method in class ij.process.ColorProcessor
  Returns the number of color channels (3).
getNChannels() - Method in class ij.process.ImageProcessor
  Returns the number of color channels in the image.
getNChannels() - Method in class ij.process.IntProcessor
  Returns the number of channels (1).
getNCoordinates() - Method in class ij.gui.PolygonRoi
  Returns the number of points that define this PolygonRoi.
getNCounters() - Method in class ij.gui.PointRoi
  Returns the number of counters.
getNDimensions() - Method in class ij.ImagePlus
  Returns the number of dimensions (2, 3, 4 or 5).
getNeighborhood(int, int, double[][]) - Method in class ij.process.ImageProcessor
  Experimental
getNextBoolean() - Method in class ij.gui.GenericDialog
  Returns the state of the next checkbox.
getNextChoice() - Method in class ij.gui.GenericDialog
  Returns the selected item in the next popup menu.
getNextChoiceIndex() - Method in class ij.gui.GenericDialog
  Returns the index of the selected item in the next popup menu.
getNextEnumChoice(Class<E>) - Method in class ij.gui.GenericDialog
  Returns the selected item in the next enum choice menu.
getNextImage() - Method in class ij.gui.GenericDialog
getNextNumber() - Method in class ij.gui.GenericDialog
  Returns the contents of the next numeric field, or NaN if the field does not contain a number.
getNextRadioButton() - Method in class ij.gui.GenericDialog
  Returns the selected item in the next radio button group.
getNextString() - Method in class ij.gui.GenericDialog
  Returns the contents of the next text field.
getNextText() - Method in class ij.gui.GenericDialog
  Returns the contents of the next text area.
getNFrames() - Method in class ij.ImagePlus
  Returns the number of frames (time-points).
getNonImageTitles() - Static method in class ij.WindowManager
  Returns an array containing the titles of non-image Frames and Dialogs.
getNonImageWindows() - Static method in class ij.WindowManager
  Returns an array containing a list of the non-image Frames.
getNonSplineCoordinates() - Method in class ij.gui.PolygonRoi
getNonSplineFloatPolygon() - Method in class ij.gui.PolygonRoi
getNScrollbars() - Method in class ij.gui.StackWindow
getNSlices() - Method in class ij.ImagePlus
  Returns the image depth (number of z-slices).
getNthImageID(int) - Static method in class ij.WindowManager
  Returns the ID of the Nth open image.
getNumber(String, double) - Static method in class ij.IJ
  Allows the user to enter a number in a dialog box.
getNumberFromList(String, String) - Static method in class ij.util.Tools
  Retrieves a number form a list of key-number pairs like "value1=1234.5 area=1.2e6".
getNumberFromList(String, String, double) - Static method in class ij.util.Tools
getNumericFields() - Method in class ij.gui.GenericDialog
  Returns the Vector containing the numeric TextFields.
getNumericProp(String) - Method in class ij.ImagePlus
  Returns the numeric property associated with the specified key or NaN if the property is not found.
getNumericProperty(String) - Method in class ij.ImagePlus
  Returns the numeric value from the "Info" property string associated with 'key', or NaN if the key is not found or the value associated with the key is not numeric.
getNumParams() - Method in class ij.measure.CurveFitter
  Get number of parameters for current fit formula Do not use before 'doFit', because the fit function would be undefined.
getNumParams(int) - Static method in class ij.measure.CurveFitter
  Returns the number of parameters for a given fit type, except for the 'custom' fit, where the number of parameters is given by the equation: see getNumParams(String)
getNumParams(String) - Static method in class ij.measure.CurveFitter
  Returns the number of parameters for a custom equation given as a macro String, like "y = a + b*x + c*x*x" .
getNumPlotObjects() - Method in class ij.gui.Plot
  Returns the number of PlotObjects (curves, labels, ...) passed with the constructor or added by 'add' or 'draw' methods.
getNumTools() - Method in class ij.gui.Toolbar
getObjectFlags(char) - Method in class ij.gui.Plot
  Gets the flags of the xLabel ('x'), yLabel('y') or the legend ('l').
getOffset() - Method in class ij.io.FileInfo
  Returns the offset as a long.
getOpacity() - Method in class ij.gui.ImageRoi
  Returns the current opacity.
getOpenAsHyperStack() - Method in class ij.ImagePlus
getOpenRecentMenu() - Static method in class ij.Menus
getOpenUsingPlugins() - Static method in class ij.io.Opener
  Returns the state of the openUsingPlugins flag.
getOptions() - Static method in class ij.Macro
  If a command started using run(name, options) is running, and the current thread is the same thread, returns the options string, otherwise, returns null.
getOrCreateResultsTable() - Method in class ij.text.TextPanel
  Returns the ResultsTable associated with this TextPanel, or attempts to create one and returns the created table.
getOrientation() - Method in class ij.gui.ScrollbarWithLabel
getOriginalFileInfo() - Method in class ij.ImagePlus
  Returns the FileInfo object that was used to open this image.
getOutline() - Method in class ij.gui.Arrow
getOutputImage() - Method in class ij.plugin.filter.ParticleAnalyzer
  Returns the "Outlines", "Masks", "Elipses" or "Count Masks" image, or null if "Nothing" is selected in the "Show:" menu.
getOutputType() - Static method in class ij.plugin.filter.EDM
  Returns the current output type (BYTE_OVERWRITE, BYTE, SHORT or FLOAT)
getOvalToolType() - Static method in class ij.gui.Toolbar
  Returns the oval tool type (OVAL_ROI, ELLIPSE_ROI or BRUSH_ROI).
getOverlay() - Method in class ij.gui.ImageCanvas
  Use ImagePlus.getOverlay().
getOverlay() - Method in class ij.ImagePlus
  Returns the current overly, or null if this image does not have an overlay.
getOverlay() - Method in class ij.process.ImageProcessor
getOverlay(ImagePlus) - Static method in class ij.io.FileSaver
getPaintPending() - Method in class ij.gui.ImageCanvas
getParams() - Method in class ij.gui.EllipseRoi
  Returns x1, y1, x2, y2 and aspectRatio as a 5 element array.
getParams() - Method in class ij.gui.RotatedRectRoi
  Returns x1, y1, x2, y2 and width as a 5 element array.
getParams() - Method in class ij.measure.CurveFitter
  Get the result of fitting, i.e.
getParams() - Method in class ij.measure.Minimizer
  Get the result, i.e., the set of parameter values (i.e., variable values) from the best corner of the simplex.
getPasteMode() - Method in class ij.gui.Roi
  Returns the current paste transfer mode, or NOT_PASTING (-1) if no paste operation is in progress.
getPath() - Method in class ij.io.OpenDialog
  Returns the selected file path or null if the dialog was canceled.
getPath(ImagePlus, String) - Static method in class ij.io.SaveDialog
getPixel(int, int) - Method in class ij.ImagePlus
  Returns the pixel value at (x,y) as a 4 element array.
getPixel(int, int) - Method in class ij.process.ByteProcessor
getPixel(int, int) - Method in class ij.process.ColorProcessor
getPixel(int, int) - Method in class ij.process.FloatProcessor
  Returns a pixel value that must be converted using Float.intBitsToFloat().
getPixel(int, int) - Method in class ij.process.ImageProcessor
  Returns the value of the pixel at (x,y).
getPixel(int, int) - Method in class ij.process.ShortProcessor
getPixel(int, int) - Method in class ij.process.SignedShortProcessor
getPixel(int, int, int[]) - Method in class ij.process.ColorProcessor
  Returns the 3 samples for the pixel at (x,y) in an array of int.
getPixel(int, int, int[]) - Method in class ij.process.FloatProcessor
  Returns the value of the pixel at (x,y) in a one element int array.
getPixel(int, int, int[]) - Method in class ij.process.ImageProcessor
  Returns the samples for the pixel at (x,y) in an int array.
getPixelCount() - Method in class ij.process.ImageProcessor
getPixelInterpolated(double, double) - Method in class ij.process.ByteProcessor
getPixelInterpolated(double, double) - Method in class ij.process.ColorProcessor
getPixelInterpolated(double, double) - Method in class ij.process.FloatProcessor
getPixelInterpolated(double, double) - Method in class ij.process.ImageProcessor
  Uses the current interpolation method to find the pixel value at real coordinates (x,y).
getPixelInterpolated(double, double) - Method in class ij.process.ShortProcessor
getPixels() - Method in class ij.gui.Line
  Returns the pixel values along this line.
getPixels() - Method in class ij.process.ByteProcessor
  Returns a reference to the byte array containing this image's pixel data.
getPixels() - Method in class ij.process.ColorProcessor
  Returns a reference to the int array containing this image's pixel data.
getPixels() - Method in class ij.process.FloatProcessor
  Returns a reference to the float array containing this image's pixel data.
getPixels() - Method in class ij.process.ImageProcessor
  Returns a reference to this image's pixel array.
getPixels() - Method in class ij.process.ShortProcessor
  Returns a reference to the short array containing this image's pixel data.
getPixels(int) - Method in class ij.gui.PlotVirtualStack
  Returns the pixel array for the specified slice, where 1<=n<=nslices.
getPixels(int) - Method in class ij.ImageStack
  Returns the pixel array for the specified slice, where 1<=n<=nslices.
getPixels(int) - Method in class ij.VirtualStack
  Returns the pixel array for the specified slice, where 1<=n<=nslices.
getPixelsCopy() - Method in class ij.process.ByteProcessor
  Returns a copy of the pixel data.
getPixelsCopy() - Method in class ij.process.ColorProcessor
  Returns a copy of the pixel data.
getPixelsCopy() - Method in class ij.process.FloatProcessor
  Returns a copy of the pixel data.
getPixelsCopy() - Method in class ij.process.ImageProcessor
  Returns a copy of the pixel data.
getPixelsCopy() - Method in class ij.process.ShortProcessor
  Returns a copy of the pixel data.
getPixelValue(int, int) - Method in class ij.process.ByteProcessor
getPixelValue(int, int) - Method in class ij.process.ColorProcessor
  Converts the specified pixel to grayscale using the formula g=(r+g+b)/3 and returns it as a float.
getPixelValue(int, int) - Method in class ij.process.FloatProcessor
  Returns the value of the pixel at (x,y) as a float.
getPixelValue(int, int) - Method in class ij.process.ImageProcessor
  Returns the value of the pixel at (x,y).
getPixelValue(int, int) - Method in class ij.process.IntProcessor
getPixelValue(int, int) - Method in class ij.process.ShortProcessor
  Returns the value of the pixel at (x,y) as a float.
getPlot() - Method in class ij.gui.PlotCanvas
  Returns the Plot displayed in this canvas
getPlot() - Method in interface ij.gui.PlotMaker
  Returns a profile plot.
getPlot() - Method in class ij.gui.PlotWindow
  Returns the Plot associated with this PlotWindow.
getPlot() - Method in class ij.gui.ProfilePlot
getPlot() - Method in class ij.ImagePlus
getPlot() - Method in class ij.measure.CurveFitter
getPlot() - Method in class ij.plugin.Profiler
getPlot() - Method in class ij.plugin.ZAxisProfiler
getPlot(int) - Method in class ij.measure.CurveFitter
getPlot(ImagePlus) - Static method in class ij.plugin.ZAxisProfiler
  Returns a Plot of the selection mean gray value versus slice number.
getPlot(ImagePlus, String) - Static method in class ij.plugin.ZAxisProfiler
  Returns a Plot of the selection mean versus slice number for the specified hyperstack, where 'options' can be "time" or "z-axis".
getPlotObjectDesignations() - Method in class ij.gui.Plot
  Gets an array with human-readable designations of the PlotObjects (curves, labels, ...) in the sequence they were added (the object passed with the constructor is first, even though it is plotted last).
getPlotObjectIndex(float[][]) - Method in class ij.gui.Plot
  Returns the index of the first plot object with x,y data (points, line) or arrows with all data equal to those given.
getPlotObjectLabel(int) - Method in class ij.gui.Plot
  Get the label the i-th PlotObject (in the sequence how they were added, including hidden ones).
getPlotObjectStyle(int) - Method in class ij.gui.Plot
  Get the style of the i-th PlotObject (curve, label, ...) in the sequence they were added (including hidden ones), as String with comma delimiters: Main Color, Secondary Color (or "none"), Line Width [, Symbol shape for XY_DATA] [,hidden] PlotObjects here refers to curves, arrows, labels etc.
getPlotSize() - Method in class ij.gui.ProfilePlot
  Returns the size of the plot that createWindow() creates.
getPluginCount() - Method in class ij.Menus
getPlugins() - Static method in class ij.Menus
  Returns a list of the plugins in the plugins menu.
getPluginsDirProperty() - Static method in class ij.Prefs
getPlugInsPath() - Static method in class ij.Menus
  Returns the path to the user plugins directory or null if the plugins directory was not found.
getPlugInTool() - Static method in class ij.gui.Toolbar
getPointPosition(int) - Method in class ij.gui.PointRoi
  Returns the stack slice of the point with the given index, or 0 if no slice defined for this point
getPoints() - Method in class ij.gui.Line
  Returns, as a Polygon, the two points that define this line.
getPointType() - Method in class ij.gui.PointRoi
  Returns the point type (0=hybrid, 1=cross, 2=dot, 3=circle).
getPolygon() - Method in class ij.gui.Line
  If the width of this line is less than or equal to one, returns the starting and ending coordinates as a 2-point Polygon, or, if the width is greater than one, returns an outline of the line as a 4-point Polygon.
getPolygon() - Method in class ij.gui.OvalRoi
  Returns this OvalRoi as a Polygon that outlines the mask, in image pixel coordinates.
getPolygon() - Method in class ij.gui.PolygonRoi
  Returns this PolygonRoi as a Polygon.
getPolygon() - Method in class ij.gui.Roi
  Returns the outline of this selection as a Polygon.
getPolygon() - Method in class ij.gui.ShapeRoi
getPopupMenu() - Static method in class ij.Menus
getPort() - Static method in class ij.ImageJ
  Returns the port that ImageJ checks on startup to see if another instance is running.
getPosition() - Method in class ij.gui.Roi
  Returns the stack position (image number) of this ROI, or zero if the ROI is not associated with a particular stack image.
getPowerSpectrum() - Method in class ij.process.FHT
  Returns an 8-bit power spectrum, log-scaled to 1-254.
getPrecision() - Static method in class ij.plugin.filter.Analyzer
  Returns the number of digits displayed to the right of decimal point.
getPreferredLocation() - Method in class ij.ImageJ
getPreferredSize() - Method in class ij.gui.ImageCanvas
getPreferredSize() - Method in class ij.gui.ImagePanel
getPreferredSize() - Method in class ij.gui.MultiLineLabel
getPreferredSize() - Method in class ij.gui.ProgressBar
getPreferredSize() - Method in class ij.gui.ScrollbarWithLabel
getPreferredSize() - Method in class ij.gui.Toolbar
getPreferredSize() - Method in class ij.gui.TrimmedButton
getPrefsDir() - Static method in class ij.Prefs
  Returns the path to the directory where the preferences file (IJPrefs.txt) is saved.
getPrefsDirectory() - Static method in class ij.OtherInstance
getPreviewCheckbox() - Method in class ij.gui.GenericDialog
  Returns a reference to the Preview checkbox.
getPreviousRoi() - Static method in class ij.gui.Roi
  Returns the Roi saved by setPreviousRoi().
getProcessor() - Method in class ij.gui.ImageRoi
getProcessor() - Method in class ij.gui.Plot
  Draws the plot (if not done before) in an ImageProcessor and returns the ImageProcessor with the plot.
getProcessor() - Static method in class ij.IJ
  Returns the active image or stack slice as an ImageProcessor, or displays an error message and aborts the plugin or macro if no images are open.
getProcessor() - Method in class ij.ImagePlus
  Returns a reference to the current ImageProcessor.
getProcessor(int) - Method in class ij.CompositeImage
getProcessor(int) - Method in class ij.gui.PlotVirtualStack
  Returns an ImageProcessor for the specified slice, where 1<=n<=nslices.
getProcessor(int) - Method in class ij.ImageStack
  Returns an ImageProcessor for the specified slice, where 1<=n<=nslices.
getProcessor(int) - Method in class ij.plugin.AVI_Reader
  Returns an ImageProcessor for the specified slice of this virtual stack (if it is one) where 1<=n<=nslices.
getProcessor(int) - Method in class ij.plugin.FileInfoVirtualStack
  Returns an ImageProcessor for the specified image, where 1<=n<=nImages.
getProcessor(int) - Method in class ij.plugin.ListVirtualStack
  Returns an ImageProcessor for the specified slice, where 1<=n<=nslices.
getProcessor(int) - Method in class ij.VirtualStack
  Returns an ImageProcessor for the specified slice, where 1<=n<=nslices.
getProfile() - Method in class ij.gui.ProfilePlot
  Returns the profile plot data.
getProgram() - Method in class ij.plugin.MacroInstaller
getProgressBar() - Method in class ij.ImageJ
getProgressIncrement(int, int) - Method in class ij.process.ImageProcessor
getProjection() - Method in class ij.plugin.ZProjector
  Retrieve results of most recent projection operation.
getProp(String) - Method in class ij.ImagePlus
  Returns as a string the image property associated with the specified key or null if the property is not found.
getProperties() - Method in class ij.gui.Roi
getProperties() - Method in class ij.ImagePlus
  Returns this image's Properties.
getProperties() - Method in class ij.VirtualStack
  Returns the ImagePlus Properties assoctated with the current slice, or null.
getPropertiesAsArray() - Method in class ij.ImagePlus
  Used for saving string properties in TIFF header.
getProperty(String) - Method in class ij.gui.Roi
getProperty(String) - Static method in class ij.IJ
  Returns the object in IJ.properties associated with 'key', or null if 'key' is not found.
getProperty(String) - Method in class ij.ImagePlus
  Returns the property associated with 'key', or null if it is not found.
getPropertyCount() - Method in class ij.gui.Roi
getPropsInfo() - Method in class ij.ImagePlus
  Returns information displayed by Image/Show Info command.
getPrototypeOverlay() - Method in class ij.gui.Roi
getQuality() - Static method in class ij.plugin.JpegWriter
getRadioButtonGroups() - Method in class ij.gui.GenericDialog
  Returns the Vector that contains the RadioButtonGroups.
getRawInstance() - Static method in class ij.plugin.frame.RoiManager
getRawLength() - Method in class ij.gui.Line
  Returns the length of this line in pixels.
getRawPowerSpectrum() - Method in class ij.process.FHT
  Returns the unscaled 32-bit power spectrum.
getRawStatistics() - Method in class ij.ImagePlus
getRawType(int) - Static method in class ij.macro.ExtensionDescriptor
getRawValue(double) - Method in class ij.measure.Calibration
  Converts a density calibrated value into a raw pixel value.
getRawX(double) - Method in class ij.measure.Calibration
  Converts a x-coordinate in physical units to pixels.
getRawY(double) - Method in class ij.measure.Calibration
  Converts a y-coodinate in physical units to pixels.
getRawY(double, int) - Method in class ij.measure.Calibration
  Converts a y-coodinate in physical units to pixels, taking into account the 'invertY' flag.
getRawZ(double) - Method in class ij.measure.Calibration
  Converts a z-coodinate in physical units to pixels.
getRectToolType() - Static method in class ij.gui.Toolbar
  Returns the rectangle tool type (RECT_ROI, ROUNDED_RECT_ROI or ROTATED_RECT_ROI).
getRed(String) - Static method in class ij.plugin.Colors
getRedirectImage(ImagePlus) - Static method in class ij.plugin.filter.Analyzer
  Returns the image selected in the "Redirect To:" popup menu of the Analyze/Set Measurements dialog, or null if "None" is selected, the image was not found or the image is not the same size as `currentImage`.
getReds() - Method in class ij.LookUpTable
getRejectMacrosMsg() - Method in class ij.plugin.frame.Editor
getResiduals() - Method in class ij.measure.CurveFitter
  Returns residuals array, i.e., differences between data and curve.
getRestarts() - Method in class ij.measure.CurveFitter
  Get maximum number of simplex restarts to do.
getResultsTable() - Method in class ij.gui.HistogramWindow
  Returns the histogram values as a ResultsTable.
getResultsTable() - Method in class ij.gui.Plot
  Creates a ResultsTable with the plot data.
getResultsTable() - Method in class ij.gui.PlotWindow
  Returns the plot values with simple headings (X, Y, Y1 etc, not the labels) as a ResultsTable.
getResultsTable() - Static method in class ij.measure.ResultsTable
  Returns the ResultsTable used by the Measure command.
getResultsTable() - Static method in class ij.plugin.filter.Analyzer
  Returns the default results table.
getResultsTable() - Method in class ij.text.TextPanel
  Returns the ResultsTable associated with this TextPanel, or null.
getResultsTable() - Method in class ij.text.TextWindow
  Returns the ResultsTable associated with this TextWindow, or null.
getResultsTable(boolean) - Method in class ij.gui.Plot
  Creates a ResultsTable with the data of the plot.
getResultsTable(String) - Static method in class ij.measure.ResultsTable
  Returns the ResultsTable with the specified title, or null if it does not exist,
getResultsTableWithLabels() - Method in class ij.gui.Plot
  Creates a ResultsTable with the data of the plot.
getResultString() - Method in class ij.measure.CurveFitter
  Get a string with detailed description of the curve fitting results (several lines, including the fit parameters).
getResultsWindow() - Static method in class ij.measure.ResultsTable
  Obsolete.
getReturnValue() - Method in class ij.plugin.PlugInInterpreter
  Returns the value returned by the script, if any, or null.
getRGB(byte[], byte[], byte[]) - Method in class ij.process.ColorProcessor
  Returns the red, green and blue planes as 3 byte arrays.
getRGBWeights() - Method in class ij.process.ColorProcessor
  Returns the values set by setRGBWeights(), or null if setRGBWeights() has not been called.
getRoi() - Method in class ij.ImagePlus
  Returns the current selection, or null if there is no selection.
getRoi() - Method in class ij.ImageStack
getRoi() - Method in class ij.io.RoiDecoder
  Returns the ROI.
getRoi() - Method in class ij.process.ImageProcessor
  Returns a Rectangle that represents the current region of interest.
getRoi(int) - Method in class ij.plugin.frame.RoiManager
  Returns a reference to the ROI at the specified index.
getRoiIndex(Roi) - Method in class ij.plugin.frame.RoiManager
  Returns the index of the specified Roi, or -1 if it is not found.
getRoiManager() - Static method in class ij.plugin.frame.RoiManager
  Returns a reference to the ROI Manager if it open or opens it if it is not already open.
getRois() - Method in class ij.gui.ShapeRoi
  Converts a Shape into Roi object(s).
getROIs() - Method in class ij.plugin.frame.RoiManager
  Deprecated.
getRoisAsArray() - Method in class ij.plugin.frame.RoiManager
  Returns the ROIs as an array.
getRoot() - Method in class ij.plugin.ControlPanel
getRotationCenter() - Method in class ij.gui.Line
getRotationCenter() - Method in class ij.gui.Roi
getRoundRectArcSize() - Method in class ij.gui.Roi
  Obsolete; replaced by getCornerDiameter().
getRoundRectArcSize() - Static method in class ij.gui.Toolbar
  Returns the rounded rectangle arc size, or 0 if the rounded rectangle tool is not enabled.
getRow(int, int, float[], int) - Method in class ij.process.ImageProcessor
  Returns the pixel values along the horizontal line starting at (x,y).
getRow(int, int, int[], int) - Method in class ij.process.ImageProcessor
  Returns the pixel values along the horizontal line starting at (x,y).
getRowAsString(int) - Method in class ij.measure.ResultsTable
  Returns a tab or comma delimited string representing the given row, where 0invalid input: '<'=rowinvalid input: '<'=size()-1.
getRSquared() - Method in class ij.measure.CurveFitter
  Returns R^2, where 1.0 is best.
getSampleImageNames() - Static method in class ij.plugin.URLOpener
getSaveAsMenu() - Static method in class ij.Menus
getScale(float[]) - Static method in class ij.plugin.filter.Convolver
getScaledStroke() - Method in class ij.gui.Roi
getScaleStrokeWidth() - Method in class ij.gui.Roi
  Returns 'true' if the stroke width is scaled as images are zoomed.
getScaleToFit() - Method in class ij.gui.ImageCanvas
getScreenBounds() - Static method in class ij.gui.GUI
getScreenBounds(Component) - Static method in class ij.gui.GUI
getScreenBounds(Component, boolean) - Static method in class ij.gui.GUI
  Get maximum bounds for the screen that contains a given component.
getScreenBounds(Point) - Static method in class ij.gui.GUI
getScreenBounds(Point, boolean) - Static method in class ij.gui.GUI
  Get maximum bounds for the screen that contains a given point.
getScreenSize() - Static method in class ij.IJ
  Returns the size, in pixels, of the primary display.
getSD() - Method in class ij.measure.CurveFitter
  Returns the standard deviation of the residuals.
getSD() - Static method in class ij.plugin.filter.Filters
  Returns the default standard deviation used by Process/Noise/Add Specified Noise.
getSelectedIndex() - Method in class ij.plugin.frame.RoiManager
  Returns the index of the first selected ROI or -1 if no ROI is selected.
getSelectedIndexes() - Method in class ij.plugin.frame.RoiManager
  Returns an array of the selected indexes.
getSelectedRoisAsArray() - Method in class ij.plugin.frame.RoiManager
  Returns the selected ROIs as an array, or all the ROIs if none are selected.
getSelectionCoordinates() - Method in class ij.gui.ShapeRoi
  Used by the getSelectionCoordinates macro function
getSelectionEnd() - Method in class ij.text.TextPanel
  Returns the index of the last selected line, or -1 if there is no slection.
getSelectionStart() - Method in class ij.text.TextPanel
  Returns the index of the first selected line, or -1 if there is no slection.
getSerializedImage() - Method in class ij.gui.ImageRoi
  Returns a serialized version of the image.
getShape() - Method in class ij.gui.ShapeRoi
  Returns a reference to the Shape object encapsulated by this ShapeRoi.
getShapeAsArray() - Method in class ij.gui.ShapeRoi
  Retrieves the end points and control points of the path as a float array.
getShapeRoi() - Method in class ij.io.RoiDecoder
getShortcuts() - Static method in class ij.Menus
  Returns the hashtable that associates shortcuts with commands.
getShortcuts() - Method in class ij.plugin.CommandLister
getShortSliceLabel(int) - Method in class ij.ImageStack
  Returns a shortened version (up to the first 60 characters or first newline), with the extension removed, of the specified slice label, or null if the slice does not have a label.
getShortSliceLabel(int, int) - Method in class ij.ImageStack
  Returns a shortened version (up to the first 'max' characters or first newline), with the extension removed, of the specified slice label, or null if the slice does not have a label.
getShortTitle() - Method in class ij.ImagePlus
  If the image title is a file name, returns the name without the extension and with spaces removed, otherwise returns the title shortened to the first space.
getShowAllColor() - Static method in class ij.gui.ImageCanvas
  Obsolete
getShowAllList() - Method in class ij.gui.ImageCanvas
getShowAllROIs() - Method in class ij.gui.ImageCanvas
  Obsolete
getShowLabels() - Method in class ij.gui.PointRoi
getSimilarFontsList(String) - Static method in class ij.util.FontUtil
  For a few basic font types, gets a list of replacement font families Note that java's 'SansSerif' has wider characters (significantly different metrics) than the other sans-serif fonts in the list; thus it should be considered a fallback option only.
getSingleWildcardChar() - Method in class ij.util.WildcardMatch
  Returns the character used to specify exactly one character.
getSixteenBitRanges() - Static method in class ij.plugin.frame.ContrastAdjuster
getSize() - Method in class ij.gui.Plot
  The size of the plot including borders with axis labels etc., in pixels
getSize() - Method in class ij.gui.PlotVirtualStack
  Returns the number of slices in this stack.
getSize() - Method in class ij.gui.PointRoi
  Returns the current point size 0-6 (Tiny-XXXL).
getSize() - Static method in class ij.gui.TextRoi
  Deprecated.
  Replaced by getDefaultFontSize
getSize() - Method in class ij.ImageStack
getSize() - Method in class ij.macro.Program
getSize() - Method in class ij.plugin.AVI_Reader
  Returns the number of images in this virtual stack (if it is one)
getSize() - Method in class ij.plugin.FileInfoVirtualStack
getSize() - Method in class ij.plugin.ListVirtualStack
  Returns the number of images in this stack.
getSize() - Method in class ij.VirtualStack
getSizeInBytes() - Method in class ij.ImagePlus
  Returns the size of this image in bytes.
getSlice() - Method in class ij.ImagePlus
getSliceLabel(int) - Method in class ij.gui.PlotVirtualStack
getSliceLabel(int) - Method in class ij.ImageStack
  Returns the label of the specified slice, where 1<=n<=nslices.
getSliceLabel(int) - Method in class ij.plugin.AVI_Reader
  Returns the label of the specified slice in this virtual stack (if it is one).
getSliceLabel(int) - Method in class ij.plugin.FileInfoVirtualStack
  Returns the label of the Nth image.
getSliceLabel(int) - Method in class ij.plugin.ListVirtualStack
  Returns the name of the specified image.
getSliceLabel(int) - Method in class ij.VirtualStack
  Returns the label of the Nth image.
getSliceLabels() - Method in class ij.ImageStack
  Returns the slice labels as an array of Strings.
getSliceNumber() - Method in class ij.plugin.filter.PlugInFilterRunner
  Return the slice number currently processed by the calling thread.
getSliceNumber() - Method in class ij.process.ImageProcessor
  Returns the current stack position (1-n) of this image.
getSliceNumber(String) - Method in class ij.gui.ImageCanvas
getSliceNumber(String) - Method in class ij.plugin.frame.RoiManager
  Returns the slice number associated with the specified name, or -1 if the name does not include a slice number.
getSliderHeight() - Method in class ij.gui.ImageWindow
getSliders() - Method in class ij.gui.GenericDialog
  Returns the Vector containing the sliders (Scrollbars).
getSnapshotPixels() - Method in class ij.process.ByteProcessor
getSnapshotPixels() - Method in class ij.process.ColorProcessor
  Returns a reference to the snapshot pixel array.
getSnapshotPixels() - Method in class ij.process.FloatProcessor
getSnapshotPixels() - Method in class ij.process.ImageProcessor
  Returns a reference to the snapshot (undo) buffer, or null.
getSnapshotPixels() - Method in class ij.process.ShortProcessor
getSortedFitList() - Static method in class ij.measure.CurveFitter
  Returns an array of fit names with nicer sorting
getSourceImage() - Method in interface ij.gui.PlotMaker
  Returns the ImagePlus used to generate the profile plots.
getSourceImage() - Method in class ij.plugin.Profiler
getSourceImage() - Method in class ij.plugin.ZAxisProfiler
getSrcRect() - Method in class ij.gui.ImageCanvas
getStack() - Method in class ij.gui.Plot
  Returns the virtual stack created by addToStack().
getStack() - Method in class ij.ImagePlus
  Returns the image stack.
getStackIndex(int, int, int) - Method in class ij.ImagePlus
  Returns that stack index (one-based) corresponding to the specified position.
getStackSize() - Method in class ij.ImagePlus
  Returns the number of stack images.
getStartTime() - Method in class ij.ImagePlus
  Returns the time in milliseconds when startTiming() was last called.
getStartupMacro() - Method in class ij.plugin.Startup
getState() - Method in class ij.gui.Roi
getStaticGlobalCalibration() - Static method in class ij.ImagePlus
  This is a version of getGlobalCalibration() that can be called from a static context.
getStatistics() - Method in class ij.gui.Roi
getStatistics() - Method in class ij.ImagePlus
  Get calibrated statistics for this image or ROI, including histogram, area, mean, min and max, standard deviation and mode.
getStatistics() - Method in class ij.process.ImageProcessor
  Calculates and returns complete uncalibrated (raw) statistics for this image or ROI but it is up to 70 times slower than getStats().
getStatistics(double[]) - Static method in class ij.util.Tools
getStatistics(int) - Method in class ij.ImagePlus
  Returns an ImageStatistics object generated using the specified measurement options.
getStatistics(int, int) - Method in class ij.ImagePlus
  Returns an ImageStatistics object generated using the specified measurement options and histogram bin count.
getStatistics(int, int, double, double) - Method in class ij.ImagePlus
  Returns an ImageStatistics object generated using the specified measurement options, histogram bin count and histogram range.
getStatistics(ImageProcessor) - Static method in class ij.process.ImageStatistics
  Calculates and returns uncalibrated (raw) statistics for the specified image, including histogram, area, mean, min and max, standard deviation and mode.
getStatistics(ImageProcessor, int, Calibration) - Static method in class ij.process.ImageStatistics
  Calculates and returns statistics for the specified image using the specified measurent options and calibration.
getStats() - Method in class ij.process.ImageProcessor
  Calculates and returns uncalibrated statistics for this image or ROI, including histogram, area, mean, min and max, standard deviation, and mode.
getStatus() - Method in class ij.measure.CurveFitter
getStatusBar() - Method in class ij.ImageJ
getStatusBarText() - Static method in class ij.ImageJ
getStatusString() - Method in class ij.measure.CurveFitter
  Get a short text with a short description of the status.
getString() - Method in class ij.macro.Variable
getString(String) - Static method in class ij.Prefs
  Retrieves a string from string in IJ_Props or IJ_Prefs.txt.
getString(String, String) - Static method in class ij.IJ
  Allows the user to enter a string in a dialog box.
getString(String, String) - Static method in class ij.Prefs
  Retrieves a string from IJ_Props or IJ_Prefs.txt.
getStringBounds(String) - Method in class ij.process.ImageProcessor
  Returns a rectangle enclosing the pixels affected by drawString assuming it is drawn at (x=0, y=0).
getStringFields() - Method in class ij.gui.GenericDialog
  Returns the Vector containing the string TextFields.
getStringFromList(String, String) - Static method in class ij.util.Tools
  Retrieves a String form a list of key-number pairs like "value1="abc" str='the Text'".
getStringFromList(String, String, String) - Static method in class ij.util.Tools
getStringProperty(String) - Method in class ij.ImagePlus
  Returns the string value from the "Info" property string associated with 'key', or null if the key is not found.
getStringValue(int, int) - Method in class ij.measure.ResultsTable
  Returns the string value of the given column and row, where column must be less than or equal the value returned by getLastColumn() and row must be greater than or equal zero and less than the value returned by size().
getStringValue(String, int) - Method in class ij.measure.ResultsTable
  Returns the string value of the given column and row, where row must be greater than or equal zero and less than the value returned by size().
getStringVariable(String) - Method in class ij.macro.Interpreter
getStringWidth(String) - Method in class ij.process.ImageProcessor
  Returns the width in pixels of the specified string, including any background space (whitespace) between the x drawing coordinate and the string, not necessarily including all whitespace at the right.
getStringWidth(String, FontMetrics, Graphics) - Static method in class ij.util.Java2
getStroke() - Method in class ij.gui.Roi
  Returns the Stroke used to draw this ROI, or null if no Stroke is used.
getStrokeColor() - Method in class ij.gui.Roi
  Returns the the color used to draw the ROI outline or null if the default color is being used.
getStrokeWidth() - Method in class ij.gui.Roi
  Returns the line width.
getStubPath() - Static method in class ij.OtherInstance
getStyle() - Method in class ij.gui.Arrow
getStyle() - Static method in class ij.gui.TextRoi
  Deprecated.
  Replaced by getDefaultFontStyle
getSumResidualsSqr() - Method in class ij.measure.CurveFitter
  Returns the sum of the residuals (may be NaN if the minimizer could not start properly i.e., if getStatus() returns Minimizer.INITILIZATION_FAILURE).
getSymbolTable() - Method in class ij.macro.Program
getT() - Method in class ij.ImagePlus
  Returns the current hyperstack frame position.
getTableAsImage() - Method in class ij.measure.ResultsTable
  Returns the contents of this ResultsTable as a FloatProcessor.
getTag(ImagePlus, String) - Static method in class ij.util.DicomTools
  Returns the value (as a string) of the specified DICOM tag id (in the form "0018,0050") of the specified image or stack slice.
getTagName(String) - Static method in class ij.plugin.DICOM
  Returns the name of the specified DICOM tag id.
getTagName(String) - Static method in class ij.util.DicomTools
  Returns the name of the specified DICOM tag id.
getTempCurrentImage() - Static method in class ij.WindowManager
  Returns the temporary current image for this thread, or null.
getText() - Method in class ij.gui.TextRoi
getText() - Method in class ij.plugin.frame.Editor
getText() - Method in class ij.plugin.frame.Recorder
getText() - Method in class ij.text.TextPanel
  Returns all the text as a string.
getTextArea() - Method in class ij.plugin.frame.Editor
getTextArea1() - Method in class ij.gui.GenericDialog
  Returns a reference to textArea1.
getTextArea2() - Method in class ij.gui.GenericDialog
  Returns a reference to textArea2.
getTextPanel() - Static method in class ij.IJ
  Returns a reference to the "Results" window TextPanel.
getTextPanel() - Method in class ij.text.TextWindow
  Returns a reference to this TextWindow's TextPanel.
getThread() - Method in class ij.macro.MacroRunner
getThreads() - Static method in class ij.Prefs
  Returns the number of threads used by PlugInFilters to process images and stacks.
getThreshold(AutoThresholder.Method, int[]) - Method in class ij.process.AutoThresholder
  Calculates and returns a threshold using the specified method and histogram.
getThreshold(String, int[]) - Method in class ij.process.AutoThresholder
getThresholdColorModel(byte[], byte[], byte[]) - Static method in class ij.process.ImageProcessor
  Returns a color model based on the colors of the input from 0 to 254 (inclusive).
getTiffFileInfo(String) - Static method in class ij.io.Opener
  Returns the FileInfo of the specified TIFF file.
getTiffInfo() - Method in class ij.io.TiffDecoder
getTimeUnit() - Method in class ij.measure.Calibration
  Returns the distance unit (e.g.
getTitle() - Method in class ij.gui.Plot
  Returns the title of the image showing the plot (if any) or title of the plot
getTitle() - Method in class ij.ImagePlus
  Returns the image name.
getTitle() - Method in class ij.measure.ResultsTable
getTolerance() - Static method in class ij.plugin.WandToolOptions
getToolIcon() - Method in class ij.plugin.tool.ArrowTool
getToolIcon() - Method in class ij.plugin.tool.BrushTool
getToolIcon() - Method in class ij.plugin.tool.OverlayBrushTool
getToolIcon() - Method in class ij.plugin.tool.PixelInspectionTool
getToolIcon() - Method in class ij.plugin.tool.PlugInTool
  Return the string encoding of the tool icon.
getToolIcon() - Method in class ij.plugin.tool.RoiRotationTool
getToolId() - Static method in class ij.gui.Toolbar
  Returns the ID of the current tool (Toolbar.RECTANGLE, Toolbar.OVAL, etc.).
getToolId(String) - Method in class ij.gui.Toolbar
  Returns the ID of the tool whose name (the description displayed in the status bar) starts with the specified string, or -1 if the tool is not found.
getToolName() - Static method in class ij.gui.Toolbar
  Returns the name of the current tool.
getToolName() - Static method in class ij.IJ
  Returns the name of the current tool.
getToolName() - Method in class ij.plugin.tool.ArrowTool
getToolName() - Method in class ij.plugin.tool.BrushTool
getToolName() - Method in class ij.plugin.tool.OverlayBrushTool
getToolName() - Method in class ij.plugin.tool.PixelInspectionTool
getToolName() - Method in class ij.plugin.tool.PlugInTool
  Return the tool name.
getToolName() - Method in class ij.plugin.tool.RoiRotationTool
getTPosition() - Method in class ij.gui.Roi
  Returns the frame position of this ROI, or zero if this ROI is not associated with a particular frame.
getTransferData(DataFlavor) - Method in class ij.plugin.Clipboard
getTransferDataFlavors() - Method in class ij.plugin.Clipboard
getTransparentIndex() - Static method in class ij.Prefs
  Returns the transparent index (0-255), or -1 if transparency is disabled.
getType() - Method in class ij.gui.Roi
getType() - Method in class ij.ImagePlus
  Returns the current image type (ImagePlus.GRAY8, ImagePlus.GRAY16, ImagePlus.GRAY32, ImagePlus.COLOR_256 or ImagePlus.COLOR_RGB).
getTypeAsString() - Method in class ij.gui.Roi
  Convenience method that converts Roi type to a human-readable form.
getTypeName(int) - Static method in class ij.macro.ExtensionDescriptor
getTypes() - Method in class ij.gui.Plot
  Returns an array of the available curve types ("Line", "Bar", "Circle", etc).
getUMeans() - Static method in class ij.plugin.filter.Analyzer
  Returns an array containing the first 20 uncalibrated means.
getUncalibratedLength() - Method in class ij.gui.PolygonRoi
getUnionOfBounds() - Static method in class ij.gui.GUI
getUniqueName(ImagePlus, String) - Static method in class ij.WindowManager
getUniqueName(String) - Static method in class ij.WindowManager
  Returns a unique name by adding, before the extension, -1, -2, etc.
getUnit() - Method in class ij.measure.Calibration
  Returns the default length unit (e.g.
getUnitIncrement() - Method in class ij.gui.ScrollbarWithLabel
getUnits() - Method in class ij.measure.Calibration
  Returns the plural form of the length unit (e.g.
getValue() - Method in class ij.gui.ScrollbarWithLabel
getValue() - Method in class ij.macro.Variable
getValue(int, int) - Method in class ij.measure.ResultsTable
  Deprecated.
  replaced by getValueAsDouble
getValue(int, int) - Method in class ij.process.ImageProcessor
  Returns the value of the pixel at (x,y), a calibrated value from 8-bit and 16-bit images, an intensity value from RGB images and a double value from 32-bit images.
getValue(ImagePlus, String) - Static method in class ij.IJ
  Returns a measurement result, where 'measurement' is "Area", "Mean", "StdDev", "Mode", "Min", "Max", "X", "Y", "XM", "YM", "Perim.", "BX", "BY", "Width", "Height", "Major", "Minor", "Angle", "Circ.", "Feret", "IntDen", "Median", "Skew", "Kurt", "%Area", "RawIntDen", "Ch", "Slice", "Frame", "FeretX", "FeretY", "FeretAngle", "MinFeret", "AR", "Round", "Solidity", "MinThr" or "MaxThr".
getValue(String) - Method in class ij.gui.GenericDialog
getValue(String, int) - Method in class ij.measure.ResultsTable
  Returns the value of the specified column and row, where column is the column heading and row is a number greater than or equal zero and less than value returned by size().
getValue(String, String, String) - Static method in class ij.Macro
getValueAsDouble(int, int) - Method in class ij.measure.ResultsTable
  Returns the value of the given column and row, where column must be less than or equal the value returned by getLastColumn() and row must be greater than or equal zero and less than the value returned by size().
getValueUnit() - Method in class ij.measure.Calibration
  Returns the value unit.
getVariable(String) - Method in class ij.macro.Interpreter
getVariable2(String) - Method in class ij.macro.Interpreter
getVariableAsString(String) - Method in class ij.macro.Interpreter
getVariableNames() - Method in class ij.macro.Interpreter
  Returns the names of all variables, without any annotation
getVariables() - Method in class ij.macro.Interpreter
  Returns the names of all variables and functions with human-readable annotations
getVariance() - Method in class ij.util.ArrayUtil
  Variance value
getVersion() - Static method in class ij.IJ
  Returns the ImageJ version number as a string.
getVersion() - Method in class ij.plugin.PlugInInterpreter
  Returns the version of ImageJ at the time this plugin was created.
getVisibleAmount() - Method in class ij.gui.ScrollbarWithLabel
getVoxel(int, int, int) - Method in class ij.ImageStack
  Returns, as a double, the value of the specified voxel.
getVoxelDepth(ImageStack) - Static method in class ij.util.DicomTools
  Calculates the voxel depth of the specified DICOM stack based on the distance between the first and last slices.
getVoxels(int, int, int, int, int, int, float[]) - Method in class ij.ImageStack
getVoxels(int, int, int, int, int, int, float[], int) - Method in class ij.ImageStack
getWeightingFactors() - Static method in class ij.process.ColorProcessor
  Returns the three weighting factors used by getPixelValue(), getHistogram() and convertToByte() to do color conversions.
getWidth() - Static method in class ij.gui.Line
  Returns the default line width.
getWidth() - Method in class ij.ImagePlus
  Returns the width of this image in pixels.
getWidth() - Method in class ij.ImageStack
getWidth() - Method in class ij.plugin.AVI_Reader
  Returns the image width of the virtual stack
getWidth() - Method in class ij.plugin.FileInfoVirtualStack
getWidth() - Method in class ij.plugin.ListVirtualStack
getWidth() - Method in class ij.process.ImageProcessor
  Returns the width of this image in pixels.
getWindow() - Method in class ij.ImagePlus
  Returns the ImageWindow that is being used to display this image.
getWindow(String) - Static method in class ij.WindowManager
  Returns the window (a Frame or a Dialog) with the specified title, or null if a window with that title is not found.
getWindowCount() - Static method in class ij.WindowManager
  Returns the number of open image windows.
getX(double) - Method in class ij.measure.Calibration
  Converts a x-coodinate in pixels to physical units (e.g.
getXBase() - Method in class ij.gui.Roi
getXCoordinates() - Method in class ij.gui.PolygonRoi
  Obsolete; replaced by either getPolygon() or getFloatPolygon().
getXPoints() - Method in class ij.measure.CurveFitter
  returns the array with the x data
getXUnit() - Method in class ij.measure.Calibration
  Returns the X length unit.
getXUnits() - Method in class ij.measure.Calibration
  Returns the plural form of the X length unit (e.g.
getXValues() - Method in class ij.gui.HistogramPlot
getXValues() - Method in class ij.gui.HistogramWindow
getXValues() - Method in class ij.gui.Plot
  Get the x coordinates of the data set passed with the constructor (if not null) or otherwise of the data set of the first 'addPoints'.
getXValues() - Method in class ij.gui.PlotWindow
getXZImage() - Method in class ij.plugin.Orthogonal_Views
getY(double) - Method in class ij.measure.Calibration
  Converts a y-coordinate in pixels to physical units (e.g.
getY(double, int) - Method in class ij.measure.Calibration
  Converts a y-coordinate in pixels to physical units (e.g.
getYBase() - Method in class ij.gui.Roi
getYCoordinates() - Method in class ij.gui.PolygonRoi
  Obsolete; replaced by either getPolygon() or getFloatPolygon().
getYPoints() - Method in class ij.measure.CurveFitter
  returns the array with the y data
getYUnit() - Method in class ij.measure.Calibration
  Returns the Y length unit, or the default unit if 'yunit' is null.
getYUnits() - Method in class ij.measure.Calibration
  Returns the plural form of the Y length unit (e.g.
getYUV(ImageProcessor, byte[], byte[], byte[]) - Method in class ij.plugin.frame.ColorThresholder
getYValues() - Method in class ij.gui.Plot
  Get the y coordinates of the data set passed with the constructor (if not null) or otherwise of the data set of the first 'addPoints'.
getYValues() - Method in class ij.gui.PlotWindow
getYZImage() - Method in class ij.plugin.Orthogonal_Views
getZ() - Method in class ij.ImagePlus
  Returns the current hyperstack slice position.
getZ(double) - Method in class ij.measure.Calibration
  Converts a z-coordinate in pixels to physical units (e.g.
getZeroBasedMaxBounds() - Static method in class ij.gui.GUI
getZeroTransparent() - Method in class ij.gui.ImageRoi
getZPosition() - Method in class ij.gui.Roi
  Returns the slice position of this ROI, or zero if this ROI is not associated with a particular slice.
getZUnit() - Method in class ij.measure.Calibration
  Returns the Z length unit, or the default unit if 'zunit' is null.
getZUnits() - Method in class ij.measure.Calibration
  Returns the plural form of the Z length unit (e.g.
GIF - Static variable in class ij.io.Opener
GIF_OR_JPG - Static variable in class ij.io.FileInfo
GIF_Reader - Class in ij.plugin
  This plugin opens GIFs and Animated GIFs.
GIF_Reader() - Constructor for class ij.plugin.GIF_Reader
GifWriter - Class in ij.plugin
  Saves the active image in GIF format, or as an animated GIF if the image is a stack.
GifWriter() - Constructor for class ij.plugin.GifWriter
gLUT1 - Variable in class ij.process.ImageProcessor
gLUT2 - Variable in class ij.process.ImageProcessor
GRAY10_UNSIGNED - Static variable in class ij.io.FileInfo
  10-bit unsigned integer (0-1023).
GRAY12_UNSIGNED - Static variable in class ij.io.FileInfo
  12-bit unsigned integer (0-4095).
GRAY16 - Static variable in class ij.gui.NewImage
GRAY16 - Static variable in class ij.ImagePlus
  16-bit grayscale (unsigned)
GRAY16_SIGNED - Static variable in class ij.io.FileInfo
  16-bit signed integer (-32768-32767).
GRAY16_UNSIGNED - Static variable in class ij.io.FileInfo
  16-bit unsigned integer (0-65535).
GRAY24_UNSIGNED - Static variable in class ij.io.FileInfo
  24-bit unsigned integer.
GRAY32 - Static variable in class ij.gui.NewImage
GRAY32 - Static variable in class ij.ImagePlus
  32-bit floating-point grayscale
GRAY32_FLOAT - Static variable in class ij.io.FileInfo
  32-bit floating-point.
GRAY32_INT - Static variable in class ij.io.FileInfo
  32-bit signed integer.
GRAY32_UNSIGNED - Static variable in class ij.io.FileInfo
  32-bit unsigned integer.
GRAY64_FLOAT - Static variable in class ij.io.FileInfo
  64-bit floating-point.
GRAY8 - Static variable in class ij.gui.NewImage
GRAY8 - Static variable in class ij.ImagePlus
  8-bit grayscale (unsigned)
GRAY8 - Static variable in class ij.io.FileInfo
  8-bit unsigned integer (0-255).
GRAYSCALE - Static variable in class ij.CompositeImage
  Display modes (note: TRANSPARENT mode has not yet been implemented)
GRAYSCALE - Static variable in class ij.IJ
  Image display modes
green - Variable in class ij.plugin.filter.RGBStackSplitter
greens - Variable in class ij.io.FileInfo
Grid - Class in ij.plugin
  This class implements the Analyze/Tools/Grid command.
Grid() - Constructor for class ij.plugin.Grid
GRID - Static variable in class ij.plugin.filter.Rotator
GROUP - Static variable in class ij.io.RoiDecoder
GroupedZProjector - Class in ij.plugin
  Implements the Image/Stacks/Tools/Grouped Z Project command.
GroupedZProjector() - Constructor for class ij.plugin.GroupedZProjector
groupZProject(ImagePlus, int, int) - Method in class ij.plugin.GroupedZProjector
grow(int, int) - Method in class ij.gui.EllipseRoi
grow(int, int) - Method in class ij.gui.FreehandRoi
grow(int, int) - Method in class ij.gui.Line
grow(int, int) - Method in class ij.gui.PolygonRoi
grow(int, int) - Method in class ij.gui.Roi
grow(int, int) - Method in class ij.gui.RotatedRectRoi
GT - Static variable in interface ij.macro.MacroConstants
GTE - Static variable in interface ij.macro.MacroConstants
GUI - Class in ij.gui
  This class consists of static GUI utility methods.
GUI() - Constructor for class ij.gui.GUI
GUI_SCALE - Static variable in class ij.Prefs

## H

HAMMING - Static variable in class ij.process.FHT
HAND - Static variable in class ij.gui.Toolbar
handCursor - Static variable in class ij.gui.ImageCanvas
handle(Throwable) - Method in interface ij.IJ.ExceptionHandler
handle(Throwable) - Method in class ij.ImageJ.ExceptionHandler
HANDLE_SIZE - Static variable in class ij.gui.Roi
handleColor - Variable in class ij.gui.Roi
handleException(String, Throwable) - Method in class ij.ImageJ.ExceptionHandler
handleException(Throwable) - Static method in class ij.IJ
  Displays a stack trace.
handleExtension(String, Object[]) - Method in interface ij.macro.MacroExtension
handleMouseDown(int, int) - Method in class ij.gui.Arrow
handleMouseDown(int, int) - Method in class ij.gui.Line
handleMouseDown(int, int) - Method in class ij.gui.Roi
handleMouseDrag(int, int, int) - Method in class ij.gui.Roi
handleMouseUp(int, int) - Method in class ij.gui.EllipseRoi
handleMouseUp(int, int) - Method in class ij.gui.FreehandRoi
handleMouseUp(int, int) - Method in class ij.gui.Line
handleMouseUp(int, int) - Method in class ij.gui.PointRoi
handleMouseUp(int, int) - Method in class ij.gui.PolygonRoi
  With segmented selections, ignore first mouse up and finalize when user double-clicks, control-clicks or clicks in start box.
handleMouseUp(int, int) - Method in class ij.gui.Roi
handleMouseUp(int, int) - Method in class ij.gui.RotatedRectRoi
handleMouseUp(int, int) - Method in class ij.gui.TextRoi
handlePopupMenu(MouseEvent) - Method in class ij.gui.ImageCanvas
handler - Variable in class ij.macro.ExtensionDescriptor
handleRoiMouseDown(MouseEvent) - Method in class ij.gui.ImageCanvas
HANN - Static variable in class ij.process.FHT
hasCustomLuts() - Method in class ij.CompositeImage
hasHyperStackPosition() - Method in class ij.gui.Roi
  Returns 'true' if setPosition(C,Z,T) has been called.
hasImageStack() - Method in class ij.ImagePlus
  Returns 'true' if this ImagePlus contains an ImageStack.
hasNext() - Method in class ij.gui.Line.PointIterator
hasVars() - Method in class ij.macro.Program
hasWord(String) - Method in class ij.macro.Program
HEADER2_OFFSET - Static variable in class ij.io.RoiDecoder
HEADLESS - Static variable in class ij.gui.Arrow
height - Variable in class ij.ImagePlus
height - Variable in class ij.io.FileInfo
height - Variable in class ij.process.ImageProcessor
height - Variable in class ij.process.ImageStatistics
HEIGHT - Static variable in class ij.gui.ProgressBar
HEIGHT_KEY - Static variable in class ij.text.TextWindow
HEIGHTD - Static variable in class ij.io.RoiDecoder
help - Static variable in class ij.plugin.frame.Channels
help - Static variable in class ij.plugin.PointToolOptions
hexDigits - Static variable in class ij.util.Tools
  This array contains the 16 hex digits '0'-'F'.
hexToColor(String) - Static method in class ij.plugin.Colors
  Converts a hex color (e.g., "ffff00") into "red", "green", "yellow", etc.
hexToColor2(String) - Static method in class ij.plugin.Colors
  Converts a hex color (e.g., "ffff00" or "#ffff00") into a color name "Red", "Green", "Yellow", etc.
HGAP - Static variable in class ij.gui.ImageWindow
HI_RESOLUTION - Static variable in class ij.gui.PlotDialog
  Types of dialog.
hide() - Method in class ij.ImagePlus
  Closes the window, if any, that is displaying this image.
hideCancelButton() - Method in class ij.gui.GenericDialog
  Do not display "Cancel" button.
hideErrorMessages() - Method in class ij.plugin.TextReader
hideProcessStackDialog - Static variable in class ij.IJ
hideProgress() - Method in class ij.process.ImageProcessor
  Deprecated.
hideRangeArrows() - Method in class ij.gui.PlotWindow
hideZoomIndicator(boolean) - Method in class ij.gui.ImageCanvas
histMax - Variable in class ij.process.ImageStatistics
histMin - Variable in class ij.process.ImageStatistics
histogram - Variable in class ij.gui.HistogramWindow
histogram - Variable in class ij.process.ImageStatistics
  Use the hIstogram() method to get the histogram as a double array.
histogram() - Method in class ij.process.ImageStatistics
  Returns the histogram as an array of doubles.
Histogram - Class in ij.plugin
  This plugin implements the Analyze/Histogram command.
Histogram() - Constructor for class ij.plugin.Histogram
histogram16 - Variable in class ij.process.ImageStatistics
  Bin width 1 histogram of 16-bit images
histogramMax - Variable in class ij.process.ImageProcessor
histogramMin - Variable in class ij.process.ImageProcessor
HistogramPlot - Class in ij.gui
HistogramPlot() - Constructor for class ij.gui.HistogramPlot
histogramSize - Variable in class ij.process.ImageProcessor
HistogramWindow - Class in ij.gui
  This class is an extended ImageWindow that displays histograms.
HistogramWindow(HistogramPlot, ImagePlus) - Constructor for class ij.gui.HistogramWindow
HistogramWindow(ImagePlus) - Constructor for class ij.gui.HistogramWindow
  Displays a histogram using the title "Histogram of ImageName".
HistogramWindow(String, ImagePlus, int) - Constructor for class ij.gui.HistogramWindow
  Displays a histogram using the specified title and number of bins.
HistogramWindow(String, ImagePlus, int, double, double) - Constructor for class ij.gui.HistogramWindow
  Displays a histogram using the specified title, number of bins and histogram range.
HistogramWindow(String, ImagePlus, int, double, double, int) - Constructor for class ij.gui.HistogramWindow
  Displays a histogram using the specified title, number of bins, histogram range and yMax.
HistogramWindow(String, ImagePlus, ImageStatistics) - Constructor for class ij.gui.HistogramWindow
  Displays a histogram using the specified title and ImageStatistics.
histYMax - Variable in class ij.process.ImageStatistics
HOST_COMPUTER - Static variable in class ij.io.TiffDecoder
Hotkeys - Class in ij.plugin
  Implements the Plugins/Hotkeys/Create Shortcut and Remove commands.
Hotkeys() - Constructor for class ij.plugin.Hotkeys
HSBtoRGB(double[]) - Method in class ij.process.ColorSpaceConverter
HSBtoRGB(double, double, double) - Method in class ij.process.ColorSpaceConverter
HTMLDialog - Class in ij.gui
  This is modal or non-modal dialog box that displays HTML formated text.
HTMLDialog(Dialog, String, String) - Constructor for class ij.gui.HTMLDialog
HTMLDialog(String, String) - Constructor for class ij.gui.HTMLDialog
HTMLDialog(String, String, boolean) - Constructor for class ij.gui.HTMLDialog
Huang - Enum constant in enum class ij.process.AutoThresholder.Method
Huang(int[]) - Static method in class ij.process.AutoThresholder
Huang2(int[]) - Static method in class ij.process.AutoThresholder
HYBRID - Static variable in class ij.gui.PointRoi
hyperlinkUpdate(HyperlinkEvent) - Method in class ij.gui.HTMLDialog
HyperStackConverter - Class in ij.plugin
  Implements the "Stack to HyperStack", "RGB to HyperStack" and "HyperStack to Stack" commands.
HyperStackConverter() - Constructor for class ij.plugin.HyperStackConverter
HyperStackMaker - Class in ij.plugin
  This plugin implements the File/New/Hyperstack command.
HyperStackMaker() - Constructor for class ij.plugin.HyperStackMaker
HyperStackReducer - Class in ij.plugin
  Implements the Image/HyperStacks/Reduce Dimensionality command.
HyperStackReducer() - Constructor for class ij.plugin.HyperStackReducer
  Default constructor
HyperStackReducer(ImagePlus) - Constructor for class ij.plugin.HyperStackReducer
  Constructs a HyperStackReducer using the specified source image.

## I

ic - Variable in class ij.gui.ImageWindow
ic - Variable in class ij.gui.Roi
IF - Static variable in interface ij.macro.MacroConstants
ignoreClipRect - Variable in class ij.gui.Roi
ignoreNextSelection() - Static method in class ij.plugin.Duplicator
ignoreNonImageWidths(boolean) - Method in class ij.gui.ImageLayout
  Determines whether to ignore the width of non-image components when calculating the preferred width (default false, i.e.
ignoreRescaleSlope - Static variable in class ij.Prefs
  Ignore Rescale Slope when opening DICOMs
ij - module ij
ij - package ij
ij - Variable in class ij.gui.ImageCanvas
ij - Variable in class ij.gui.ImageWindow
IJ - Class in ij
  This class consists of static utility methods.
IJ() - Constructor for class ij.IJ
IJ_CALL - Static variable in interface ij.macro.MacroConstants
IJ_IsoData - Enum constant in enum class ij.process.AutoThresholder.Method
IJ.ExceptionHandler - Interface in ij
ij.gui - package ij.gui
ij.io - package ij.io
ij.macro - package ij.macro
ij.measure - package ij.measure
ij.plugin - package ij.plugin
ij.plugin.filter - package ij.plugin.filter
ij.plugin.frame - package ij.plugin.frame
ij.plugin.tool - package ij.plugin.tool
ij.process - package ij.process
ij.text - package ij.text
ij.util - package ij.util
IJDefault(int[]) - Static method in class ij.process.AutoThresholder
IJEventListener - Interface in ij
  Plugins that implement this interface are notified when the user changes the foreground color, changes the background color, closes the color picker, closes the Log window or switches to another tool.
ijInstance - Variable in class ij.plugin.frame.SyncWindows
  reference to current instance of ImageJ (to avoid repeated IJ.getInstance() s)
IJMath - Class in ij.util
IJMath() - Constructor for class ij.util.IJMath
image - Variable in class ij.process.ImageProcessor
IMAGE - Static variable in class ij.io.RoiDecoder
IMAGE - Static variable in interface ij.macro.MacroConstants
IMAGE_DESCRIPTION - Static variable in class ij.io.TiffDecoder
IMAGE_LENGTH - Static variable in class ij.io.TiffDecoder
IMAGE_OPACITY - Static variable in class ij.io.RoiDecoder
IMAGE_SIZE - Static variable in class ij.io.RoiDecoder
IMAGE_WIDTH - Static variable in class ij.io.TiffDecoder
ImageCalculator - Class in ij.plugin
  This plugin implements the Process/Image Calculator command.
ImageCalculator() - Constructor for class ij.plugin.ImageCalculator
ImageCanvas - Class in ij.gui
  This is a Canvas used to display images in a Window.
ImageCanvas(ImagePlus) - Constructor for class ij.gui.ImageCanvas
imageClosed(ImagePlus) - Method in class ij.gui.HistogramWindow
imageClosed(ImagePlus) - Method in class ij.gui.PlotWindow
  For live plots, if either the source image or this image are closed, exit live mode
imageClosed(ImagePlus) - Method in interface ij.ImageListener
imageClosed(ImagePlus) - Method in class ij.plugin.EventListener
imageClosed(ImagePlus) - Method in class ij.plugin.frame.Recorder
imageClosed(ImagePlus) - Method in class ij.plugin.frame.SyncWindows
  Implementation of ImageListener interface: update window list, if image is opened or closed
imageClosed(ImagePlus) - Method in class ij.plugin.frame.ThresholdAdjuster
imageClosed(ImagePlus) - Method in class ij.plugin.Orthogonal_Views
ImageConverter - Class in ij.process
  This class converts an ImagePlus object to a different type.
ImageConverter(ImagePlus) - Constructor for class ij.process.ImageConverter
  Constructs an ImageConverter based on an ImagePlus object.
imageHeight - Variable in class ij.gui.ImageCanvas
ImageInfo - Class in ij.plugin
  This plugin implements the Image/Show Info command.
ImageInfo() - Constructor for class ij.plugin.ImageInfo
IMAGEIO - Static variable in class ij.io.FileInfo
ImageJ - Class in ij
  This frame is the main ImageJ class.
ImageJ() - Constructor for class ij.ImageJ
  Creates a new ImageJ frame that runs as an application.
ImageJ(int) - Constructor for class ij.ImageJ
  Creates a new ImageJ frame that runs as an application in the specified mode.
ImageJ(Applet) - Constructor for class ij.ImageJ
  Creates a new ImageJ frame that runs as an applet.
ImageJ(Applet, int) - Constructor for class ij.ImageJ
  If 'applet' is not null, creates a new ImageJ frame that runs as an applet.
IMAGEJ_APP - Static variable in class ij.ImageJ
  Run as the ImageJ application.
ImageJ_Updater - Class in ij.plugin
  This plugin implements the Help/Update ImageJ command.
ImageJ_Updater() - Constructor for class ij.plugin.ImageJ_Updater
ImageJ.ExceptionHandler - Class in ij
  Handles exceptions on the EDT.
ImageJApplet - Class in ij
  Runs ImageJ as an applet and optionally opens up to nine images using URLs passed as a parameters.
ImageJApplet() - Constructor for class ij.ImageJApplet
ImageLayout - Class in ij.gui
  This is a custom layout manager that supports resizing of zoomed images.
ImageLayout(ImageCanvas) - Constructor for class ij.gui.ImageLayout
  Creates a new ImageLayout with center alignment.
ImageListener - Interface in ij
  Plugins that implement this interface are notified when an image is opened, closed or updated.
ImageMath - Class in ij.plugin.filter
  This plugin implements ImageJ's Process/Math submenu.
ImageMath() - Constructor for class ij.plugin.filter.ImageMath
imageOpened(ImagePlus) - Method in class ij.gui.HistogramWindow
imageOpened(ImagePlus) - Method in class ij.gui.PlotWindow
imageOpened(ImagePlus) - Method in interface ij.ImageListener
imageOpened(ImagePlus) - Method in class ij.plugin.EventListener
imageOpened(ImagePlus) - Method in class ij.plugin.frame.Recorder
imageOpened(ImagePlus) - Method in class ij.plugin.frame.SyncWindows
  Implementation of ImageListener interface: update window list, if image is opened or closed
imageOpened(ImagePlus) - Method in class ij.plugin.frame.ThresholdAdjuster
imageOpened(ImagePlus) - Method in class ij.plugin.Orthogonal_Views
ImagePanel - Class in ij.gui
  This class is used by GenericDialog to add images to dialogs.
ImagePanel(ImagePlus) - Constructor for class ij.gui.ImagePanel
ImagePlus - Class in ij
  An ImagePlus contain an ImageProcessor (2D image) or an ImageStack (3D, 4D or 5D image).
ImagePlus() - Constructor for class ij.ImagePlus
  Constructs an uninitialized ImagePlus.
ImagePlus(String) - Constructor for class ij.ImagePlus
  Constructs an ImagePlus from a TIFF, BMP, DICOM, FITS, PGM, GIF or JPRG specified by a path or from a TIFF, DICOM, GIF or JPEG specified by a URL.
ImagePlus(String, ImageStack) - Constructor for class ij.ImagePlus
  Constructs an ImagePlus from a stack.
ImagePlus(String, ImageProcessor) - Constructor for class ij.ImagePlus
  Constructs an ImagePlus from an ImageProcessor.
ImagePlus(String, Image) - Constructor for class ij.ImagePlus
  Constructs an ImagePlus from an Image or BufferedImage.
ImageProcessor - Class in ij.process
  This abstract class is the superclass for classes that process the four data types (byte, short, float and RGB) supported by ImageJ.
ImageProcessor() - Constructor for class ij.process.ImageProcessor
ImageProperties - Class in ij.plugin.filter
ImageProperties() - Constructor for class ij.plugin.filter.ImageProperties
ImageReader - Class in ij.io
  Reads raw 8-bit, 16-bit or 32-bit (float or RGB) images from a stream or URL.
ImageReader(FileInfo) - Constructor for class ij.io.ImageReader
  Constructs a new ImageReader using a FileInfo object to describe the file to be read.
ImageRoi - Class in ij.gui
  An ImageRoi is an Roi that overlays an image.
ImageRoi(int, int, ImageProcessor) - Constructor for class ij.gui.ImageRoi
  Creates a new ImageRoi from a ImageProcessor.
ImageRoi(int, int, BufferedImage) - Constructor for class ij.gui.ImageRoi
  Creates a new ImageRoi from a BufferedImage.
imageSaved - Variable in class ij.io.FileInfo
imageSaved(ImagePlus) - Method in class ij.plugin.EventListener
ImageStack - Class in ij
  This class represents an expandable array of images.
ImageStack() - Constructor for class ij.ImageStack
  Default constructor.
ImageStack(int, int) - Constructor for class ij.ImageStack
  Creates a new, empty image stack.
ImageStack(int, int, int) - Constructor for class ij.ImageStack
  Creates a new, empty image stack with a capacity of 'size'.
ImageStack(int, int, ColorModel) - Constructor for class ij.ImageStack
  Creates a new, empty image stack using the specified color model.
ImageStatistics - Class in ij.process
  Statistics, including the histogram, of an image or selection.
ImageStatistics() - Constructor for class ij.process.ImageStatistics
ImagesToStack - Class in ij.plugin
  Implements the Image/Stacks/Images to Stack" command.
ImagesToStack() - Constructor for class ij.plugin.ImagesToStack
imageUpdate(Image, int, int, int, int, int) - Method in class ij.ImagePlus
  Used by ImagePlus to monitor loading of images.
imageUpdated - Variable in class ij.gui.ImageCanvas
imageUpdated(ImagePlus) - Method in class ij.gui.HistogramWindow
imageUpdated(ImagePlus) - Method in class ij.gui.PlotWindow
  For live plots, this method is called if the source image content is changed.
imageUpdated(ImagePlus) - Method in interface ij.ImageListener
imageUpdated(ImagePlus) - Method in class ij.plugin.EventListener
imageUpdated(ImagePlus) - Method in class ij.plugin.frame.Recorder
imageUpdated(ImagePlus) - Method in class ij.plugin.frame.SyncWindows
imageUpdated(ImagePlus) - Method in class ij.plugin.frame.ThresholdAdjuster
imageUpdated(ImagePlus) - Method in class ij.plugin.Orthogonal_Views
imageWidth - Variable in class ij.gui.ImageCanvas
ImageWindow - Class in ij.gui
  A frame for displaying images.
ImageWindow(ImagePlus) - Constructor for class ij.gui.ImageWindow
ImageWindow(ImagePlus, ImageCanvas) - Constructor for class ij.gui.ImageWindow
ImageWindow(String) - Constructor for class ij.gui.ImageWindow
ImageWriter - Class in ij.io
  Writes a raw image described by a FileInfo object to an OutputStream.
ImageWriter(FileInfo) - Constructor for class ij.io.ImageWriter
img - Variable in class ij.ImagePlus
img - Variable in class ij.process.ImageProcessor
imp - Variable in class ij.gui.ImageCanvas
imp - Variable in class ij.gui.ImageWindow
imp - Variable in class ij.gui.ProfilePlot
imp - Variable in class ij.gui.Roi
imp - Variable in class ij.plugin.filter.ParticleAnalyzer
IMPORT_MENU - Static variable in class ij.Menus
importData(JComponent, Transferable) - Method in class ij.io.DragAndDropHandler
  Imports the draginvalid input: '&drop' file or list of files and sets the JFileChooser to this.
ImportDialog - Class in ij.io
  This is a dialog box used to imports raw 8, 16, 24 and 32-bit images.
ImportDialog() - Constructor for class ij.io.ImportDialog
ImportDialog(String, String) - Constructor for class ij.io.ImportDialog
in - Variable in class ij.io.TiffDecoder
in(ImagePlus) - Static method in class ij.plugin.Zoom
IN_PLACE - Static variable in class ij.plugin.Resizer
IN_SITU_SHOW - Static variable in class ij.plugin.filter.ParticleAnalyzer
  Replace original image with masks.
IN_TOLERANCE - Static variable in class ij.plugin.filter.MaximumFinder
  Output type all points around the maximum within the tolerance
INCLUDE_HOLES - Static variable in class ij.plugin.filter.ParticleAnalyzer
  Flood fill to ignore interior holes.
incrementCounter() - Method in class ij.measure.ResultsTable
  Adds a row to the table.
INDEX_OF - Static variable in interface ij.macro.MacroConstants
indexAt(int, int) - Method in class ij.gui.Overlay
  Returns the index of the last ROI that contains the point (x,y) or null if no ROI contains the point.
indices - Variable in class ij.process.DownsizeTable
  For each source point between srcStart and srcEnd, indices of destination points where the data should be added.
info - Variable in class ij.io.FileInfo
info - Variable in class ij.measure.Calibration
  Plugin writers can use this string to store information about the image.
Info - Class in ij.plugin.filter
  Deprecated.
  replaced by ij.plugin.ImageInfo
Info() - Constructor for class ij.plugin.filter.Info
  Deprecated.
init() - Method in class ij.gui.Toolbar
init() - Method in class ij.ImageJApplet
  Starts ImageJ if it's not already running.
init(int, int) - Method in class ij.gui.ProgressBar
INITIALIZATION_FAILURE - Static variable in class ij.measure.Minimizer
  Status returned: Could not initialize the simplex because either the initialParams resulted in the target function returning NaN or all attempts to find starting parameters for the other simplex points resulted in the target function returning NaN.
inputStream - Variable in class ij.io.FileInfo
insert(ImagePlus, ImagePlus, int, int) - Method in class ij.plugin.StackInserter
insert(ImageProcessor, int, int) - Method in class ij.process.ImageProcessor
  Inserts the image contained in 'ip' at (xloc, yloc).
insertText(String) - Method in class ij.plugin.frame.Editor
inSituShow - Variable in class ij.plugin.filter.ParticleAnalyzer
install(String) - Method in class ij.plugin.MacroInstaller
install(String) - Method in class ij.plugin.PluginInstaller
install(String, Menu) - Method in class ij.plugin.MacroInstaller
INSTALL_BUTTON - Static variable in class ij.plugin.frame.Editor
installFile(String) - Method in class ij.plugin.MacroInstaller
installFromIJJar(String) - Method in class ij.plugin.MacroInstaller
  Installs a macro set contained in ij.jar.
installFromJar(String) - Static method in class ij.plugin.MacroInstaller
  Installs a macro set contained in ij.jar.
installLibrary(String) - Method in class ij.plugin.MacroInstaller
installPlugin(String, char, String, String, ImageJ) - Static method in class ij.Menus
  Adds a plugin based command to the end of a specified menu.
installSingleTool(String) - Method in class ij.plugin.MacroInstaller
installStartupMacros(String) - Method in class ij.plugin.MacroInstaller
  Installs startup macros and runs AutoRun macro on current thread.
installStartupMacrosTools() - Static method in class ij.gui.Toolbar
installStartupTools() - Method in class ij.gui.Toolbar
installTool(String) - Method in class ij.plugin.MacroInstaller
installUserPlugin(String, boolean) - Method in class ij.Menus
instance - Static variable in class ij.gui.GenericDialog
instanceColor - Variable in class ij.gui.Roi
int2hex(int, int) - Static method in class ij.util.Tools
  Converts an int to a zero-padded hex string of fixed length 'digits'.
INTEGRATED_DENSITY - Static variable in interface ij.measure.Measurements
INTEGRATED_DENSITY - Static variable in class ij.measure.ResultsTable
intelByteOrder - Variable in class ij.io.FileInfo
intelByteOrder - Static variable in class ij.Prefs
  Export TIFF and Raw using little-endian byte order.
INTERACTIVE_NAME - Static variable in class ij.plugin.frame.Editor
Intermodes - Enum constant in enum class ij.process.AutoThresholder.Method
Intermodes(int[]) - Static method in class ij.process.AutoThresholder
interpolate - Static variable in class ij.gui.PlotWindow
  Interpolate line profiles.
interpolate - Variable in class ij.process.ImageProcessor
interpolateScaledImages - Static variable in class ij.Prefs
  Display images scaled invalid input: '<'100% using bilinear interpolation
interpolationMethod - Variable in class ij.process.ImageProcessor
Interpreter - Class in ij.macro
  This is the recursive descent parser/interpreter for the ImageJ macro language.
Interpreter() - Constructor for class ij.macro.Interpreter
IntProcessor - Class in ij.process
  This is an extended ColorProcessor that supports signed 32-bit int images.
IntProcessor(int, int) - Constructor for class ij.process.IntProcessor
  Creates a blank IntProcessor with the specified dimensions.
IntProcessor(int, int, int[]) - Constructor for class ij.process.IntProcessor
  Creates an IntProcessor from a pixel array.
INV_RODBARD - Static variable in class ij.measure.CurveFitter
  Constants for the built-in fit functions
INVALID_SHORTCUT - Static variable in class ij.Menus
invalidNumber() - Method in class ij.gui.GenericDialog
  Returns true if one or more of the numeric fields contained an invalid number.
inverse(ImagePlus) - Static method in class ij.plugin.FFT
  Performs an inverse FHT transform.
inverseTransform() - Method in class ij.process.FHT
  Performs an inverse transform, converting this image into the space domain.
inverseTransform1D(float[]) - Method in class ij.process.FHT
  Performs an inverse 1D Fast Hartley Transform (FHT) of an array
inversionTested - Variable in class ij.process.ImageProcessor
invert() - Method in class ij.process.FloatProcessor
  Each pixel in the image or ROI is inverted using p=max-(p-min), where 'min' and 'max' are the minimum and maximum displayed pixel values.
invert() - Method in class ij.process.ImageProcessor
  Inverts the image or ROI.
invert() - Method in class ij.process.ShortProcessor
  If "Full range 16-bit inversions" (Prefs.fullRange16bitInversions) is set in Edit/Options/Conversions, the image or ROI is inverted using the full pixel value range (0-65535) or, if set, using the "Unsigned 16-bit range" in the "Set" option of the Image>Adjust>Brightness/Contrast dialog.
  Otherwise, each pixel in the image or ROI is inverted using v2=max-(v1-min), where 'min' and 'max' are the image's minimum and maximum pixel values.
invert() - Method in class ij.process.StackProcessor
INVERT - Static variable in interface ij.macro.MacroConstants
INVERT_PROJECTION - Static variable in class ij.process.ImageProcessor
  Composite image projection modes.
INVERT_Y - Static variable in interface ij.measure.Measurements
invertedLut - Variable in class ij.process.ImageProcessor
invertLut() - Method in class ij.process.ColorProcessor
  Does nothing since RGB images do not use LUTs.
invertLut() - Method in class ij.process.ImageProcessor
  Inverts the values in this image's LUT (indexed color model).
ip - Variable in class ij.ImagePlus
IPLAB - Static variable in class ij.io.TiffDecoder
IS - Static variable in interface ij.macro.MacroConstants
IS_ACTIVE - Static variable in interface ij.macro.MacroConstants
IS_KEY_DOWN - Static variable in interface ij.macro.MacroConstants
IS_NAN - Static variable in interface ij.macro.MacroConstants
IS_OPEN - Static variable in interface ij.macro.MacroConstants
is64Bit() - Static method in class ij.IJ
  Returns true if ImageJ is running a 64-bit version of Java.
isActiveOverlayRoi() - Method in class ij.gui.Roi
  Returns 'true' if this ROI is displayed and is also in an overlay.
isAntialiased() - Static method in class ij.gui.TextRoi
  Returns the state of the global 'antialiasedText' variable, which is used by the "Fonts" widget.
isArea() - Method in class ij.gui.Roi
  Returns 'true' if this is an area selection.
isAutoRunAndHide() - Method in class ij.plugin.MacroInstaller
  Returns true if an "AutoRunAndHide" macro was run/installed.
isBatchMode() - Static method in class ij.macro.Interpreter
isBatchModeRoiManager() - Static method in class ij.macro.Interpreter
  Returns true if there is an internal batch mode RoiManager.
isBinary() - Method in class ij.process.ByteProcessor
  Returns 'true' if this is a binary image (8-bit-image with only 0 and 255).
isBinary() - Method in class ij.process.ImageProcessor
  Returns 'true' if this is a binary image (8-bit-image with only 0 and 255).
isCalibrationBar() - Method in class ij.gui.Overlay
isClosed() - Method in class ij.gui.ImageWindow
  Has this window been closed?
isColorLut() - Method in class ij.process.ImageProcessor
  Returns true if this image uses a color LUT.
isComposite() - Method in class ij.ImagePlus
  Returns true if this is a CompositeImage.
isCursor() - Method in class ij.gui.Roi
isDarkBackground() - Static method in class ij.plugin.frame.ThresholdAdjuster
isDataFlavorSupported(DataFlavor) - Method in class ij.plugin.Clipboard
isDefaultLut() - Method in class ij.process.ImageProcessor
  Returns true if the image is using the default grayscale LUT.
isDisplayedHyperStack() - Method in class ij.ImagePlus
  Returns 'true' if this is a hyperstack currently being displayed in a StackWindow.
isDraggable() - Method in class ij.gui.Overlay
  Returns 'true' if ROIs in this overlay can be dragged by their labels.
isDrawingTool() - Method in class ij.gui.Arrow
isDrawingTool() - Method in class ij.gui.Roi
  Returns 'true' if this is an ROI primarily used from drawing (e.g., TextRoi or Arrow).
isDrawingTool() - Method in class ij.gui.TextRoi
isFrozen() - Method in class ij.gui.Plot
isFrozen() - Method in class ij.gui.PlotCanvas
  Whether the plot is frozen, i.e.
isFullPath(String) - Static method in class ij.io.Opener
isGrayscale() - Method in class ij.LookUpTable
  Returns `true` if this is a 256 entry grayscale LUT.
isGrayscale() - Method in class ij.process.ColorProcessor
  Returns 'true' if this is a grayscale image.
isGrayscale() - Method in class ij.process.ImageProcessor
  Returns 'true' if this is an image with a grayscale LUT or an RGB image with identical red, green and blue channels.
isHandle(int, int) - Method in class ij.gui.EllipseRoi
isHandle(int, int) - Method in class ij.gui.Line
  Returns a handle number if the specified screen coordinates are inside or near a handle, otherwise returns -1.
isHandle(int, int) - Method in class ij.gui.OvalRoi
  Returns a handle number if the specified screen coordinates are inside or near a handle, otherwise returns -1.
isHandle(int, int) - Method in class ij.gui.PointRoi
  Returns a point index if it has been at least one second since the last point was added and the specified screen coordinates are inside or near a point, otherwise returns -1.
isHandle(int, int) - Method in class ij.gui.PolygonRoi
  Returns a handle number if the specified screen coordinates are inside or near a handle, otherwise returns -1.
isHandle(int, int) - Method in class ij.gui.Roi
  Returns a handle number if the specified screen coordinates are inside or near a handle, otherwise returns -1.
isHandle(int, int) - Method in class ij.gui.RotatedRectRoi
isHandle(int, int) - Method in class ij.gui.ShapeRoi
  Always returns -1 since ShapeRois do not have handles.
isHSB() - Method in class ij.ImageStack
  Returns true if this is a 3-slice HSB stack.
isHSB32() - Method in class ij.ImageStack
  Returns true if this is a 3-slice 32-bit HSB stack.
isHyperStack() - Method in class ij.gui.StackWindow
isHyperStack() - Method in class ij.ImagePlus
  Returns 'true' if this image has more than three dimensions.
isInteger(double) - Static method in class ij.gui.Roi
  Returns whether a number is an integer
isInvertedLut() - Method in class ij.ImagePlus
  Returns true is this image uses an inverting LUT that displays zero as white and 255 as black.
isInvertedLut() - Method in class ij.process.ColorProcessor
  Always returns false since RGB images do not use LUTs.
isInvertedLut() - Method in class ij.process.ImageProcessor
  Returns true if this image uses an inverting LUT that displays zero as white and 255 as black.
isJava14() - Static method in class ij.IJ
  Always returns true.
isJava15() - Static method in class ij.IJ
  Always returns true.
isJava16() - Static method in class ij.IJ
  Returns true if ImageJ is running on a Java 1.6 or greater JVM.
isJava17() - Static method in class ij.IJ
  Returns true if ImageJ is running on a Java 1.7 or greater JVM.
isJava18() - Static method in class ij.IJ
  Returns true if ImageJ is running on a Java 1.8 or greater JVM.
isJava19() - Static method in class ij.IJ
  Returns true if ImageJ is running on a Java 1.9 or greater JVM.
isJava2() - Static method in class ij.IJ
  Always returns true.
isKillable() - Method in class ij.process.ImageProcessor
  Deprecated.
isLab() - Method in class ij.ImageStack
  Returns true if this is a Lab stack.
isLine() - Method in class ij.gui.Roi
  Returns 'true' if this is a line selection.
isLineOrPoint() - Method in class ij.gui.Roi
  Return 'true' if this is a line or point selection.
isLinux() - Static method in class ij.IJ
  Returns true if ImageJ is running on Linux.
isLocked() - Method in class ij.ImagePlus
  Returns 'true' if the image is locked.
isLockedByAnotherThread() - Method in class ij.ImagePlus
  Returns 'true' if the image was locked on another thread.
isMacintosh() - Static method in class ij.IJ
  Returns true if this machine is a Macintosh.
isMacOSX() - Static method in class ij.IJ
  Returns true if this machine is a Macintosh running OS X.
isMacro() - Method in class ij.gui.GenericDialog
isMacro() - Static method in class ij.IJ
  Returns true if a macro is running, or if the run(), open() or newImage() method is executing.
isMacroCommand(String) - Static method in class ij.plugin.MacroInstaller
  Returns 'true' if the macro command 'name' exists.
isMaximum(double) - Method in class ij.util.ArrayUtil
IsoData - Enum constant in enum class ij.process.AutoThresholder.Method
IsoData(int[]) - Static method in class ij.process.AutoThresholder
ISODATA - Static variable in class ij.process.ImageProcessor
  Isodata thresholding method
ISODATA2 - Static variable in class ij.process.ImageProcessor
  Modified isodata method used in Image/Adjust/Threshold tool
isOptionalArg(int) - Static method in class ij.macro.ExtensionDescriptor
isOrthoViewsImage(ImagePlus) - Static method in class ij.plugin.Orthogonal_Views
isOutputArg(int) - Static method in class ij.macro.ExtensionDescriptor
isPowerOf2(int) - Static method in class ij.process.FHT
isPreviewActive() - Method in class ij.gui.GenericDialog
  Returns 'true' if this dialog has a "Preview" checkbox and it is enabled.
isProcessor() - Method in class ij.ImagePlus
isPseudoColorLut() - Method in class ij.process.ImageProcessor
  Returns true if this image uses a pseudocolor or grayscale LUT, in other words, is this an image that can be filtered.
isRedirectImage() - Static method in class ij.plugin.filter.Analyzer
  Returns `true` if an image is selected in the "Redirect To:" popup menu of the Analyze/Set Measurements dialog box.
isResultsTable - Variable in class ij.measure.ResultsTable
isResultsWindow() - Static method in class ij.IJ
  Returns true if the "Results" window is open.
isRGB() - Method in class ij.ImagePlus
isRGB() - Method in class ij.ImageStack
  Returns true if this is a 3-slice, 8-bit RGB stack.
isRMIEnabled() - Static method in class ij.OtherInstance
isSelectable() - Method in class ij.gui.Overlay
  Returns 'true' if ROIs in this overlay can be activated by clicking on their labels or by a long press.
isSelected(int) - Method in class ij.plugin.frame.RoiManager
  Returns 'true' if the index is valid and the indexed ROI is selected.
isSigned16Bit() - Method in class ij.measure.Calibration
  Returns true if this is a signed 16-bit image.
isSigned16Bit() - Method in class ij.process.ImageProcessor
  Returns 'true' if this is a signed 16-bit image.
isSigned16Bit() - Method in class ij.process.ShortProcessor
  Returns 'true' if this is a signed 16-bit image.
isSplineFit() - Method in class ij.gui.PolygonRoi
  Returns 'true' if this selection has been fitted with a spline.
isStack() - Method in class ij.ImagePlus
  Deprecated.
  Replaced by ImagePlus.hasImageStack()
isSupportedTransferFlavor(DataFlavor) - Method in class ij.io.DragAndDropHandler
  Returns whether this transfer flavor is supported.
isThreshold() - Method in class ij.ImagePlus
  Returns 'true' if this image is thresholded.
isThreshold() - Method in class ij.process.ImageProcessor
  Returns 'true' if this image is thresholded.
isVirtual() - Method in class ij.ImageStack
  Returns true if this is a virtual (disk resident) stack.
isVirtual() - Method in class ij.VirtualStack
  Always return true.
isVisible() - Method in class ij.gui.Roi
  Returns true if this ROI is currently displayed on an image.
isVisible() - Method in class ij.ImagePlus
  Returns true if this image is currently being displayed in a window.
isVista() - Static method in class ij.IJ
  Obsolete; always returns false.
isWindows() - Static method in class ij.IJ
  Returns true if this machine is running Windows.
itemStateChanged(ItemEvent) - Method in class ij.gui.GenericDialog
itemStateChanged(ItemEvent) - Method in class ij.gui.PlotWindow
  Called if the user activates/deactivates a CheckboxMenuItem
itemStateChanged(ItemEvent) - Method in class ij.gui.Toolbar
itemStateChanged(ItemEvent) - Method in class ij.ImageJ
  Handles CheckboxMenuItem state changes.
itemStateChanged(ItemEvent) - Method in class ij.macro.FunctionFinder
itemStateChanged(ItemEvent) - Method in class ij.plugin.BatchProcessor
itemStateChanged(ItemEvent) - Method in class ij.plugin.Colors
  Callback listener for Choice modifications in the dialog
itemStateChanged(ItemEvent) - Method in class ij.plugin.CommandFinder
itemStateChanged(ItemEvent) - Method in class ij.plugin.Concatenator
itemStateChanged(ItemEvent) - Method in class ij.plugin.Duplicator
itemStateChanged(ItemEvent) - Method in class ij.plugin.frame.Channels
itemStateChanged(ItemEvent) - Method in class ij.plugin.frame.ColorThresholder
itemStateChanged(ItemEvent) - Method in class ij.plugin.frame.Commands
itemStateChanged(ItemEvent) - Method in class ij.plugin.frame.ContrastAdjuster
itemStateChanged(ItemEvent) - Method in class ij.plugin.frame.Editor
itemStateChanged(ItemEvent) - Method in class ij.plugin.frame.Fitter
itemStateChanged(ItemEvent) - Method in class ij.plugin.frame.LineWidthAdjuster
itemStateChanged(ItemEvent) - Method in class ij.plugin.frame.PasteController
itemStateChanged(ItemEvent) - Method in class ij.plugin.frame.Recorder
itemStateChanged(ItemEvent) - Method in class ij.plugin.frame.RoiManager
itemStateChanged(ItemEvent) - Method in class ij.plugin.frame.SyncWindows
  Item Listener method
itemStateChanged(ItemEvent) - Method in class ij.plugin.frame.ThresholdAdjuster
itemStateChanged(ItemEvent) - Method in class ij.plugin.Resizer
itemStateChanged(ItemEvent) - Method in class ij.plugin.Slicer
itemStateChanged(ItemEvent) - Method in class ij.plugin.Startup
itemStateChanged(ItemEvent) - Method in class ij.plugin.Thresholder
itemStateChanged(ItemEvent) - Method in class ij.text.TextWindow
iterator() - Method in class ij.gui.Line
iterator() - Method in class ij.gui.Overlay
iterator() - Method in class ij.gui.PointRoi
  Custom iterator for points contained in a `PointRoi`.
iterator() - Method in class ij.gui.Roi
  Required by the `Iterable` interface.
iterator() - Method in class ij.plugin.frame.RoiManager
IterFactor - Static variable in class ij.measure.CurveFitter
  Deprecated.
  now in the Minimizer class (since ImageJ 1.46f). (probably of not much value for anyone anyhow?)

## J

JAVA_OR_TEXT - Static variable in class ij.io.Opener
Java2 - Class in ij.util
  This class contains static methods that use the Java 2 API.
Java2() - Constructor for class ij.util.Java2
JavaProperties - Class in ij.plugin
  Displays the Java system properties in a text window.
JavaProperties() - Constructor for class ij.plugin.JavaProperties
JAVASCRIPT - Static variable in class ij.plugin.NewPlugin
JavaScriptEvaluator - Class in ij.plugin
  Implements the text editor's Macros/Run command, and the IJ.runMacroFile() method, when the file name ends with ".js".
JavaScriptEvaluator() - Constructor for class ij.plugin.JavaScriptEvaluator
JavaScriptIncludes - Static variable in class ij.plugin.frame.Editor
  ImportPackage statements added in front of scripts.
javaVersion() - Static method in class ij.IJ
  Returns the Java version (6, 7, 8, 9, 10, etc.).
jFileChooserSettingChanged - Static variable in class ij.Prefs
  Use JFileChooser setting changed/
joinAll(Future[]) - Static method in class ij.util.ThreadUtil
  Waits for completion of all `Callable`s corresponding to the `Future`s given.
JPEG - Static variable in class ij.io.FileInfo
JPEG - Static variable in class ij.io.Opener
JPEG - Static variable in class ij.Prefs
JPEG_COMPRESSION - Static variable in class ij.plugin.filter.AVI_Writer
JPEG_TABLES - Static variable in class ij.io.TiffDecoder
JpegWriter - Class in ij.plugin
  The File/Save As/Jpeg command (FileSaver.saveAsJpeg() method) uses this plugin to save images in JPEG format.
JpegWriter() - Constructor for class ij.plugin.JpegWriter
justification - Variable in class ij.process.ImageProcessor

## K

KEEP_PREVIEW - Static variable in interface ij.plugin.filter.ExtendedPlugInFilter
  Set this flag if the last preview image may be kept as a result.
KEEP_THRESHOLD - Static variable in interface ij.plugin.filter.PlugInFilter
  Set this flag to keep the invisible binary threshold from being reset.
keepArrowSelections - Static variable in class ij.Prefs
  Keep arrow selection after adding to overlay
keepUndoBuffers - Static variable in class ij.Prefs
  Preserve undo (snapshot) buffers when switching images
kernel(double) - Method in class ij.process.DownsizeTable
kernelSize - Variable in class ij.process.DownsizeTable
  Number of kernel points per source data point
KEY_PREFIX - Static variable in class ij.Prefs
keyPressed(KeyEvent) - Method in class ij.gui.GenericDialog
keyPressed(KeyEvent) - Method in class ij.gui.HTMLDialog
keyPressed(KeyEvent) - Method in class ij.gui.MessageDialog
keyPressed(KeyEvent) - Method in class ij.gui.NonBlockingGenericDialog
keyPressed(KeyEvent) - Method in class ij.gui.SaveChangesDialog
keyPressed(KeyEvent) - Method in class ij.gui.WaitForUserDialog
keyPressed(KeyEvent) - Method in class ij.gui.YesNoCancelDialog
keyPressed(KeyEvent) - Method in class ij.ImageJ
keyPressed(KeyEvent) - Method in class ij.macro.FunctionFinder
keyPressed(KeyEvent) - Method in class ij.measure.ResultsTableMacros
keyPressed(KeyEvent) - Method in class ij.plugin.CommandFinder
keyPressed(KeyEvent) - Method in class ij.plugin.frame.Editor
keyPressed(KeyEvent) - Method in class ij.plugin.frame.Fitter
keyPressed(KeyEvent) - Method in class ij.plugin.frame.ThresholdAdjuster
keyPressed(KeyEvent) - Method in class ij.plugin.Orthogonal_Views
keyPressed(KeyEvent) - Method in class ij.text.TextPanel
keyReleased(KeyEvent) - Method in class ij.gui.GenericDialog
keyReleased(KeyEvent) - Method in class ij.gui.HTMLDialog
keyReleased(KeyEvent) - Method in class ij.gui.MessageDialog
keyReleased(KeyEvent) - Method in class ij.gui.SaveChangesDialog
keyReleased(KeyEvent) - Method in class ij.gui.WaitForUserDialog
keyReleased(KeyEvent) - Method in class ij.gui.YesNoCancelDialog
keyReleased(KeyEvent) - Method in class ij.ImageJ
keyReleased(KeyEvent) - Method in class ij.macro.FunctionFinder
keyReleased(KeyEvent) - Method in class ij.measure.ResultsTableMacros
keyReleased(KeyEvent) - Method in class ij.plugin.CommandFinder
keyReleased(KeyEvent) - Method in class ij.plugin.frame.Editor
keyReleased(KeyEvent) - Method in class ij.plugin.frame.Fitter
keyReleased(KeyEvent) - Method in class ij.plugin.frame.ThresholdAdjuster
keyReleased(KeyEvent) - Method in class ij.plugin.Orthogonal_Views
keyReleased(KeyEvent) - Method in class ij.text.TextPanel
keyTyped(KeyEvent) - Method in class ij.gui.GenericDialog
keyTyped(KeyEvent) - Method in class ij.gui.HTMLDialog
keyTyped(KeyEvent) - Method in class ij.gui.MessageDialog
keyTyped(KeyEvent) - Method in class ij.gui.SaveChangesDialog
keyTyped(KeyEvent) - Method in class ij.gui.WaitForUserDialog
keyTyped(KeyEvent) - Method in class ij.gui.YesNoCancelDialog
keyTyped(KeyEvent) - Method in class ij.ImageJ
keyTyped(KeyEvent) - Method in class ij.macro.FunctionFinder
keyTyped(KeyEvent) - Method in class ij.measure.ResultsTableMacros
keyTyped(KeyEvent) - Method in class ij.plugin.CommandFinder
keyTyped(KeyEvent) - Method in class ij.plugin.frame.Editor
keyTyped(KeyEvent) - Method in class ij.plugin.frame.Fitter
keyTyped(KeyEvent) - Method in class ij.plugin.frame.ThresholdAdjuster
keyTyped(KeyEvent) - Method in class ij.plugin.Orthogonal_Views
keyTyped(KeyEvent) - Method in class ij.text.TextPanel
keywordIDs - Static variable in interface ij.macro.MacroConstants
keywords - Static variable in interface ij.macro.MacroConstants
killPlotObjectsSnapshot() - Method in class ij.gui.Plot
  Deletes the snapshot of the plot contents to make space
killPlotPropertiesSnapshot() - Method in class ij.gui.Plot
  Deletes the snapshot of the plot properties to make space
killRoi() - Method in class ij.ImagePlus
  Deletes the current region of interest.
killStack() - Method in class ij.ImagePlus
kurtosis - Variable in class ij.process.ImageStatistics
KURTOSIS - Static variable in interface ij.measure.Measurements
KURTOSIS - Static variable in class ij.measure.ResultsTable

## L

label - Variable in class ij.gui.MessageDialog
label - Variable in class ij.gui.WaitForUserDialog
label(ImageProcessor) - Method in class ij.plugin.filter.Filler
labelHyperstack(ImagePlus) - Static method in class ij.plugin.HyperStackMaker
LABELS - Static variable in interface ij.measure.Measurements
LabToRGB(ImagePlus) - Method in class ij.process.ColorSpaceConverter
  Converts a Lab stack into an RGB image.
LABtoRGB(double[]) - Method in class ij.process.ColorSpaceConverter
LABtoRGB(double, double, double) - Method in class ij.process.ColorSpaceConverter
  Convert LAB to RGB.
LABtoXYZ(double[]) - Method in class ij.process.ColorSpaceConverter
  Convert LAB to XYZ.
LABtoXYZ(double, double, double) - Method in class ij.process.ColorSpaceConverter
  Convert LAB to XYZ.
LAST_HEADING - Static variable in class ij.measure.ResultsTable
LAST_INDEX_OF - Static variable in interface ij.macro.MacroConstants
lastZoomSX - Variable in class ij.gui.ImageCanvas
  Screen coordinates where the last zoom operation was done (initialized to impossible value)
lastZoomSY - Variable in class ij.gui.ImageCanvas
layoutContainer(Container) - Method in class ij.gui.ImageLayout
  Lays out the container and calls ImageCanvas.resizeCanvas() to adjust the image canvas size as needed.
LEFT - Static variable in class ij.gui.Plot
  Text justification.
LEFT - Static variable in class ij.gui.TextRoi
LEFT - Static variable in class ij.io.RoiDecoder
LEFT_JUSTIFY - Static variable in class ij.process.ImageProcessor
  Left justify text.
LEFT_MARGIN - Static variable in class ij.gui.Plot
  Deprecated.
  Not a fixed value any more, use getDrawingFrame() to get the drawing area
LEGACY_MODE - Static variable in class ij.gui.Wand
  Wand operation type similar to that of ImageJ 1.42p and before; for backwards compatibility.
LEGEND - Static variable in class ij.gui.PlotDialog
  Types of dialog.
LEGEND_BOTTOM_UP - Static variable in class ij.gui.Plot
  Legend has its curves in bottom-to-top sequence (otherwise top to bottom)
LEGEND_TRANSPARENT - Static variable in class ij.gui.Plot
  Legend erases background (otherwise transparent)
LENGTH_OF - Static variable in interface ij.macro.MacroConstants
Li - Enum constant in enum class ij.process.AutoThresholder.Method
Li(int[]) - Static method in class ij.process.AutoThresholder
LIMIT - Static variable in interface ij.measure.Measurements
Line - Class in ij.gui
  This class represents a straight line selection.
Line(double, double, double, double) - Constructor for class ij.gui.Line
  Creates a new straight line selection using the specified starting and ending offscreen double coordinates.
Line(int, int, int, int) - Constructor for class ij.gui.Line
  Creates a new straight line selection using the specified starting and ending offscreen integer coordinates.
Line(int, int, int, int, ImagePlus) - Constructor for class ij.gui.Line
  Deprecated.
  replaced by Line(int, int, int, int)
Line(int, int, ImagePlus) - Constructor for class ij.gui.Line
  Starts the process of creating a new user-generated straight line selection.
LINE - Static variable in class ij.gui.Plot
  Connect points with solid lines.
LINE - Static variable in class ij.gui.PlotWindow
  Deprecated.
LINE - Static variable in class ij.gui.Roi
LINE - Static variable in class ij.gui.Toolbar
LINE_TO - Static variable in interface ij.macro.MacroConstants
Line.PointIterator - Class in ij.gui
  Dedicated point iterator for thin lines.
lineCircleIntersection(double, double, double, double, double, double, double, boolean) - Static method in class ij.gui.Roi
  Calculates intersections of a line segment with a circle Author N.Vischer ax, ay, bx, by: points A and B of line segment cx, cy, rad: Circle center and radius.
LineGraphAnalyzer - Class in ij.plugin.filter
  Implements ImageJ's Analyze/Tools/Analyze Line Graph command.
LineGraphAnalyzer() - Constructor for class ij.plugin.filter.LineGraphAnalyzer
lineTo(int, int) - Method in class ij.process.ImageProcessor
  Draws a line from the current drawing location to (x2,y2).
lineToArea(Roi) - Static method in class ij.plugin.Selection
  Converts a line selection into an area selection.
lineWidth - Static variable in class ij.gui.Roi
lineWidth - Variable in class ij.process.ImageProcessor
LineWidthAdjuster - Class in ij.plugin.frame
  Adjusts the width of line selections.
LineWidthAdjuster() - Constructor for class ij.plugin.frame.LineWidthAdjuster
list - Variable in class ij.gui.HistogramWindow
LIST - Static variable in interface ij.macro.MacroConstants
LIST - Static variable in class ij.plugin.filter.MaximumFinder
  Do not create an image, just list x, y of maxima in the Results table
listAllThreads(PrintWriter) - Static method in class ij.plugin.ThreadLister
listCommands() - Method in class ij.plugin.CommandLister
listRois(Roi[]) - Static method in class ij.plugin.OverlayCommands
listShortcuts() - Method in class ij.plugin.CommandLister
listValues - Static variable in class ij.gui.PlotWindow
  Display the XY coordinates in a separate window.
ListVirtualStack - Class in ij.plugin
  This plugin opens images specified by list of file paths as a virtual stack.
ListVirtualStack() - Constructor for class ij.plugin.ListVirtualStack
live - Variable in class ij.gui.HistogramWindow
ln() - Method in class ij.process.ImageProcessor
  Does a natural logarithmic (base e) transform of the image or ROI.
load(BufferedReader) - Method in class ij.text.TextWindow
  Appends the text in the specified file to the end of this TextWindow.
load(Object, Applet) - Static method in class ij.Prefs
  Finds and loads the configuration file ("IJ_Props.txt") and the preferences file ("IJ_Prefs.txt").
loadLut(String) - Static method in class ij.Executer
  Opens a .lut file from the ImageJ/luts directory and returns 'true' if successful.
loadPrefs() - Static method in class ij.OtherInstance
LOC_KEY - Static variable in class ij.gui.ImageWindow
LOC_KEY - Static variable in class ij.plugin.frame.Commands
LOC_KEY - Static variable in class ij.plugin.frame.ContrastAdjuster
LOC_KEY - Static variable in class ij.plugin.frame.LineWidthAdjuster
LOC_KEY - Static variable in class ij.plugin.frame.RoiManager
LOC_KEY - Static variable in class ij.plugin.frame.ThresholdAdjuster
LOC_KEY - Static variable in class ij.text.TextWindow
lock() - Method in class ij.ImagePlus
  Locks the image so other threads can test to see if it is in use.
locked - Variable in class ij.ImagePlus
lockSilently() - Method in class ij.ImagePlus
  Similar to lock, but doesn't beep and display an error message if the attempt to lock the image fails.
log - Variable in class ij.gui.HistogramWindow
log() - Method in class ij.process.FloatProcessor
log() - Method in class ij.process.ImageProcessor
  Does a natural logarithmic (base e) transform of the image or ROI.
log() - Method in class ij.process.ShortProcessor
log(String) - Static method in class ij.IJ
LOG - Static variable in interface ij.macro.MacroConstants
LOG - Static variable in class ij.measure.Calibration
LOG - Static variable in class ij.measure.CurveFitter
  Constants for the built-in fit functions
LOG_HEIGHT_KEY - Static variable in class ij.text.TextWindow
LOG_LOC_KEY - Static variable in class ij.text.TextWindow
LOG_WIDTH_KEY - Static variable in class ij.text.TextWindow
LOG_WINDOW_CLOSED - Static variable in interface ij.IJEventListener
LOG2 - Static variable in class ij.measure.Calibration
LOG2 - Static variable in class ij.measure.CurveFitter
  Constants for the built-in fit functions
LOGICAL_AND - Static variable in interface ij.macro.MacroConstants
LOGICAL_OR - Static variable in interface ij.macro.MacroConstants
logImageListeners() - Static method in class ij.ImagePlus
  For debug purposes, writes all registered (and possibly, forgotten) ImageListeners to the log window
logProperties() - Method in class ij.plugin.ProxySettings
logScale - Variable in class ij.gui.HistogramWindow
LogStream - Class in ij.io
  This class provides the functionality to divert output sent to the System.out and System.err streams to ImageJ's log console.
LogStream() - Constructor for class ij.io.LogStream
longGap - Variable in class ij.io.FileInfo
longHistogram - Variable in class ij.process.ImageStatistics
  Long histogram; use getHIstogram() to retrieve.
longOffset - Variable in class ij.io.FileInfo
longPixelCount - Variable in class ij.process.ImageStatistics
  Long pixel count
lookupPathVariable(String) - Static method in class ij.io.OpenDialog
LookUpTable - Class in ij
  This class represents a color look-up table.
LookUpTable(Image) - Constructor for class ij.LookUpTable
  Constructs a LookUpTable object from an AWT Image.
LookUpTable(ColorModel) - Constructor for class ij.LookUpTable
  Constructs a LookUpTable object from a ColorModel.
loop - Variable in class ij.measure.Calibration
lostOwnership(Clipboard, Transferable) - Method in class ij.gui.HistogramWindow
lostOwnership(Clipboard, Transferable) - Method in class ij.gui.PlotWindow
lostOwnership(Clipboard, Transferable) - Method in class ij.plugin.frame.Editor
lostOwnership(Clipboard, Transferable) - Method in class ij.plugin.frame.Fitter
lostOwnership(Clipboard, Transferable) - Method in class ij.text.TextPanel
lowerThreshold - Variable in class ij.process.ImageStatistics
  Minimum threshold when "Limit to threshold" enabled
LT - Static variable in interface ij.macro.MacroConstants
LTE - Static variable in interface ij.macro.MacroConstants
lut - Variable in class ij.gui.HistogramWindow
LUT - Class in ij.process
  This is an indexed color model that allows an lower and upper bound to be specified.
LUT - Static variable in class ij.io.Opener
LUT(byte[], byte[], byte[]) - Constructor for class ij.process.LUT
  Constructs a LUT from red, green and blue byte arrays, which must have a length of 256.
LUT(int, int, byte[], byte[], byte[]) - Constructor for class ij.process.LUT
  Constructs a LUT from red, green and blue byte arrays, where 'bits' must be 8 and 'size' must be less than or equal to 256.
LUT(IndexColorModel, double, double) - Constructor for class ij.process.LUT
LUT_Editor - Class in ij.plugin
LUT_Editor() - Constructor for class ij.plugin.LUT_Editor
lutAnimation - Variable in class ij.process.ImageProcessor
LutApplier - Class in ij.plugin.filter
  This plugin implements the Image/Lookup Tables/Apply LUT command.
LutApplier() - Constructor for class ij.plugin.filter.LutApplier
LutLoader - Class in ij.plugin
  Opens NIH Image look-up tables (LUTs), 768 byte binary LUTs (256 reds, 256 greens and 256 blues), LUTs in text format, or generates the LUT specified by the string argument passed to the run() method.
LutLoader() - Constructor for class ij.plugin.LutLoader
lutMessage - Static variable in class ij.plugin.ZProjector
lutSize - Variable in class ij.io.FileInfo
lutUpdateMode - Variable in class ij.process.ImageProcessor
LutViewer - Class in ij.plugin.filter
  Displays the active image's look-up table.
LutViewer() - Constructor for class ij.plugin.filter.LutViewer
LZW - Static variable in class ij.io.FileInfo
LZW_WITH_DIFFERENCING - Static variable in class ij.io.FileInfo
lzwUncompress(byte[]) - Method in class ij.io.ImageReader
  Utility method for decoding an LZW-compressed image strip.

## M

M - Variable in class ij.process.ColorSpaceConverter
  sRGB to XYZ conversion matrix
Macro - Class in ij
  The class contains static methods that perform macro operations.
Macro() - Constructor for class ij.Macro
MACRO - Static variable in interface ij.macro.MacroConstants
MACRO - Static variable in class ij.plugin.NewPlugin
MACRO - Static variable in class ij.Undo
MACRO_CANCELED - Static variable in class ij.Macro
MACRO_KEY - Static variable in class ij.plugin.filter.ImageMath
Macro_Runner - Class in ij.plugin
  This class runs macros and scripts installed in the Plugins menu as well as macros and scripts opened using the Plugins/Macros/Run command.
Macro_Runner() - Constructor for class ij.plugin.Macro_Runner
MACRO_TOOL - Static variable in class ij.plugin.NewPlugin
MacroConstants - Interface in ij.macro
macroCount() - Method in class ij.macro.Program
MacroExtension - Interface in ij.macro
MacroInstaller - Class in ij.plugin
  This plugin implements the Plugins/Macros/Install Macros command.
MacroInstaller() - Constructor for class ij.plugin.MacroInstaller
MacroRunner - Class in ij.macro
  This class runs macros in a separate thread.
MacroRunner() - Constructor for class ij.macro.MacroRunner
  Create a MacroRunner.
MacroRunner(Program, int, String) - Constructor for class ij.macro.MacroRunner
  Runs a tokenized macro in a separate thread.
MacroRunner(Program, int, String, Editor) - Constructor for class ij.macro.MacroRunner
  Runs a tokenized macro in debug mode if 'editor' is not null.
MacroRunner(Program, int, String, String) - Constructor for class ij.macro.MacroRunner
  Runs a tokenized macro in a separate thread, passing a string argument.
MacroRunner(File) - Constructor for class ij.macro.MacroRunner
  Interprets a macro file in a separate thread.
MacroRunner(String) - Constructor for class ij.macro.MacroRunner
  Create a new object that interprets macro source in a separate thread.
MacroRunner(String, String) - Constructor for class ij.macro.MacroRunner
  Interprets macro source in a separate thread, passing a string argument.
macroRunning() - Static method in class ij.IJ
  Returns true if the run(), open() or newImage() method is executing.
MACROS_MENU_ITEMS - Static variable in class ij.plugin.frame.Editor
MacroToolRunner - Class in ij.plugin.tool
MacroToolRunner(MacroInstaller) - Constructor for class ij.plugin.tool.MacroToolRunner
mag - Variable in class ij.gui.Roi
magnification - Variable in class ij.gui.ImageCanvas
magnification - Variable in class ij.gui.ProfilePlot
magnificationForSubPixel() - Method in class ij.gui.Roi
  Returns whether a roi created interactively should have subpixel resolution, (if the roi type supports it), i.e., whether the magnification is high enough
magnificationForSubPixel(double) - Static method in class ij.gui.Roi
MAGNIFIER - Static variable in class ij.gui.Toolbar
main(String[]) - Static method in class ij.ImageJ
major - Variable in class ij.process.EllipseFitter
  Length of major axis
major - Variable in class ij.process.ImageStatistics
  Length of major axis of fitted ellipse
MAJOR - Static variable in class ij.measure.ResultsTable
MAKE_ARROW - Static variable in interface ij.macro.MacroConstants
MAKE_ELLIPSE - Static variable in interface ij.macro.MacroConstants
MAKE_LINE - Static variable in interface ij.macro.MacroConstants
MAKE_OVAL - Static variable in interface ij.macro.MacroConstants
MAKE_POINT - Static variable in interface ij.macro.MacroConstants
MAKE_POLYGON - Static variable in interface ij.macro.MacroConstants
MAKE_RECTANGLE - Static variable in interface ij.macro.MacroConstants
MAKE_ROTATED_RECT - Static variable in interface ij.macro.MacroConstants
MAKE_SELECTION - Static variable in interface ij.macro.MacroConstants
MAKE_TEXT - Static variable in interface ij.macro.MacroConstants
make16bitEDM(ImageProcessor) - Method in class ij.plugin.filter.EDM
  Calculates a 16-bit grayscale Euclidean Distance Map for a binary 8-bit image.
makeComposite(ImagePlus) - Static method in class ij.plugin.CompositeConverter
makeDefaultColorModel() - Method in class ij.process.ImageProcessor
makeFilePrivate(String) - Static method in class ij.OtherInstance
makeFloatEDM(ImageProcessor, int, boolean) - Method in class ij.plugin.filter.EDM
  Creates the Euclidian Distance Map of a (binary) byte image.
makeFullPath(String) - Static method in class ij.io.Opener
makeGaussianKernel(double, double, int) - Method in class ij.plugin.filter.GaussianBlur
  Create a 1-dimensional normalized Gaussian kernel with standard deviation sigma and the running sum over the kernel Note: this is one side of the kernel only, not the full kernel as used by the Convolver class of ImageJ.
makeHighResolution(String, float, boolean, boolean) - Method in class ij.gui.Plot
  Creates a new high-resolution plot by scaling it and displays that plot if showIt is true.
makeKernel(double) - Method in class ij.plugin.filter.RankFilters
  Deprecated.
  Not needed any more, use the rank(ip, ...) method, which creates the kernel
makeLine(double, double, double, double) - Static method in class ij.IJ
  Creates a straight line selection using floating point coordinates.
makeLine(int, int, int, int) - Static method in class ij.IJ
  Creates a straight line selection.
makeLineRadii(double) - Method in class ij.plugin.filter.RankFilters
  Create a circular kernel (structuring element) of a given radius.
makeMask(ImageProcessor, Rectangle) - Method in class ij.plugin.filter.Filler
makeMontage(ImagePlus) - Method in class ij.plugin.MontageMaker
makeMontage(ImagePlus, int, int, double, int, int, int, int, boolean) - Method in class ij.plugin.MontageMaker
  Creates a montage and displays it.
makeMontage2(ImagePlus, int, int, double, int, int, int, int, boolean) - Method in class ij.plugin.MontageMaker
  Creates a montage and returns it as an ImagePlus.
makeOval(double, double, double, double) - Static method in class ij.IJ
  Creates an subpixel resolution oval selection.
makeOval(int, int, int, int) - Static method in class ij.IJ
  Creates an oval selection.
makePoint(double, double) - Static method in class ij.IJ
  Creates a point selection using floating point coordinates.
makePoint(int, int) - Static method in class ij.IJ
  Creates a point selection using integer coordinates..
makeRectangle(double, double, double, double) - Static method in class ij.IJ
  Creates a subpixel resolution rectangular selection.
makeRectangle(int, int, int, int) - Static method in class ij.IJ
  Creates a rectangular selection.
makeRoi(ImageProcessor) - Method in class ij.process.EllipseFitter
  Generates the xCoordinates, yCoordinates public arrays that can be used to create an ROI.
makeRow(String, CommandFinder.CommandAction) - Method in class ij.plugin.CommandFinder
makeStack(ImageProcessor, int, int, int) - Method in class ij.plugin.StackMaker
makeStack(String, int, int, boolean, boolean, boolean) - Method in class ij.plugin.AVI_Reader
  Create an ImageStack from an avi file with given path.
makeSubhyperstack(ImagePlus, String, String, String) - Static method in class ij.plugin.SubHyperstackMaker
makeSubhyperstack(ImagePlus, List<Integer>, List<Integer>, List<Integer>) - Static method in class ij.plugin.SubHyperstackMaker
makeSubstack(ImagePlus, String) - Method in class ij.plugin.SubstackMaker
makeSurfacePlot(ImageProcessor) - Method in class ij.plugin.SurfacePlotter
makeThumbnail(int, int, double) - Method in class ij.process.ColorProcessor
  Uses averaging to creates a new ColorProcessor containing a downsized copy of this image or selection.
makeUniqueName(String) - Static method in class ij.WindowManager
  If 'name' is not unique, adds -1, -2, etc.
markWidth - Static variable in class ij.plugin.filter.Analyzer
MASKS - Static variable in class ij.plugin.filter.ParticleAnalyzer
maskSizeError(ImageProcessor) - Method in class ij.process.ImageProcessor
match(String, String) - Method in class ij.util.WildcardMatch
  Matches a string against a pattern with wildcards.
MATCHES - Static variable in interface ij.macro.MacroConstants
MATH - Static variable in interface ij.macro.MacroConstants
max - Variable in class ij.io.ImageReader
max - Variable in class ij.process.ColorProcessor
max - Variable in class ij.process.ImageStatistics
max - Variable in class ij.process.LUT
max - Variable in class ij.process.ShortProcessor
max(double) - Method in class ij.process.FloatProcessor
max(double) - Method in class ij.process.ImageProcessor
  Pixels greater than 'value' are set to 'value'.
max(double) - Method in class ij.process.ShortProcessor
MAX - Static variable in class ij.measure.ResultsTable
MAX - Static variable in class ij.plugin.Binner
MAX - Static variable in class ij.plugin.filter.RankFilters
MAX - Static variable in class ij.plugin.Filters3D
MAX - Static variable in interface ij.process.Blitter
  dst=max(dst,src)
MAX - Static variable in class ij.process.ImageProcessor
MAX_CHANNELS - Static variable in class ij.CompositeImage
MAX_COLUMNS - Static variable in class ij.measure.ResultsTable
  Obsolete; use getLastColumn().
MAX_COMMANDS - Static variable in class ij.plugin.frame.Commands
MAX_COUNTERS - Static variable in class ij.gui.PointRoi
MAX_ITERATIONS_EXCEEDED - Static variable in class ij.measure.Minimizer
  Status returned: no convergence detected after maximum iteration count
MAX_MACROS - Static variable in class ij.plugin.MacroInstaller
MAX_METHOD - Static variable in class ij.plugin.ZProjector
MAX_MOUSEMOVE_ZOOM - Static variable in class ij.gui.ImageCanvas
  If the mouse moves less than this in screen pixels, successive zoom operations are on the same image pixel
MAX_OF - Static variable in interface ij.macro.MacroConstants
MAX_OPEN_RECENT_ITEMS - Static variable in class ij.Menus
MAX_PROJECTION - Static variable in class ij.process.ImageProcessor
  Composite image projection modes.
MAX_RESTARTS_EXCEEDED - Static variable in class ij.measure.Minimizer
  Status returned: not two equal solutions after maximum number of restarts
MAX_SIZE - Static variable in class ij.plugin.frame.Editor
MAX_SIZE - Static variable in class ij.plugin.MacroInstaller
MAX_STANDARDS - Static variable in interface ij.measure.Measurements
  Maximum number of calibration standard (20)
MAX_THRESHOLD - Static variable in class ij.measure.ResultsTable
maxCount - Variable in class ij.process.ImageStatistics
maxEntries - Variable in class ij.plugin.Concatenator
MaxEntropy - Enum constant in enum class ij.process.AutoThresholder.Method
MaxEntropy(int[]) - Static method in class ij.process.AutoThresholder
maximize() - Method in class ij.gui.ImageWindow
maximize(ImagePlus) - Static method in class ij.plugin.Zoom
MaximumFinder - Class in ij.plugin.filter
  This ImageJ plug-in filter finds the maxima (or minima) of an image.
MaximumFinder() - Constructor for class ij.plugin.filter.MaximumFinder
MAXLOCAL - Static variable in class ij.plugin.Filters3D
maxMemory() - Static method in class ij.IJ
  Returns the maximum amount of memory available to ImageJ or zero if ImageJ is unable to determine this limit.
maxMemory() - Method in class ij.plugin.Memory
  Returns the maximum amount of memory this JVM will attempt to use.
maxPoints - Variable in class ij.gui.PolygonRoi
maxThreshold - Variable in class ij.process.ImageProcessor
maxValue() - Method in class ij.process.FloatProcessor
  Returns the largest possible positive finite pixel value.
maxValue() - Method in class ij.process.ImageProcessor
  Returns the maximum possible pixel value.
maxValue() - Method in class ij.process.ShortProcessor
  Returns the maximum possible pixel value.
mean - Variable in class ij.process.ImageStatistics
Mean - Enum constant in enum class ij.process.AutoThresholder.Method
Mean(int[]) - Static method in class ij.process.AutoThresholder
MEAN - Static variable in interface ij.measure.Measurements
MEAN - Static variable in class ij.measure.ResultsTable
MEAN - Static variable in class ij.plugin.filter.RankFilters
MEAN - Static variable in class ij.plugin.Filters3D
measure() - Method in class ij.gui.MultiLineLabel
measure() - Method in class ij.plugin.filter.Analyzer
  Measures the image or selection and adds the results to the default results table.
measure(ImagePlus) - Method in class ij.gui.Overlay
  Measures the ROIs in this overlay on the specified image and returns the results as a ResultsTable.
Measurements - Interface in ij.measure
MeasurementsWriter - Class in ij.plugin
  Saves a table as a csv or tab-delimited text file.
MeasurementsWriter() - Constructor for class ij.plugin.MeasurementsWriter
median - Variable in class ij.process.ImageStatistics
MEDIAN - Static variable in interface ij.measure.Measurements
MEDIAN - Static variable in class ij.measure.ResultsTable
MEDIAN - Static variable in class ij.plugin.Binner
MEDIAN - Static variable in class ij.plugin.filter.RankFilters
MEDIAN - Static variable in class ij.plugin.Filters3D
MEDIAN_FILTER - Static variable in class ij.process.ImageProcessor
MEDIAN_METHOD - Static variable in class ij.plugin.ZProjector
MedianCut - Class in ij.process
  Converts an RGB image to 8-bit index color using Heckbert's median-cut color quantization algorithm.
MedianCut(int[], int, int) - Constructor for class ij.process.MedianCut
MedianCut(ColorProcessor) - Constructor for class ij.process.MedianCut
medianFilter() - Method in class ij.process.ByteProcessor
medianFilter() - Method in class ij.process.ColorProcessor
medianFilter() - Method in class ij.process.FloatProcessor
  Not implemented.
medianFilter() - Method in class ij.process.ImageProcessor
  A 3x3 median filter.
medianFilter() - Method in class ij.process.ShortProcessor
  Not implemented.
medianSort() - Method in class ij.util.ArrayUtil
  The median (sorted array)
Memory - Class in ij.plugin
  This plugin implements the Edit/Options/Memory command.
Memory() - Constructor for class ij.plugin.Memory
MemoryMonitor - Class in ij.plugin.frame
  This plugin continuously plots ImageJ's memory utilization.
MemoryMonitor() - Constructor for class ij.plugin.frame.MemoryMonitor
MENU_BAR - Static variable in class ij.plugin.frame.Editor
MENU_SIZE - Static variable in class ij.Prefs
Menus - Class in ij
  This class installs and updates ImageJ's menus.
mergeChannels(ImagePlus[], boolean) - Static method in class ij.plugin.RGBStackMerge
mergeHyperstacks(ImagePlus[], boolean) - Method in class ij.plugin.RGBStackMerge
mergeStacks() - Method in class ij.plugin.RGBStackMerge
  Combines up to seven grayscale stacks into one RGB or composite stack.
mergeStacks(int, int, int, ImageStack, ImageStack, ImageStack, boolean) - Method in class ij.plugin.RGBStackMerge
mergeStacks(ImageStack, ImageStack, ImageStack, boolean) - Static method in class ij.plugin.RGBStackMerge
MessageDialog - Class in ij.gui
  A modal dialog box that displays information.
MessageDialog(Frame, String, String) - Constructor for class ij.gui.MessageDialog
META_DATA - Static variable in class ij.io.TiffDecoder
META_DATA_BYTE_COUNTS - Static variable in class ij.io.TiffDecoder
metaData - Variable in class ij.io.FileInfo
metaDataTypes - Variable in class ij.io.FileInfo
METAMORPH1 - Static variable in class ij.io.TiffDecoder
METAMORPH2 - Static variable in class ij.io.TiffDecoder
methods - Static variable in class ij.plugin.Thresholder
METHODS - Static variable in class ij.plugin.ZProjector
Mi - Variable in class ij.process.ColorSpaceConverter
  XYZ to sRGB conversion matrix
micronSymbol - Static variable in class ij.IJ
min - Variable in class ij.io.ImageReader
min - Variable in class ij.process.ColorProcessor
min - Variable in class ij.process.ImageStatistics
min - Variable in class ij.process.LUT
min - Variable in class ij.process.ShortProcessor
min(double) - Method in class ij.process.FloatProcessor
min(double) - Method in class ij.process.ImageProcessor
  Pixels less than 'value' are set to 'value'.
min(double) - Method in class ij.process.ShortProcessor
MIN - Static variable in class ij.measure.ResultsTable
MIN - Static variable in class ij.plugin.Binner
MIN - Static variable in class ij.plugin.filter.RankFilters
MIN - Static variable in class ij.plugin.Filters3D
MIN - Static variable in interface ij.process.Blitter
  dst=min(dst,src)
MIN - Static variable in class ij.process.ImageProcessor
MIN_FERET - Static variable in class ij.measure.ResultsTable
MIN_FRAMEHEIGHT - Static variable in class ij.gui.Plot
  minimum width of frame area in plot
MIN_FRAMEWIDTH - Static variable in class ij.gui.Plot
  minimum width of frame area in plot
MIN_HEIGHT - Static variable in class ij.gui.ImageWindow
MIN_MAX - Static variable in interface ij.measure.Measurements
MIN_METHOD - Static variable in class ij.plugin.ZProjector
MIN_OF - Static variable in interface ij.macro.MacroConstants
MIN_PROJECTION - Static variable in class ij.process.ImageProcessor
  Composite image projection modes.
MIN_THRESHOLD - Static variable in class ij.measure.ResultsTable
MIN_WIDTH - Static variable in class ij.gui.ImageWindow
MinError - Enum constant in enum class ij.process.AutoThresholder.Method
MinErrorI(int[]) - Static method in class ij.process.AutoThresholder
minimize() - Method in class ij.gui.ImageWindow
minimize(double[], double[]) - Method in class ij.measure.Minimizer
  Perform minimization with the gradient-enhanced simplex method once or a few times, depending on the value of 'restarts'.
minimizeOnce(double[], double[]) - Method in class ij.measure.Minimizer
  Perform minimization with the simplex method once, including re-initialization until we have a stable solution.
Minimizer - Class in ij.measure
  Minimizer based on Nelder-Mead simplex method (also known as polytope method), including the 'outside contraction' as described in: J.C.
Minimizer() - Constructor for class ij.measure.Minimizer
Minimum - Enum constant in enum class ij.process.AutoThresholder.Method
Minimum(int[]) - Static method in class ij.process.AutoThresholder
minimumLayoutSize(Container) - Method in class ij.gui.ImageLayout
  Returns the minimum dimensions for this layout.
minMaxSet - Variable in class ij.process.ImageProcessor
minor - Variable in class ij.process.EllipseFitter
  Length of minor axis
minor - Variable in class ij.process.ImageStatistics
  Length of minor axis of fitted ellipse
MINOR - Static variable in class ij.measure.ResultsTable
minThreshold - Variable in class ij.process.ImageProcessor
MINUS_EQUAL - Static variable in interface ij.macro.MacroConstants
MINUS_MINUS - Static variable in interface ij.macro.MacroConstants
minValue() - Method in class ij.process.FloatProcessor
  Returns the smallest possible positive nonzero pixel value.
minValue() - Method in class ij.process.ImageProcessor
  Returns the minimum possible pixel value.
mode - Variable in class ij.process.ImageStatistics
  Mode of 256 bin histogram (counts limited to 2^31-1)
MODE - Static variable in interface ij.measure.Measurements
MODE - Static variable in class ij.measure.ResultsTable
MODE_KEY - Static variable in class ij.plugin.frame.ThresholdAdjuster
MODIFIED - Static variable in interface ij.gui.RoiListener
modifiers(int) - Static method in class ij.ImageJ
  Return the current list of modifier keys.
Moments - Enum constant in enum class ij.process.AutoThresholder.Method
Moments(int[]) - Static method in class ij.process.AutoThresholder
MONOSPACED - Static variable in class ij.plugin.frame.Editor
MontageMaker - Class in ij.plugin
  Implements the Image/Stacks/Make Montage command.
MontageMaker() - Constructor for class ij.plugin.MontageMaker
mouseClicked(ImagePlus, MouseEvent) - Method in class ij.plugin.tool.PlugInTool
mouseClicked(MouseEvent) - Method in class ij.gui.ImageCanvas
mouseClicked(MouseEvent) - Method in class ij.gui.Toolbar
mouseClicked(MouseEvent) - Method in class ij.ImageJ
mouseClicked(MouseEvent) - Method in class ij.plugin.CommandFinder
mouseClicked(MouseEvent) - Method in class ij.plugin.frame.Editor
mouseClicked(MouseEvent) - Method in class ij.plugin.frame.RoiManager
mouseClicked(MouseEvent) - Method in class ij.plugin.frame.SyncWindows
  Propagate mouse clicked events to all synchronized windows.
mouseClicked(MouseEvent) - Method in class ij.plugin.Orthogonal_Views
mouseClicked(MouseEvent) - Method in class ij.text.TextPanel
mouseDownInHandle(int, int, int) - Method in class ij.gui.Line
mouseDownInHandle(int, int, int) - Method in class ij.gui.PolygonRoi
mouseDownInHandle(int, int, int) - Method in class ij.gui.Roi
mouseDragged(ImagePlus, MouseEvent) - Method in class ij.plugin.tool.ArrowTool
mouseDragged(ImagePlus, MouseEvent) - Method in class ij.plugin.tool.BrushTool
mouseDragged(ImagePlus, MouseEvent) - Method in class ij.plugin.tool.OverlayBrushTool
mouseDragged(ImagePlus, MouseEvent) - Method in class ij.plugin.tool.PixelInspectionTool
mouseDragged(ImagePlus, MouseEvent) - Method in class ij.plugin.tool.PlugInTool
mouseDragged(ImagePlus, MouseEvent) - Method in class ij.plugin.tool.RoiRotationTool
mouseDragged(MouseEvent) - Method in class ij.gui.ImageCanvas
mouseDragged(MouseEvent) - Method in class ij.gui.Roi
mouseDragged(MouseEvent) - Method in class ij.gui.Toolbar
mouseDragged(MouseEvent) - Method in class ij.plugin.frame.SyncWindows
  Propagate mouse dragged events to all synchronized windows.
mouseDragged(MouseEvent) - Method in class ij.plugin.Orthogonal_Views
mouseDragged(MouseEvent) - Method in class ij.text.TextPanel
mouseEntered(ImagePlus, MouseEvent) - Method in class ij.plugin.tool.PlugInTool
mouseEntered(MouseEvent) - Method in class ij.gui.ImageCanvas
mouseEntered(MouseEvent) - Method in class ij.gui.Toolbar
mouseEntered(MouseEvent) - Method in class ij.ImageJ
mouseEntered(MouseEvent) - Method in class ij.plugin.CommandFinder
mouseEntered(MouseEvent) - Method in class ij.plugin.frame.Editor
mouseEntered(MouseEvent) - Method in class ij.plugin.frame.RoiManager
mouseEntered(MouseEvent) - Method in class ij.plugin.frame.SyncWindows
  Propagate mouse entered events to all synchronized windows.
mouseEntered(MouseEvent) - Method in class ij.plugin.Orthogonal_Views
mouseEntered(MouseEvent) - Method in class ij.text.TextPanel
mouseExited(ImagePlus, MouseEvent) - Method in class ij.plugin.tool.PlugInTool
mouseExited(MouseEvent) - Method in class ij.gui.ImageCanvas
mouseExited(MouseEvent) - Method in class ij.gui.PlotCanvas
  overrides ImageCanvas.mouseExited; removes 'range' arrows
mouseExited(MouseEvent) - Method in class ij.gui.Toolbar
mouseExited(MouseEvent) - Method in class ij.ImageJ
mouseExited(MouseEvent) - Method in class ij.plugin.CommandFinder
mouseExited(MouseEvent) - Method in class ij.plugin.frame.Editor
mouseExited(MouseEvent) - Method in class ij.plugin.frame.RoiManager
mouseExited(MouseEvent) - Method in class ij.plugin.frame.SyncWindows
  Propagate mouse exited events to all synchronized windows.
mouseExited(MouseEvent) - Method in class ij.plugin.Orthogonal_Views
mouseExited(MouseEvent) - Method in class ij.text.TextPanel
mouseMoved(int, int) - Method in class ij.gui.HistogramWindow
mouseMoved(int, int) - Method in class ij.gui.ImageWindow
  This method is called by ImageCanvas.mouseMoved(MouseEvent).
mouseMoved(int, int) - Method in class ij.gui.PlotWindow
  Updates the X and Y values when the mouse is moved and, if appropriate, shows/hides the overlay with the triangular buttons for changing the axis range limits.
mouseMoved(int, int) - Method in class ij.ImagePlus
  Displays the cursor coordinates and pixel value in the status bar.
mouseMoved(ImagePlus, MouseEvent) - Method in class ij.plugin.tool.PlugInTool
mouseMoved(MouseEvent) - Method in class ij.gui.ImageCanvas
mouseMoved(MouseEvent) - Method in class ij.gui.Line
mouseMoved(MouseEvent) - Method in class ij.gui.PolygonRoi
mouseMoved(MouseEvent) - Method in class ij.gui.Roi
mouseMoved(MouseEvent) - Method in class ij.gui.Toolbar
mouseMoved(MouseEvent) - Method in class ij.plugin.frame.SyncWindows
  Draws the "synchronize" cursor in each of the synchronized windows.
mouseMoved(MouseEvent) - Method in class ij.plugin.Orthogonal_Views
mouseMoved(MouseEvent) - Method in class ij.text.TextPanel
mousePressed(ImagePlus, MouseEvent) - Method in class ij.plugin.tool.ArrowTool
mousePressed(ImagePlus, MouseEvent) - Method in class ij.plugin.tool.BrushTool
mousePressed(ImagePlus, MouseEvent) - Method in class ij.plugin.tool.OverlayBrushTool
mousePressed(ImagePlus, MouseEvent) - Method in class ij.plugin.tool.PixelInspectionTool
mousePressed(ImagePlus, MouseEvent) - Method in class ij.plugin.tool.PlugInTool
mousePressed(ImagePlus, MouseEvent) - Method in class ij.plugin.tool.RoiRotationTool
mousePressed(MouseEvent) - Method in class ij.gui.ImageCanvas
mousePressed(MouseEvent) - Method in class ij.gui.PlotCanvas
  overrides ImageCanvas.mousePressed: no further processing of clicks on 'range' arrows
mousePressed(MouseEvent) - Method in class ij.gui.Toolbar
mousePressed(MouseEvent) - Method in class ij.ImageJ
mousePressed(MouseEvent) - Method in class ij.plugin.CommandFinder
mousePressed(MouseEvent) - Method in class ij.plugin.frame.Editor
mousePressed(MouseEvent) - Method in class ij.plugin.frame.RoiManager
mousePressed(MouseEvent) - Method in class ij.plugin.frame.SyncWindows
  Propagate mouse pressed events to all synchronized windows.
mousePressed(MouseEvent) - Method in class ij.plugin.Orthogonal_Views
mousePressed(MouseEvent) - Method in class ij.text.TextPanel
mouseReleased(ImagePlus, MouseEvent) - Method in class ij.plugin.tool.ArrowTool
mouseReleased(ImagePlus, MouseEvent) - Method in class ij.plugin.tool.BrushTool
mouseReleased(ImagePlus, MouseEvent) - Method in class ij.plugin.tool.OverlayBrushTool
mouseReleased(ImagePlus, MouseEvent) - Method in class ij.plugin.tool.PlugInTool
mouseReleased(ImagePlus, MouseEvent) - Method in class ij.plugin.tool.RoiRotationTool
mouseReleased(MouseEvent) - Method in class ij.gui.ImageCanvas
mouseReleased(MouseEvent) - Method in class ij.gui.PlotCanvas
  Overrides ImageCanvas.mouseReleased, handles clicks on 'range' arrows
mouseReleased(MouseEvent) - Method in class ij.gui.Roi
mouseReleased(MouseEvent) - Method in class ij.gui.Toolbar
mouseReleased(MouseEvent) - Method in class ij.ImageJ
mouseReleased(MouseEvent) - Method in class ij.plugin.CommandFinder
mouseReleased(MouseEvent) - Method in class ij.plugin.frame.Editor
mouseReleased(MouseEvent) - Method in class ij.plugin.frame.RoiManager
mouseReleased(MouseEvent) - Method in class ij.plugin.frame.SyncWindows
  Propagate mouse released events to all synchronized windows.
mouseReleased(MouseEvent) - Method in class ij.plugin.Orthogonal_Views
mouseReleased(MouseEvent) - Method in class ij.text.TextPanel
mouseWheelMoved(MouseWheelEvent) - Method in class ij.gui.ImageWindow
mouseWheelMoved(MouseWheelEvent) - Method in class ij.gui.PlotWindow
  Mouse wheel: zooms when shift or ctrl is pressed, scrolls in x if space bar down, in y otherwise.
mouseWheelMoved(MouseWheelEvent) - Method in class ij.gui.StackWindow
mouseWheelMoved(MouseWheelEvent) - Method in class ij.plugin.frame.RoiManager
mouseWheelMoved(MouseWheelEvent) - Method in class ij.plugin.frame.ThresholdAdjuster
mouseWheelMoved(MouseWheelEvent) - Method in class ij.plugin.Orthogonal_Views
mouseWheelMoved(MouseWheelEvent) - Method in class ij.text.TextPanel
MOVE_TO - Static variable in interface ij.macro.MacroConstants
moveCursor - Static variable in class ij.gui.ImageCanvas
MOVED - Static variable in interface ij.gui.RoiListener
moveHandle(int, int) - Method in class ij.gui.EllipseRoi
moveHandle(int, int) - Method in class ij.gui.Line
moveHandle(int, int) - Method in class ij.gui.OvalRoi
moveHandle(int, int) - Method in class ij.gui.PolygonRoi
moveHandle(int, int) - Method in class ij.gui.Roi
moveHandle(int, int) - Method in class ij.gui.RotatedRectRoi
moveRoisToOverlay(ImagePlus) - Method in class ij.plugin.frame.RoiManager
  Moves all the ROIs to the specified image's overlay.
moveTo(int, int) - Method in class ij.process.ImageProcessor
  Sets the current drawing location.
moveToMisc - Static variable in class ij.Prefs
  Move isolated plugins to Miscellaneous submenu.
MOVING - Static variable in class ij.gui.Roi
MOVING_HANDLE - Static variable in class ij.gui.Roi
MUL_EQUAL - Static variable in interface ij.macro.MacroConstants
multiCrop(String, String) - Method in class ij.plugin.frame.RoiManager
MultiLineLabel - Class in ij.gui
  Custom component for displaying multiple lines.
MultiLineLabel(String) - Constructor for class ij.gui.MultiLineLabel
MultiLineLabel(String, int) - Constructor for class ij.gui.MultiLineLabel
multiMeasure(ImagePlus) - Method in class ij.plugin.frame.RoiManager
  This method measures the selected ROIs, or all ROIs if none are selected, on all the slices of a stack and returns a ResultsTable arranged with one row per slice.
multiMeasure(ImagePlus, Roi[], boolean) - Static method in class ij.plugin.frame.RoiManager
multiply(double) - Method in class ij.process.FloatProcessor
multiply(double) - Method in class ij.process.ImageProcessor
  Multiplies each pixel in the image or ROI by 'value'.
multiply(double) - Method in class ij.process.ShortProcessor
multiply(ImagePlus, ImageProcessor) - Static method in class ij.plugin.FFT
  Multiplies a Fourier domain image by a filter
multiply(FHT) - Method in class ij.process.FHT
  Returns the image resulting from the point by point Hartley multiplication of this image and the specified image.
MULTIPLY - Static variable in interface ij.process.Blitter
  dst=src*src
multiPointMode - Static variable in class ij.Prefs
  Use MultiPoint tool.

## N

n(double) - Method in class ij.plugin.filter.Analyzer
  Converts a number to a formatted string with a tab at the end.
N_COORDINATES - Static variable in class ij.io.RoiDecoder
name - Variable in class ij.macro.ExtensionDescriptor
NAME_LENGTH - Static variable in class ij.io.RoiDecoder
NAME_OFFSET - Static variable in class ij.io.RoiDecoder
nameKey - Static variable in class ij.process.LUT
NaN - Static variable in interface ij.macro.MacroConstants
NaN_EMPTY_CELLS - Static variable in interface ij.measure.Measurements
nBins - Static variable in class ij.gui.HistogramWindow
nBins - Variable in class ij.process.ImageStatistics
nChannels - Variable in class ij.ImagePlus
nCoordinates - Variable in class ij.process.EllipseFitter
  Initialized by makeRoi()
NEAREST_NEIGHBOR - Static variable in class ij.process.ImageProcessor
  Interpolation methods
NEQ - Static variable in interface ij.macro.MacroConstants
NEW_ARRAY - Static variable in interface ij.macro.MacroConstants
NEW_IMAGE - Static variable in interface ij.macro.MacroConstants
NEW_MENU - Static variable in interface ij.macro.MacroConstants
NEW_SUBFILE_TYPE - Static variable in class ij.io.TiffDecoder
newDescriptor(String, MacroExtension) - Static method in class ij.macro.ExtensionDescriptor
newDescriptor(String, MacroExtension, int) - Static method in class ij.macro.ExtensionDescriptor
newDescriptor(String, MacroExtension, int[]) - Static method in class ij.macro.ExtensionDescriptor
newDescriptor(String, MacroExtension, int, int) - Static method in class ij.macro.ExtensionDescriptor
newDescriptor(String, MacroExtension, int, int, int) - Static method in class ij.macro.ExtensionDescriptor
newDescriptor(String, MacroExtension, int, int, int, int) - Static method in class ij.macro.ExtensionDescriptor
newDescriptor(String, MacroExtension, Integer[]) - Static method in class ij.macro.ExtensionDescriptor
newDialog(String) - Static method in class ij.gui.NonBlockingGenericDialog
  Obsolete, replaced by GUI.newNonBlockingDialog(String).
newDialog(String, ImagePlus) - Static method in class ij.gui.NonBlockingGenericDialog
  Obsolete, replaced by GUI.newNonBlockingDialog(String,ImagePlus).
newImage(String, String, int, int, int) - Static method in class ij.IJ
  Opens a new image.
NewImage - Class in ij.gui
  New image dialog box plus several static utility methods for creating images.
NewImage() - Constructor for class ij.gui.NewImage
newMaxCount - Variable in class ij.gui.HistogramWindow
newNonBlockingDialog(String) - Static method in class ij.gui.GUI
  Returns a new NonBlockingGenericDialog with the given title, except when Java is running in headless mode, in which case a GenericDialog is be returned.
newNonBlockingDialog(String, ImagePlus) - Static method in class ij.gui.GUI
  Returns a new NonBlockingGenericDialog with the given title if Prefs.nonBlockingFilterDialogs is 'true' and 'imp' is displayed, otherwise returns a GenericDialog.
newPixels - Variable in class ij.process.ImageProcessor
NewPlugin - Class in ij.plugin
  This class creates a new macro or the Java source for a new plugin.
NewPlugin() - Constructor for class ij.plugin.NewPlugin
newWindowCreated - Static variable in class ij.plugin.Converter
  obsolete
next() - Method in class ij.gui.Line.PointIterator
NextImageOpener - Class in ij.plugin
NextImageOpener() - Constructor for class ij.plugin.NextImageOpener
nFrames - Variable in class ij.ImagePlus
NIH_IMAGE_HDR - Static variable in class ij.io.TiffDecoder
nImages - Variable in class ij.io.FileInfo
NIMAGES - Static variable in interface ij.macro.MacroConstants
NO_CHANGES - Static variable in interface ij.plugin.filter.PlugInFilter
  Set this flag if the filter makes no changes to the pixel data and does not require undo.
NO_COMPRESSION - Static variable in class ij.plugin.filter.AVI_Writer
NO_IMAGE_REQUIRED - Static variable in interface ij.plugin.filter.PlugInFilter
  Set this flag if the filter does not require that an image be open.
NO_LUT_UPDATE - Static variable in class ij.process.ImageProcessor
NO_RESET - Static variable in class ij.plugin.frame.ThresholdAdjuster
NO_SHOW - Static variable in class ij.ImageJ
  Run embedded and invisible in another application.
NO_THRESHOLD - Static variable in class ij.process.ImageProcessor
  Value returned by getMinThreshold() when image is not thresholded.
NO_UNDO - Static variable in interface ij.plugin.filter.PlugInFilter
  Set this flag if the filter does not require undo.
NO_UNDO_RESET - Static variable in interface ij.plugin.filter.PlugInFilter
  Set this flag to prevent Undo from being reset when processing a stack.
NO_WINDOW - Static variable in class ij.process.FHT
noBorder - Static variable in class ij.Prefs
  Do not draw black border around image.
noClickToGC - Static variable in class ij.Prefs
  Don't run garbage collector when user clicks in status bar
noErrorBars() - Method in class ij.gui.PlotContentsDialog
  Avoids showing a selection for the error bars; must be called before showDialog.
noGridLines - Static variable in class ij.gui.PlotWindow
  Have axes with no grid lines.
noImage() - Static method in class ij.IJ
  Displays a "no images are open" dialog box.
noise(double) - Method in class ij.process.ByteProcessor
  Adds pseudorandom, Gaussian ("normally") distributed values, with mean 0.0 and the specified standard deviation, to this image or ROI.
noise(double) - Method in class ij.process.ColorProcessor
noise(double) - Method in class ij.process.FloatProcessor
noise(double) - Method in class ij.process.ImageProcessor
  Adds pseudorandom, Gaussian ("normally") distributed values, with mean 0.0 and the specified standard deviation, to this image or ROI.
noise(double) - Method in class ij.process.ShortProcessor
  Adds pseudorandom, Gaussian ("normally") distributed values, with mean 0.0 and the specified standard deviation, to this image or ROI.
NOISE_SD - Static variable in class ij.Prefs
nonBatchMacroRunning() - Static method in class ij.macro.Interpreter
nonBlockingFilterDialogs - Static variable in class ij.Prefs
  Use NonBlockingGenericDialogs in filters
NonBlockingGenericDialog - Class in ij.gui
  This is an extension of GenericDialog that is non-modal.
NonBlockingGenericDialog(String) - Constructor for class ij.gui.NonBlockingGenericDialog
NONE - Static variable in class ij.measure.Calibration
NONE - Static variable in class ij.process.ImageProcessor
  Interpolation methods
nonScalable - Variable in class ij.gui.Roi
NOP - Static variable in interface ij.macro.MacroConstants
noPointLabels - Static variable in class ij.Prefs
  Do not label multiple points created using point tool.
NORMAL - Static variable in class ij.gui.Roi
NORMAL_RETURN - Static variable in class ij.Menus
noRowNumbers - Static variable in class ij.Prefs
  Do not include row numbers when copying tables to clipboard.
north(ImageProcessor) - Method in class ij.plugin.filter.Shadows
northeast(ImageProcessor) - Method in class ij.plugin.filter.Shadows
northwest(ImageProcessor) - Method in class ij.plugin.filter.Shadows
not(ShapeRoi) - Method in class ij.gui.ShapeRoi
  Unary subtraction operator.
NOT_DEBUGGING - Static variable in interface ij.macro.Debugger
NOT_INSTALLED - Static variable in class ij.Menus
NOT_PASTING - Static variable in class ij.gui.Roi
NOTCHED - Static variable in class ij.gui.Arrow
NOTHING - Static variable in class ij.plugin.filter.ParticleAnalyzer
NOTHING - Static variable in class ij.Undo
noTicks - Static variable in class ij.gui.PlotWindow
  Have axes with no ticks.
notifyEventListeners(int) - Static method in class ij.IJ
notifyListeners(int) - Method in class ij.gui.Roi
notifyListeners(int) - Method in class ij.ImagePlus
npoints - Variable in class ij.gui.Wand
  The number of points in the generated outline.
npoints - Variable in class ij.process.FloatPolygon
  The number of points in the 'xpoints' and 'ypoints' arrays.
nPoints - Variable in class ij.gui.PolygonRoi
NRESULTS - Static variable in interface ij.macro.MacroConstants
nSlices - Variable in class ij.ImagePlus
NSLICES - Static variable in interface ij.macro.MacroConstants
nudge(int) - Method in class ij.gui.Roi
  Nudge ROI one pixel on arrow key press.
nudgeCorner(int) - Method in class ij.gui.EllipseRoi
nudgeCorner(int) - Method in class ij.gui.Line
  Nudge end point of line by one pixel.
nudgeCorner(int) - Method in class ij.gui.Roi
  Nudge lower right corner of rectangular and oval ROIs by one pixel based on arrow key press.
nudgeCorner(int) - Method in class ij.gui.RotatedRectRoi
NUMBER - Static variable in interface ij.macro.MacroConstants
numberField - Variable in class ij.gui.GenericDialog
NUMERIC_FUNCTION - Static variable in interface ij.macro.MacroConstants
numericFunctionIDs - Static variable in interface ij.macro.MacroConstants
numericFunctions - Static variable in interface ij.macro.MacroConstants

## O

offScreenX(int) - Method in class ij.gui.ImageCanvas
  Converts a screen x-coordinate to an offscreen x-coordinate (nearest pixel center).
offScreenX(int) - Method in class ij.gui.Roi
  Converts image canvas screen x coordinates to integer offscreen image pixel coordinates, depending on whether this roi uses the line or area convention for coordinates.
offScreenX2(int) - Method in class ij.gui.ImageCanvas
  Converts a screen x-coordinate to an offscreen x-coordinate (Roi coordinate of nearest pixel border).
offScreenXD(int) - Method in class ij.gui.ImageCanvas
  Converts a screen x-coordinate to a floating-point offscreen x-coordinate.
offScreenXD(int) - Method in class ij.gui.Roi
  Converts image canvas screen x coordinates to floating-point offscreen image pixel coordinates, depending on whether this roi uses the line or area convention for coordinates.
offScreenY(int) - Method in class ij.gui.ImageCanvas
  Converts a screen y-coordinate to an offscreen y-coordinate (nearest pixel center).
offScreenY(int) - Method in class ij.gui.Roi
  Converts image canvas screen y coordinates to integer offscreen image pixel coordinates, depending on whether this roi uses the line or area convention for coordinates.
offScreenY2(int) - Method in class ij.gui.ImageCanvas
  Converts a screen y-coordinate to an offscreen y-coordinate (Roi coordinate of nearest pixel border).
offScreenYD(int) - Method in class ij.gui.ImageCanvas
  Converts a screen y-coordinate to a floating-point offscreen y-coordinate.
offScreenYD(int) - Method in class ij.gui.Roi
  Converts image canvas screen y coordinates to floating-point offscreen image pixel coordinates, depending on whether this roi uses the line or area convention for coordinates.
offset - Variable in class ij.io.FileInfo
OJJ - Static variable in class ij.io.Opener
okForFits(ImagePlus) - Static method in class ij.io.FileSaver
okForGif(ImagePlus) - Static method in class ij.io.FileSaver
okForJpeg(ImagePlus) - Static method in class ij.io.FileSaver
  Always returns true.
okToDeleteRoi() - Method in class ij.ImagePlus
oldHeight - Variable in class ij.gui.Roi
oldWidth - Variable in class ij.gui.Roi
oldX - Variable in class ij.gui.Roi
oldX - Variable in class ij.plugin.frame.SyncWindows
oldY - Variable in class ij.gui.Roi
oldY - Variable in class ij.plugin.frame.SyncWindows
ONE - Static variable in class ij.plugin.filter.EDM
  Unit in old make16bitEDM: this pixel value corresponds to a distance of one pixel.
onePixelWide - Static variable in class ij.gui.Roi
open() - Static method in class ij.IJ
  Displays a file open dialog box and then opens the tiff, dicom, fits, pgm, jpeg, bmp, gif, lut, roi, or text file selected by the user.
open() - Method in class ij.io.FileOpener
  Opens the image and displays it.
open() - Method in class ij.io.Opener
  Displays a file open dialog box and then opens the tiff, dicom, fits, pgm, jpeg, bmp, gif, lut, roi, or text file selected by the user.
open() - Method in class ij.plugin.TextReader
  Displays a file open dialog and opens the specified text file as a float image.
open(boolean) - Method in class ij.io.FileOpener
  Obsolete, replaced by openImage() and open().
open(InputStream) - Static method in class ij.plugin.LutLoader
  Opens an ImageJ LUT using an InputStream and returns it as an IndexColorModel.
open(String) - Static method in class ij.IJ
  Opens and displays a tiff, dicom, fits, pgm, jpeg, bmp, gif, lut, roi, or text file.
open(String) - Method in class ij.io.Opener
  Opens and displays the specified tiff, dicom, fits, pgm, jpeg, bmp, gif, lut, roi, or text file.
open(String) - Static method in class ij.io.RoiDecoder
  Opens the Roi at the specified path.
open(String) - Static method in class ij.Macro
open(String) - Static method in class ij.measure.ResultsTable
  Opens a tab or comma delimited text file and returns it as a ResultsTable.
open(String) - Static method in class ij.plugin.BrowserLauncher
  Opens the specified URL in the default browser.
open(String) - Method in class ij.plugin.DICOM
  Opens the specified file as a DICOM.
open(String) - Static method in class ij.plugin.FolderOpener
  Opens the images in the specified directory as a stack.
open(String) - Method in class ij.plugin.frame.RoiManager
  Opens a single .roi file or a ZIP-compressed set of ROIs.
open(String) - Static method in class ij.plugin.LutLoader
  Opens the specified ImageJ LUT and returns it as an IndexColorModel.
open(String) - Method in class ij.plugin.TextReader
  Opens the specified text file as a float image.
open(String, boolean) - Static method in class ij.plugin.AVI_Reader
  Opens an AVI file as a stack in memory or a virtual stack.
open(String, int) - Static method in class ij.IJ
  Opens and displays the nth image in the specified tiff stack.
open(String, int, int, int, int, int) - Static method in class ij.gui.NewImage
open(String, int, int, String) - Static method in class ij.plugin.FolderOpener
  Opens the images in the specified directory as a widthxheight stack.
open(String, FileInfo) - Static method in class ij.plugin.Raw
  Opens the image at 'filePath' using the format specified by 'fi'.
open(String, String) - Static method in class ij.plugin.AVI_Reader
  Opens an AVI file, where 'options' can contain 'virtual' (open as virtual stack), 'convert' (convert color images to grayscale) or 'flip' (flip vertically).
open(String, String) - Static method in class ij.plugin.FolderOpener
  Opens the images in the specified directory as a stack.
open(String, String) - Method in class ij.plugin.frame.Editor
  Opens a file and replaces the text (if any) by the contents of the file.
OPEN - Static variable in class ij.gui.Arrow
OPEN - Static variable in interface ij.macro.MacroConstants
OPEN - Static variable in class ij.plugin.filter.RankFilters
open100Percent - Static variable in class ij.Prefs
  Open images at 100% magnification
open16bitAsciiImage(StreamTokenizer, int, int) - Method in class ij.plugin.PGM_Reader
open16bitRawImage(InputStream, int, int) - Method in class ij.plugin.PGM_Reader
open2(String) - Static method in class ij.measure.ResultsTable
  Opens a tab or comma delimited text file and returns it as a ResultsTable, without requiring a try/catch statement.
openAll(String, FileInfo) - Static method in class ij.plugin.Raw
  Opens all the images in the specified directory as a stack, using the format specified by 'fi'.
openAllVirtual(String, FileInfo) - Static method in class ij.plugin.Raw
  Opens all the images in the specified directory as a virtual stack, using the format specified by 'fi'.
openAndAddToRecent(String) - Method in class ij.io.Opener
  Opens the specified file and adds it to the File/Open Recent menu.
openAsByteBuffer(String) - Static method in class ij.IJ
openAsciiImage(StreamTokenizer, int, byte[]) - Method in class ij.plugin.PGM_Reader
openAsString(String) - Static method in class ij.IJ
  Opens a text file as a string.
openAsVirtualStack(boolean) - Method in class ij.plugin.FolderOpener
OpenDialog - Class in ij.io
  This class displays a dialog window from which the user can select an input file.
OpenDialog(String) - Constructor for class ij.io.OpenDialog
  Displays a file open dialog with 'title' as the title.
OpenDialog(String, String) - Constructor for class ij.io.OpenDialog
  Displays a file open dialog with 'title' as the title.
OpenDialog(String, String, String) - Constructor for class ij.io.OpenDialog
  Displays a file open dialog, using the specified default directory and file name.
openDicomsAsFloat - Static variable in class ij.Prefs
  Open DICOMs as 32-bit float images
OPENED - Static variable in class ij.ImagePlus
Opener - Class in ij.io
  Opens tiff (and tiff stacks), dicom, fits, pgm, jpeg, bmp or gif images, and look-up tables, using a file open dialog or a path.
Opener() - Constructor for class ij.io.Opener
openExample(String) - Static method in class ij.plugin.frame.Editor
  Opens an example from the Help/Examples menu and runs if "Autorun Exampes" is checked.
openFile(File) - Method in class ij.plugin.DragAndDrop
  Open a file.
openFile(String) - Method in class ij.plugin.PGM_Reader
openFolder(String) - Method in class ij.plugin.FolderOpener
  Opens the images in the specified directory as a stack.
openFromByteArray(byte[]) - Static method in class ij.io.RoiDecoder
  Opens an ROI from a byte array.
openFromIJJar(String) - Method in class ij.plugin.MacroInstaller
  Returns a text file contained in ij.jar.
openFromIJJarAsString(String) - Static method in class ij.util.Tools
  Opens a text file in ij.jar as a String (example path: "/macros/Circle_Tool.txt").
openHeader(StreamTokenizer) - Method in class ij.plugin.PGM_Reader
openImage() - Static method in class ij.IJ
  Opens an image using a file open dialog and returns it as an ImagePlus object.
openImage() - Method in class ij.io.FileOpener
  Opens the image and returns it has an ImagePlus object.
openImage() - Method in class ij.io.ImportDialog
  Displays the dialog and opens the specified image or images.
openImage(String) - Static method in class ij.IJ
  Opens the specified file as a tiff, bmp, dicom, fits, pgm, gif, jpeg or text image and returns an ImagePlus object if successful.
openImage(String) - Method in class ij.io.Opener
  Opens, but does not display, the specified image file and returns an ImagePlus object object if successful, or returns null if the file is not in a supported format or is not found.
openImage(String, int) - Static method in class ij.IJ
  Opens the nth image of the specified tiff stack.
openImage(String, int) - Method in class ij.io.Opener
  Open the nth image of the specified tiff stack.
openImage(String, String) - Method in class ij.io.Opener
  Attempts to open the specified file as a tiff, bmp, dicom, fits, pgm, gif or jpeg image.
openLut(String) - Static method in class ij.io.Opener
  Opens a lookup table (LUT) and returns it as a LUT object, or returns null if there is an error.
openLut(String) - Static method in class ij.plugin.LutLoader
  Opens a LUT and returns it as a LUT object.
openMacroFromJar(String) - Static method in class ij.plugin.BatchProcessor
openMultiple() - Method in class ij.io.Opener
  Displays a JFileChooser and then opens the tiff, dicom, fits, pgm, jpeg, bmp, gif, lut, roi, or text files selected by the user.
openNextDir - Variable in class ij.io.FileInfo
openNextName - Variable in class ij.io.FileInfo
openProcessor() - Method in class ij.io.FileOpener
openRawImage(InputStream, int, byte[]) - Method in class ij.plugin.PGM_Reader
openResultsTable(String) - Static method in class ij.io.Opener
  Opens a tab or comma delimited text file in the Results window.
openRoi(String) - Method in class ij.io.Opener
  Attempts to open the specified ROI, returning null if unsuccessful.
openRoi(String, String) - Method in class ij.plugin.RoiReader
openTable(String) - Static method in class ij.io.Opener
  Opens a tab or comma delimited text file.
openTempImage(String, String) - Method in class ij.io.Opener
openTextImage(String, String) - Method in class ij.io.Opener
  Opens the specified text file as a float image.
openTiff(InputStream, String) - Method in class ij.io.Opener
  Attempts to open the specified inputStream as a TIFF, returning an ImagePlus object if successful.
openTiff(String, int) - Method in class ij.io.Opener
  Opens the nth image of the specified TIFF stack.
openTiff(String, String) - Method in class ij.io.Opener
  Attempts to open the specified file as a tiff.
openTiffStack(FileInfo[]) - Method in class ij.io.Opener
  Attemps to open a tiff file as a stack.
openURL(String) - Method in class ij.io.Opener
  Attempts to open the specified url as a tiff, zip compressed tiff, dicom, gif or jpeg.
openURL(String) - Static method in class ij.plugin.BrowserLauncher
  Attempts to open the default web browser to the given URL.
openUrlAsString(String) - Static method in class ij.IJ
  Opens a URL and returns the contents as a string.
openUsingBioFormats(String) - Static method in class ij.io.Opener
  Opens an image file using the Bio-Formats plugin.
openUsingImageIO(String) - Static method in class ij.io.Opener
openVirtual(String) - Static method in class ij.IJ
  Opens the specified tiff file as a virtual stack.
openVirtual(String) - Static method in class ij.plugin.AVI_Reader
  Opens an AVI file as a virtual stack.
openVirtual(String) - Static method in class ij.plugin.FileInfoVirtualStack
  Opens the specified tiff file as a virtual stack.
openWithHandleExtraFileTypes(String, int[]) - Method in class ij.io.Opener
openZip(String) - Method in class ij.io.Opener
  Opens a single TIFF or DICOM contained in a ZIP archive, or a ZIPed collection of ".roi" files created by the ROI manager.
Options - Class in ij.plugin
  This plugin implements most of the commands in the Edit/Options sub-menu.
Options() - Constructor for class ij.plugin.Options
OPTIONS - Static variable in class ij.io.RoiDecoder
OPTIONS - Static variable in class ij.Prefs
OPTIONS2 - Static variable in class ij.Prefs
or(int) - Method in class ij.process.FloatProcessor
or(int) - Method in class ij.process.ImageProcessor
  Binary OR of each pixel in the image or ROI with 'value'.
or(int) - Method in class ij.process.ShortProcessor
or(ShapeRoi) - Method in class ij.gui.ShapeRoi
  Unary union operator.
OR - Static variable in interface ij.process.Blitter
  dst=dst OR src
ORIENTATION - Static variable in class ij.io.TiffDecoder
originalBitDepth - Variable in class ij.process.FHT
  Used by the FFT class.
originalColorModel - Variable in class ij.process.FHT
  Used by the FFT class.
originalHeight - Variable in class ij.process.FHT
  Used by the FFT class.
originalWidth - Variable in class ij.process.FHT
  Used by the FFT class.
Orthogonal_Views - Class in ij.plugin
  This plugin projects dynamically orthogonal XZ and YZ views of a stack.
Orthogonal_Views() - Constructor for class ij.plugin.Orthogonal_Views
OtherInstance - Class in ij
OtherInstance() - Constructor for class ij.OtherInstance
Otsu - Enum constant in enum class ij.process.AutoThresholder.Method
Otsu(int[]) - Static method in class ij.process.AutoThresholder
out(ImagePlus) - Static method in class ij.plugin.Zoom
OUTLIERS - Static variable in class ij.plugin.filter.RankFilters
outline() - Method in class ij.process.BinaryProcessor
outline() - Method in class ij.process.ByteProcessor
OUTLINE - Static variable in class ij.io.RoiDecoder
OUTLINE_KEY - Static variable in class ij.gui.Arrow
OUTLINES - Static variable in class ij.plugin.filter.ParticleAnalyzer
outOfMemory(String) - Static method in class ij.IJ
  Displays an "out of memory" message to the "Log" window.
OVAL - Static variable in class ij.gui.Roi
OVAL - Static variable in class ij.gui.Toolbar
OVAL_ROI - Static variable in class ij.gui.Toolbar
OvalRoi - Class in ij.gui
  Oval region of interest
OvalRoi(double, double, double, double) - Constructor for class ij.gui.OvalRoi
  Creates an OvalRoi using double arguments.
OvalRoi(int, int, int, int) - Constructor for class ij.gui.OvalRoi
  Creates an OvalRoi.
OvalRoi(int, int, int, int, ImagePlus) - Constructor for class ij.gui.OvalRoi
  Deprecated.
OvalRoi(int, int, ImagePlus) - Constructor for class ij.gui.OvalRoi
  Starts the process of creating a user-defined OvalRoi.
OvalRoi(double, double, double, double) - Static method in class ij.IJ
  Creates an OvalRoi.
OVER_UNDER_LUT - Static variable in class ij.process.ImageProcessor
overlay - Variable in class ij.gui.Roi
overlay - Variable in class ij.io.FileInfo
Overlay - Class in ij.gui
  An Overlay is a list of ROIs that can be drawn non-destructively on an Image.
Overlay() - Constructor for class ij.gui.Overlay
  Constructs an empty Overlay.
Overlay(Roi) - Constructor for class ij.gui.Overlay
  Constructs an Overlay and adds the specified ROI.
OVERLAY - Static variable in interface ij.macro.MacroConstants
OVERLAY - Static variable in class ij.plugin.filter.ParticleAnalyzer
  Use "Overlay" checkbox to display overlay.
OVERLAY_ADDITION - Static variable in class ij.Undo
OVERLAY_BACKGROUNDS - Static variable in class ij.io.RoiDecoder
OVERLAY_BOLD - Static variable in class ij.io.RoiDecoder
OVERLAY_FONT_SIZE - Static variable in class ij.io.RoiDecoder
OVERLAY_LABEL_COLOR - Static variable in class ij.io.RoiDecoder
OVERLAY_LABELS - Static variable in class ij.io.RoiDecoder
OVERLAY_MASKS - Static variable in class ij.plugin.filter.ParticleAnalyzer
OVERLAY_NAMES - Static variable in class ij.io.RoiDecoder
OVERLAY_OUTLINES - Static variable in class ij.plugin.filter.ParticleAnalyzer
OverlayBrushTool - Class in ij.plugin.tool
OverlayBrushTool() - Constructor for class ij.plugin.tool.OverlayBrushTool
OverlayCommands - Class in ij.plugin
  This plugin implements the commands in the Image/Overlay menu.
OverlayCommands() - Constructor for class ij.plugin.OverlayCommands
OverlayLabels - Class in ij.plugin
  This plugin implements the Image/Overlay/Labels command.
OverlayLabels() - Constructor for class ij.plugin.OverlayLabels

## P

PACK_BITS - Static variable in class ij.io.FileInfo
packBitsUncompress(byte[], int) - Method in class ij.io.ImageReader
  Based on the Bio-Formats PackbitsCodec written by Melissa Linkert.
pad(int, int) - Static method in class ij.IJ
  Pad 'n' with leading zeros to the specified number of digits.
pad(String, int) - Static method in class ij.IJ
  Pad 's' with leading zeros to the specified number of digits.
padEdges - Static variable in class ij.Prefs
  Extend the borders to foreground for binary erosions and closings.
paint(Graphics) - Method in class ij.gui.GenericDialog
paint(Graphics) - Method in class ij.gui.ImageCanvas
paint(Graphics) - Method in class ij.gui.ImagePanel
paint(Graphics) - Method in class ij.gui.ImageWindow
paint(Graphics) - Method in class ij.gui.MultiLineLabel
paint(Graphics) - Method in class ij.gui.ProgressBar
paint(Graphics) - Method in class ij.gui.Toolbar
paint(Graphics) - Method in class ij.gui.YesNoCancelDialog
paintDoubleBuffered - Static variable in class ij.Prefs
  Aways paint images using double buffering
panel - Variable in class ij.plugin.frame.SyncWindows
  Panel for GUI
PARALLELIZE_IMAGES - Static variable in interface ij.plugin.filter.PlugInFilter
  Set this flag if images may be processed in parallel threads.
PARALLELIZE_STACKS - Static variable in interface ij.plugin.filter.PlugInFilter
  Set this flag if the slices of a stack may be processed in parallel threads
PARSE_FLOAT - Static variable in interface ij.macro.MacroConstants
PARSE_INT - Static variable in interface ij.macro.MacroConstants
parseDouble(String) - Method in class ij.gui.GenericDialog
parseDouble(String) - Static method in class ij.util.Tools
  Returns a double containg the value represented by the specified `String`.
parseDouble(String, double) - Static method in class ij.util.Tools
  Returns a double containg the value represented by the specified `String`.
parseMenu(String, Menu) - Method in class ij.plugin.CommandFinder
partialSum(int[], int) - Static method in class ij.process.AutoThresholder
ParticleAnalyzer - Class in ij.plugin.filter
  Implements ImageJ's Analyze Particles command.
ParticleAnalyzer() - Constructor for class ij.plugin.filter.ParticleAnalyzer
  Default constructor
ParticleAnalyzer(int, int, ResultsTable, double, double) - Constructor for class ij.plugin.filter.ParticleAnalyzer
  Constructs a ParticleAnalyzer using the default min and max circularity values (0 and 1).
ParticleAnalyzer(int, int, ResultsTable, double, double, double, double) - Constructor for class ij.plugin.filter.ParticleAnalyzer
  Constructs a ParticleAnalyzer.
particleAnalyzerFill(int, int, double, double, ImageProcessor, Rectangle) - Method in class ij.process.FloodFiller
  This method is used by the particle analyzer to remove interior holes from particle masks.
paste() - Method in class ij.gui.ImageWindow
paste() - Method in class ij.ImagePlus
  Inserts the contents of the internal clipboard into this image.
paste(int, int) - Method in class ij.ImagePlus
  Inserts the contents of the internal clipboard at the specified location, without updating the display.
paste(int, int, String) - Method in class ij.ImagePlus
  Copies the contents of the internal clipboard to the specified location using the specified transfer mode ("Copy", "Blend", "Average", "Difference", "Transparent", "Transparent2", "AND", "OR", "XOR", "Add", "Subtract", "Multiply", or "Divide").
PASTE - Static variable in class ij.Undo
PasteController - Class in ij.plugin.frame
  Implements ImageJ's Paste Control window.
PasteController() - Constructor for class ij.plugin.frame.PasteController
pasteMode - Static variable in class ij.gui.Roi
path - Variable in class ij.io.PluginClassLoader
Percentile - Enum constant in enum class ij.process.AutoThresholder.Method
Percentile(int[]) - Static method in class ij.process.AutoThresholder
PERIMETER - Static variable in interface ij.measure.Measurements
PERIMETER - Static variable in class ij.measure.ResultsTable
PGM - Static variable in class ij.io.FileInfo
PGM - Static variable in class ij.io.Opener
PGM_Reader - Class in ij.plugin
  This plugin opens PxM format images.
PGM_Reader() - Constructor for class ij.plugin.PGM_Reader
ph - Variable in class ij.process.ImageStatistics
PHOTO_INTERP - Static variable in class ij.io.TiffDecoder
PI - Static variable in interface ij.macro.MacroConstants
pixelCount - Variable in class ij.process.ImageStatistics
  Int pixel count (limited to 2^31-1)
pixelDepth - Variable in class ij.io.FileInfo
pixelDepth - Variable in class ij.measure.Calibration
  Pixel depth in 'unit's
pixelHeight - Variable in class ij.io.FileInfo
pixelHeight - Variable in class ij.measure.Calibration
  Pixel height in 'unit's
PixelInspectionTool - Class in ij.plugin.tool
  This plugin continuously displays the pixel values of the cursor and its surroundings.
PixelInspectionTool() - Constructor for class ij.plugin.tool.PixelInspectionTool
pixels - Variable in class ij.io.FileInfo
pixels - Variable in class ij.process.ByteProcessor
pixels - Variable in class ij.process.ColorProcessor
pixels - Variable in class ij.process.ShortProcessor
pixels8 - Variable in class ij.process.FloatProcessor
pixels8 - Variable in class ij.process.ShortProcessor
pixelWidth - Variable in class ij.io.FileInfo
pixelWidth - Variable in class ij.measure.Calibration
  Pixel width in 'unit's
PLANAR_CONFIGURATION - Static variable in class ij.io.TiffDecoder
plot - Variable in class ij.io.FileInfo
plot(CurveFitter) - Static method in class ij.plugin.frame.Fitter
plot(CurveFitter, boolean) - Static method in class ij.plugin.frame.Fitter
Plot - Class in ij.gui
  This class creates an image that line graphs, scatter plots and plots of vector fields (arrows) can be drawn on and displayed.
Plot(ImagePlus, InputStream) - Constructor for class ij.gui.Plot
  Constructs a new plot from an InputStream and closes the stream.
Plot(String, String, String) - Constructor for class ij.gui.Plot
  Constructs a new Plot with the default options.
Plot(String, String, String, double[], double[]) - Constructor for class ij.gui.Plot
  Deprecated.
Plot(String, String, String, double[], double[], int) - Constructor for class ij.gui.Plot
  Deprecated.
Plot(String, String, String, float[], float[]) - Constructor for class ij.gui.Plot
  Deprecated.
Plot(String, String, String, float[], float[], int) - Constructor for class ij.gui.Plot
  Deprecated.
Plot(String, String, String, int) - Constructor for class ij.gui.Plot
  This version of the constructor has a 'flags' argument for controlling whether ticks, grid, etc.
Plot(String, String, String, String, float[], float[]) - Constructor for class ij.gui.Plot
  Deprecated.
PLOT - Static variable in interface ij.macro.MacroConstants
PlotCanvas - Class in ij.gui
  This subclass of ImageCanvas has special provisions for plots: - Zooming: sets the plot range - Scrolling: moves data area This behavior is suppressed if the plot is frozen
PlotCanvas(ImagePlus) - Constructor for class ij.gui.PlotCanvas
  Creates a new PlotCanvas
PlotContentsDialog - Class in ij.gui
  This class implements the Plot Window's Data>"Add from Plot", "Add form Table", "Add Fit" and "More>Contents Style" dialogs
PlotContentsDialog(Plot, int) - Constructor for class ij.gui.PlotContentsDialog
  Prepares a new PlotContentsDialog for an existing plot.
PlotContentsDialog(Plot, String[], String[], ArrayList<float[]>) - Constructor for class ij.gui.PlotContentsDialog
  Prepares a new PlotContentsDialog for adding data from float[] arrays to a plot.
PlotContentsDialog(String, ResultsTable) - Constructor for class ij.gui.PlotContentsDialog
  Prepares a new PlotContentsDialog for creating a new plot using data from a ResultsTable.
PlotContentsDialog(String, String[], String[], ArrayList<float[]>) - Constructor for class ij.gui.PlotContentsDialog
  Prepares a new PlotContentsDialog for creating a new plot using float[] arrays as data.
PlotDialog - Class in ij.gui
PlotDialog(Plot, int) - Constructor for class ij.gui.PlotDialog
  Constructs a new PlotDialog for a given plot and sets the type of dialog
plotHeight - Static variable in class ij.gui.PlotWindow
  The height of the plot in pixels.
plotHistogram() - Method in class ij.ImagePlus
  Plots a 256 bin histogram of this image and returns the PlotWindow.
plotHistogram(int) - Method in class ij.ImagePlus
  Plots a histogram of this image using the specified number of bins and returns the PlotWindow.
PlotMaker - Interface in ij.gui
  Plugins that generate "Live" profile plots (Profiler and ZAxisProfiler) displayed in PlotWindows implement this interface.
plotScale - Variable in class ij.gui.HistogramWindow
PlotVirtualStack - Class in ij.gui
  This is a virtual stack of frozen plots.
PlotVirtualStack(int, int) - Constructor for class ij.gui.PlotVirtualStack
plotWidth - Static variable in class ij.gui.PlotWindow
  The width of the plot (without frame) in pixels.
PlotWindow - Class in ij.gui
  This class implements the Analyze/Plot Profile command.
PlotWindow(ImagePlus, Plot) - Constructor for class ij.gui.PlotWindow
  Creates a PlotWindow from a given ImagePlus with a Plot object.
PlotWindow(String, String, String, double[], double[]) - Constructor for class ij.gui.PlotWindow
  Deprecated.
  replaced by the Plot class.
PlotWindow(String, String, String, float[], float[]) - Constructor for class ij.gui.PlotWindow
  Deprecated.
  replaced by the Plot class.
PlugIn - Interface in ij.plugin
  Plugins that acquire images or display windows should implement this interface.
PLUGIN - Static variable in class ij.plugin.NewPlugin
PLUGIN_FILTER - Static variable in class ij.plugin.NewPlugin
PLUGIN_FRAME - Static variable in class ij.plugin.NewPlugin
PLUGIN_TOOL - Static variable in class ij.plugin.NewPlugin
PluginClassLoader - Class in ij.io
  ImageJ uses this class loader to load plugins and resources from the plugins directory and immediate subdirectories.
PluginClassLoader(String) - Constructor for class ij.io.PluginClassLoader
  Creates a new PluginClassLoader that searches in the directory path passed as a parameter.
PluginClassLoader(String, boolean) - Constructor for class ij.io.PluginClassLoader
  This version of the constructor is used when ImageJ is launched using Java WebStart.
PlugInDialog - Class in ij.plugin.frame
  This is a non-modal dialog that plugins can extend.
PlugInDialog(String) - Constructor for class ij.plugin.frame.PlugInDialog
PlugInFilter - Interface in ij.plugin.filter
  ImageJ plugins that process an image should implement this interface.
PlugInFilterRunner - Class in ij.plugin.filter
PlugInFilterRunner(Object, String, String) - Constructor for class ij.plugin.filter.PlugInFilterRunner
  The constructor runs a PlugInFilter or ExtendedPlugInFilter by calling its setup, run, etc.
PlugInFrame - Class in ij.plugin.frame
  This is a closeable window that plugins can extend.
PlugInFrame(String) - Constructor for class ij.plugin.frame.PlugInFrame
PluginInstaller - Class in ij.plugin
  Installs plugins dragged and dropped on the "ImageJ" window, or plugins, macros or scripts opened using the Plugins/Install command.
PluginInstaller() - Constructor for class ij.plugin.PluginInstaller
PlugInInterpreter - Class in ij.plugin
  Plugins that run scripts (e.g., BeanShell, Jython) extend this class.
PlugInInterpreter() - Constructor for class ij.plugin.PlugInInterpreter
pluginName - Variable in class ij.plugin.Concatenator
PLUGINS_MENU - Static variable in class ij.Menus
PlugInTool - Class in ij.plugin.tool
PlugInTool() - Constructor for class ij.plugin.tool.PlugInTool
PLUS_EQUAL - Static variable in interface ij.macro.MacroConstants
PLUS_PLUS - Static variable in interface ij.macro.MacroConstants
PNG - Static variable in class ij.io.Opener
PNG_COMPRESSION - Static variable in class ij.plugin.filter.AVI_Writer
PNG_Writer - Class in ij.plugin
  Saves in PNG format using the ImageIO classes.
PNG_Writer() - Constructor for class ij.plugin.PNG_Writer
PNM_Writer - Class in ij.plugin
PNM_Writer() - Constructor for class ij.plugin.PNM_Writer
POINT - Static variable in class ij.gui.Roi
POINT - Static variable in class ij.gui.Toolbar
POINT_SELECTION - Static variable in class ij.plugin.filter.MaximumFinder
  Do not create image, only mark points
POINT_TYPE - Static variable in class ij.io.RoiDecoder
pointAddToManager - Static variable in class ij.Prefs
  Add points to ROI Manager.
pointAddToOverlay - Static variable in class ij.Prefs
  Add points to overlay.
pointAutoMeasure - Static variable in class ij.Prefs
  Point tool auto-measure mode.
pointAutoNextSlice - Static variable in class ij.Prefs
  Point tool auto-next slice mode (not saved in IJ_Prefs).
PointIterator(double, double, double, double) - Constructor for class ij.gui.Line.PointIterator
PointIterator(Line) - Constructor for class ij.gui.Line.PointIterator
PointRoi - Class in ij.gui
  This class represents a collection of points that can be associated with counters.
PointRoi() - Constructor for class ij.gui.PointRoi
PointRoi(double, double) - Constructor for class ij.gui.PointRoi
  Creates a new PointRoi using the specified offscreen double coordinates.
PointRoi(double, double, String) - Constructor for class ij.gui.PointRoi
  Creates a new PointRoi using the specified coordinates and options.
PointRoi(float[], float[]) - Constructor for class ij.gui.PointRoi
  Creates a new PointRoi using the specified float arrays of offscreen coordinates.
PointRoi(float[], float[], int) - Constructor for class ij.gui.PointRoi
  Creates a new PointRoi using the specified float arrays of offscreen coordinates.
PointRoi(float[], float[], String) - Constructor for class ij.gui.PointRoi
  Creates a new PointRoi using the specified coordinate arrays and options.
PointRoi(int[], int[], int) - Constructor for class ij.gui.PointRoi
  Creates a new PointRoi using the specified int arrays of offscreen coordinates.
PointRoi(int, int) - Constructor for class ij.gui.PointRoi
  Creates a new PointRoi using the specified offscreen int coordinates.
PointRoi(int, int, ImagePlus) - Constructor for class ij.gui.PointRoi
  Creates a new PointRoi using the specified screen coordinates.
PointRoi(FloatPolygon) - Constructor for class ij.gui.PointRoi
  Creates a new PointRoi from a FloatPolygon.
PointRoi(Polygon) - Constructor for class ij.gui.PointRoi
  Creates a new PointRoi from a Polygon.
PointToolOptions - Class in ij.plugin
  This plugin implements the Edit/Options/Point Tool command.
PointToolOptions() - Constructor for class ij.plugin.PointToolOptions
POLY2 - Static variable in class ij.measure.Calibration
POLY2 - Static variable in class ij.measure.CurveFitter
  Constants for the built-in fit functions
POLY3 - Static variable in class ij.measure.Calibration
POLY3 - Static variable in class ij.measure.CurveFitter
  Constants for the built-in fit functions
POLY4 - Static variable in class ij.measure.Calibration
POLY4 - Static variable in class ij.measure.CurveFitter
  Constants for the built-in fit functions
POLY5 - Static variable in class ij.measure.CurveFitter
  Constants for the built-in fit functions
POLY6 - Static variable in class ij.measure.CurveFitter
  Constants for the built-in fit functions
POLY7 - Static variable in class ij.measure.CurveFitter
  Constants for the built-in fit functions
POLY8 - Static variable in class ij.measure.CurveFitter
  Constants for the built-in fit functions
POLYGON - Static variable in class ij.gui.Roi
POLYGON - Static variable in class ij.gui.Toolbar
PolygonFiller - Class in ij.process
  This class fills polygons using the scan-line filling algorithm described at "http://www.cs.rit.edu/~icss571/filling/".
PolygonFiller() - Constructor for class ij.process.PolygonFiller
  Constructs a PolygonFiller.
PolygonFiller(float[], float[], int, double, double) - Constructor for class ij.process.PolygonFiller
  Constructs a PolygonFiller using the specified polygon with floating-point coordinates.
PolygonFiller(int[], int[], int) - Constructor for class ij.process.PolygonFiller
  Constructs a PolygonFiller using the specified polygon with integer coordinates.
PolygonRoi - Class in ij.gui
  This class represents a polygon region of interest or polyline of interest.
PolygonRoi(float[], float[], int) - Constructor for class ij.gui.PolygonRoi
  Creates a new polygon or polyline ROI from float x and y arrays.
PolygonRoi(float[], float[], int, int) - Constructor for class ij.gui.PolygonRoi
  Creates a new polygon or polyline ROI from float x and y arrays.
PolygonRoi(int[], int[], int, int) - Constructor for class ij.gui.PolygonRoi
  Creates a new polygon or polyline ROI from x and y coordinate arrays.
PolygonRoi(int[], int[], int, ImagePlus, int) - Constructor for class ij.gui.PolygonRoi
  Deprecated.
PolygonRoi(int, int, ImagePlus) - Constructor for class ij.gui.PolygonRoi
  Starts the process of creating a new user-generated polygon or polyline ROI.
PolygonRoi(FloatPolygon, int) - Constructor for class ij.gui.PolygonRoi
  Creates a new polygon or polyline ROI from a FloatPolygon.
PolygonRoi(Polygon, int) - Constructor for class ij.gui.PolygonRoi
  Creates a new polygon or polyline ROI from a Polygon.
POLYLINE - Static variable in class ij.gui.Roi
POLYLINE - Static variable in class ij.gui.Toolbar
populateList(String) - Method in class ij.macro.FunctionFinder
populateList(String) - Method in class ij.plugin.CommandFinder
POSITION - Static variable in class ij.io.RoiDecoder
positionWindow() - Method in class ij.plugin.frame.Editor
POW - Static variable in interface ij.macro.MacroConstants
POWER - Static variable in class ij.measure.Calibration
POWER - Static variable in class ij.measure.CurveFitter
  Constants for the built-in fit functions
POWER_REGRESSION - Static variable in class ij.measure.CurveFitter
  Constants for the built-in fit functions
powerOf2Size() - Method in class ij.process.FHT
  Returns true of this FHT contains a square image with a width that is a power of two.
powerSpectrumMean - Variable in class ij.process.FHT
  Used by the FFT class.
precision - Static variable in class ij.plugin.filter.Analyzer
PREDEFINED_FUNCTION - Static variable in interface ij.macro.MacroConstants
PREDICTOR - Static variable in class ij.io.TiffDecoder
preferredLayoutSize(Container) - Method in class ij.gui.ImageLayout
  Returns the preferred dimensions for this layout.
Prefs - Class in ij
  This class contains the ImageJ preferences, which are loaded from the "IJ_Props.txt" and "IJ_Prefs.txt" files.
Prefs() - Constructor for class ij.Prefs
PREFS_NAME - Static variable in class ij.Prefs
previewLUT() - Method in class ij.plugin.CommandFinder
previewRunning(boolean) - Method in class ij.gui.GenericDialog
  Used by PlugInFilterRunner to provide visable feedback whether preview is running or not by switching from "Preview" to "wait..."
previousRoi - Static variable in class ij.gui.Roi
  Get using getPreviousRoi() and set using setPreviousRoi()
print(Graphics, PageFormat, int) - Method in class ij.plugin.filter.Printer
PRINT - Static variable in interface ij.macro.MacroConstants
Printer - Class in ij.plugin.filter
  This plugin implements the File/Page Setup and File/Print commands.
Printer() - Constructor for class ij.plugin.filter.Printer
process(int, double) - Method in class ij.process.ShortProcessor
process(int, double) - Method in class ij.process.SignedShortProcessor
processStack - Variable in class ij.plugin.filter.ParticleAnalyzer
processWindowEvent(WindowEvent) - Method in class ij.plugin.frame.RoiManager
processWindowEvent(WindowEvent) - Method in class ij.text.TextWindow
profile - Variable in class ij.gui.ProfilePlot
ProfilePlot - Class in ij.gui
  Creates a density profile plot of a rectangular selection or line selection.
ProfilePlot() - Constructor for class ij.gui.ProfilePlot
ProfilePlot(ImagePlus) - Constructor for class ij.gui.ProfilePlot
ProfilePlot(ImagePlus, boolean) - Constructor for class ij.gui.ProfilePlot
Profiler - Class in ij.plugin
  Implements the Analyze/Plot Profile and Edit/Options/Profile Plot Options commands.
Profiler() - Constructor for class ij.plugin.Profiler
Program - Class in ij.macro
  An object of this type is a tokenized macro file and the associated symbol table.
Program() - Constructor for class ij.macro.Program
ProgressBar - Class in ij.gui
  This is the progress bar that is displayed in the lower right hand corner of the ImageJ window.
ProgressBar(int, int) - Constructor for class ij.gui.ProgressBar
  This constructor is called once by ImageJ at startup.
Projector - Class in ij.plugin
  This plugin creates a sequence of projections of a rotating volume (stack of slices) onto a plane using nearest-point (surface), brightest-point, or mean-value projection or a weighted combination of nearest- point projection with either of the other two methods (partial opacity).
Projector() - Constructor for class ij.plugin.Projector
PROMPT_BEFORE_DELETING - Static variable in class ij.io.RoiDecoder
promptBeforeDeleting() - Method in class ij.gui.PointRoi
promptBeforeDeleting(Boolean) - Method in class ij.gui.PointRoi
properties - Variable in class ij.io.FileInfo
PROPERTY - Static variable in interface ij.macro.MacroConstants
PROPERTY_KEY - Static variable in class ij.gui.Plot
  key in ImagePlus properties to access the plot behind an ImagePlus
PROPS_NAME - Static variable in class ij.Prefs
protectStatusBar(boolean) - Static method in class ij.IJ
ProxySettings - Class in ij.plugin
  This plugin implements the Plugins/Utilities/Proxy Settings command.
ProxySettings() - Constructor for class ij.plugin.ProxySettings
PUT_PIXEL - Static variable in interface ij.macro.MacroConstants
putBehind() - Static method in class ij.WindowManager
  Activates the next image window on the window list.
putColumn(int, int, float[], int) - Method in class ij.process.ImageProcessor
  Inserts the pixels contained in 'data' into a column starting at (x,y).
putColumn(int, int, int[], int) - Method in class ij.process.ImageProcessor
  Inserts the pixels contained in 'data' into a column starting at (x,y).
putColumn(ImageProcessor, int, int, float[], int) - Method in class ij.plugin.Slicer
putPixel(int, int, int) - Method in class ij.process.ByteProcessor
  Stores the specified value at (x,y).
putPixel(int, int, int) - Method in class ij.process.ColorProcessor
  Stores the specified value at (x,y).
putPixel(int, int, int) - Method in class ij.process.FloatProcessor
  Stores the specified value at (x,y).
putPixel(int, int, int) - Method in class ij.process.ImageProcessor
  Stores the specified value at (x,y).
putPixel(int, int, int) - Method in class ij.process.ShortProcessor
  Stores the specified value at (x,y).
putPixel(int, int, int[]) - Method in class ij.process.ColorProcessor
  Sets a pixel in the image using a 3 element (R, G and B) int array of samples.
putPixel(int, int, int[]) - Method in class ij.process.FloatProcessor
  Sets a pixel in the image using a one element int array.
putPixel(int, int, int[]) - Method in class ij.process.ImageProcessor
  Sets a pixel in the image using an int array of samples.
putPixelValue(int, int, double) - Method in class ij.process.ByteProcessor
  Stores the specified real value at (x,y).
putPixelValue(int, int, double) - Method in class ij.process.ColorProcessor
  Stores the specified real grayscale value at (x,y).
putPixelValue(int, int, double) - Method in class ij.process.FloatProcessor
  Stores the specified real value at (x,y).
putPixelValue(int, int, double) - Method in class ij.process.ImageProcessor
  Stores the specified value at (x,y).
putPixelValue(int, int, double) - Method in class ij.process.ShortProcessor
  Stores the specified real value at (x,y).
putRow(int, int, float[], int) - Method in class ij.process.ImageProcessor
  Inserts the pixels contained in 'data' into a horizontal line starting at (x,y).
putRow(int, int, int[], int) - Method in class ij.process.ImageProcessor
  Inserts the pixels contained in 'data' into a horizontal line starting at (x,y).
putRow(ImageProcessor, int, int, float[], int) - Method in class ij.plugin.Slicer
putValue(int, float) - Method in class ij.util.ArrayUtil
  put a value to a index
pw - Variable in class ij.process.ImageStatistics

## Q

quadrantSwapNeeded - Variable in class ij.process.FHT
  Used by the FFT class.
quit() - Method in class ij.ImageJ
  Called by ImageJ when the user selects Quit.
quitting() - Method in class ij.ImageJ
  Returns true if ImageJ is exiting.
quittingViaMacro() - Method in class ij.ImageJ
  Returns true if ImageJ is quitting as a result of a run("Quit") macro call.

## R

radioButtonGroups - Variable in class ij.gui.GenericDialog
rand(int, int) - Method in class ij.plugin.filter.SaltAndPepper
RANDOM - Static variable in interface ij.macro.MacroConstants
RandomAccessStream - Class in ij.io
  This class uses a memory cache to allow seeking within an InputStream.
RandomAccessStream(InputStream) - Constructor for class ij.io.RandomAccessStream
  Constructs a RandomAccessStream from an InputStream.
RandomAccessStream(RandomAccessFile) - Constructor for class ij.io.RandomAccessStream
  Constructs a RandomAccessStream from an RandomAccessFile.
rank(double[]) - Static method in class ij.util.Tools
  Returns a sorted list of indices of the specified double array.
rank(ImageProcessor, double, int) - Method in class ij.plugin.filter.RankFilters
  Filters an image by any method except 'despecle', 'remove outliers', or top-hat
rank(ImageProcessor, double, int, int, float) - Method in class ij.plugin.filter.RankFilters
  Filters an image by any method except 'despecle' and top-hat (for 'despeckle', use 'median' and radius=1)
rank(ImageProcessor, double, int, int, float, boolean, boolean) - Method in class ij.plugin.filter.RankFilters
  Filters an image by any method except 'despecle' (for 'despeckle', use 'median' and radius=1)
rank(String[]) - Static method in class ij.util.Tools
  Returns a sorted list of indices of the specified String array.
RankFilters - Class in ij.plugin.filter
  This plugin implements the Mean, Minimum, Maximum, Variance, Median, Remove Outliers, Remove NaNs and Despeckle commands.
RankFilters() - Constructor for class ij.plugin.filter.RankFilters
raster - Variable in class ij.process.ImageProcessor
Raw - Class in ij.plugin
  This plugin implements the File/Import/Raw command.
Raw() - Constructor for class ij.plugin.Raw
RAW - Static variable in class ij.io.FileInfo
RAW - Static variable in class ij.io.Opener
RAW_INTEGRATED_DENSITY - Static variable in class ij.measure.ResultsTable
RAW_VALUES - Static variable in class ij.plugin.frame.ThresholdAdjuster
rc2DFHT(float[], boolean, int) - Method in class ij.process.FHT
  Performs a 2D FHT (Fast Hartley Transform).
read() - Method in class ij.io.RandomAccessStream
read(byte[], int, int) - Method in class ij.io.RandomAccessStream
readDouble() - Method in class ij.io.RandomAccessStream
readFloat() - Method in class ij.io.RandomAccessStream
readFully(byte[]) - Method in class ij.io.RandomAccessStream
readFully(byte[], int) - Method in class ij.io.RandomAccessStream
readInt() - Method in class ij.io.RandomAccessStream
readLong() - Method in class ij.io.RandomAccessStream
readPixels(InputStream) - Method in class ij.io.ImageReader
  Reads the image from the InputStream and returns the pixel array (byte, short, int or float).
readPixels(InputStream, long) - Method in class ij.io.ImageReader
  Skips the specified number of bytes, then reads an image and returns the pixel array (byte, short, int or float).
readPixels(String) - Method in class ij.io.ImageReader
  Reads the image from a URL and returns the pixel array (byte, short, int or float).
readShort() - Method in class ij.io.RandomAccessStream
RecentOpener - Class in ij
  Opens, in a separate thread, files selected from the File/Open Recent submenu.
record - Static variable in class ij.plugin.frame.Recorder
  This variable is true if the recorder is running.
record() - Static method in class ij.process.ImageConverter
record(ImagePlus, int, int, int, int) - Static method in class ij.plugin.Scaler
record(String) - Static method in class ij.plugin.frame.Recorder
record(String, double, double) - Static method in class ij.plugin.frame.Recorder
record(String, int) - Static method in class ij.plugin.frame.Recorder
record(String, int, int) - Static method in class ij.plugin.frame.Recorder
record(String, int, int, int) - Static method in class ij.plugin.frame.Recorder
record(String, int, int, int, int) - Static method in class ij.plugin.frame.Recorder
record(String, int, int, int, int, double) - Static method in class ij.plugin.frame.Recorder
record(String, int, int, int, int, int) - Static method in class ij.plugin.frame.Recorder
record(String, int, int, String) - Static method in class ij.plugin.frame.Recorder
record(String, String) - Static method in class ij.plugin.frame.Recorder
record(String, String, int) - Static method in class ij.plugin.frame.Recorder
record(String, String, int, int) - Static method in class ij.plugin.frame.Recorder
record(String, String, String) - Static method in class ij.plugin.frame.Recorder
record(String, String, String, int, int, int, int, int) - Static method in class ij.plugin.frame.Recorder
record(String, String, String, String) - Static method in class ij.plugin.frame.Recorder
RECORD_STARTS - Static variable in class ij.plugin.filter.ParticleAnalyzer
  Record starting coordinates so outline can be recreated later using doWand(x,y).
recordCall(String) - Static method in class ij.plugin.frame.Recorder
recordCall(String, boolean) - Static method in class ij.plugin.frame.Recorder
recordCall(String, String) - Static method in class ij.plugin.frame.Recorder
Recorder - Class in ij.plugin.frame
  This is ImageJ's macro recorder.
Recorder() - Constructor for class ij.plugin.frame.Recorder
Recorder(boolean) - Constructor for class ij.plugin.frame.Recorder
recordInMacros - Static variable in class ij.plugin.frame.Recorder
  Set this variable true to allow recording within IJ.run() calls.
recordOpen(String) - Static method in class ij.plugin.frame.Recorder
recordOption(String) - Static method in class ij.plugin.frame.Recorder
recordOption(String, String) - Static method in class ij.plugin.frame.Recorder
recordPath(String, String) - Static method in class ij.plugin.frame.Recorder
recordRoi(Roi) - Static method in class ij.plugin.frame.Recorder
recordRoi(Polygon, int) - Static method in class ij.plugin.frame.Recorder
recordScriptRoi(Polygon, int) - Static method in class ij.plugin.frame.Recorder
recordSetMinAndMax(double, double) - Static method in class ij.plugin.frame.ContrastAdjuster
recordStarts - Variable in class ij.plugin.filter.ParticleAnalyzer
recordString(String) - Static method in class ij.plugin.frame.Recorder
RECT - Static variable in interface ij.measure.Measurements
RECT_ROI - Static variable in class ij.gui.Toolbar
RECTANGLE - Static variable in class ij.gui.Roi
RECTANGLE - Static variable in class ij.gui.Toolbar
RectToolOptions - Class in ij.plugin
  This plugin implements the rounded rectangle tool dialog box.
RectToolOptions() - Constructor for class ij.plugin.RectToolOptions
red - Variable in class ij.plugin.filter.RGBStackSplitter
RED_LUT - Static variable in class ij.process.ImageProcessor
redirectErrorMessages() - Static method in class ij.IJ
  Causes IJ.error() output to be temporarily redirected to the "Log" window.
redirectErrorMessages(boolean) - Static method in class ij.IJ
  Set 'true' and IJ.error() output will be temporarily redirected to the "Log" window.
redirectingErrorMessages() - Static method in class ij.IJ
  Returns the state of the 'redirectErrorMessages' flag, which is set by File/Import/Image Sequence.
redirectSystem() - Static method in class ij.io.LogStream
  Redirects all output sent to `System.out` and `System.err` to ImageJ's log console using the default prefixes.
redirectSystem(boolean) - Static method in class ij.io.LogStream
  Redirects all output sent to `System.out` and `System.err` to ImageJ's log console using the default prefixes.
redirectSystemErr(String) - Static method in class ij.io.LogStream
  Redirects all output sent to `System.err` to ImageJ's log console.
redirectSystemOut(String) - Static method in class ij.io.LogStream
  Redirects all output sent to `System.out` to ImageJ's log console.
redrawGrid() - Method in class ij.gui.Plot
reds - Variable in class ij.io.FileInfo
reduce(int) - Method in class ij.plugin.ListVirtualStack
reduce(int) - Method in class ij.VirtualStack
  Reduces the number of slices in this stack by a factor.
reduce(ImagePlus) - Method in class ij.plugin.HyperStackReducer
reduceHyperstack(ImagePlus, int, boolean) - Method in class ij.plugin.StackReducer
reduceStack(ImagePlus, int) - Method in class ij.plugin.StackReducer
reflexAngle - Static variable in class ij.Prefs
  Angle tool measures reflex angle
register(Class) - Static method in class ij.IJ
  Obsolete
register(Class) - Method in class ij.ImageJ
  Adds the specified class to a Vector to keep it from being garbage collected, causing static fields to be reset.
registerExtensions(MacroExtension) - Static method in class ij.macro.Functions
REINITIALIZATION_FAILURE - Static variable in class ij.measure.Minimizer
  Status returned: Could not reinitialize the simplex because all attempts to find restarting parameters resulted in the target function returning NaN.
remove() - Method in class ij.gui.Line.PointIterator
remove(int) - Method in class ij.gui.Overlay
  Removes the ROI with the specified index from this Overlay.
remove(Roi) - Method in class ij.gui.Overlay
  Removes the specified ROI from this Overlay.
remove(String) - Method in class ij.gui.Overlay
  Removes all ROIs that have the specified name.
REMOVE_NAN - Static variable in class ij.plugin.filter.RankFilters
removeAdjustmentListener(AdjustmentListener) - Method in class ij.gui.ScrollbarWithLabel
removeBatchModeImage(ImagePlus) - Static method in class ij.macro.Interpreter
removeCommandListener(CommandListener) - Static method in class ij.Executer
  Removes the specified command listener.
removeEventListener(IJEventListener) - Static method in class ij.IJ
removeImageListener(ImageListener) - Static method in class ij.ImagePlus
removeKeyListener(KeyListener) - Method in class ij.gui.ScrollbarWithLabel
removeLast(int) - Method in class ij.util.FloatArray
  Deletes the last `n` element from this FloatArray.
removeLayoutComponent(Component) - Method in class ij.gui.ImageLayout
  Not used by this class.
removeMacroTools() - Static method in class ij.gui.Toolbar
removeNaNs() - Method in class ij.gui.Plot
  Removes NaNs from the xValues and yValues arrays of all plot objects.
removeRoiListener(RoiListener) - Static method in class ij.gui.Roi
removeScale() - Method in class ij.ImagePlus
  Removes the spatial scaling of this image.
removeSplineFit() - Method in class ij.gui.PolygonRoi
removeWindow(Frame) - Static method in class ij.WindowManager
  Removes the specified Frame from the Window menu.
removeWindow(Window) - Static method in class ij.WindowManager
  Removes the specified window from the Window menu.
rename(int, String) - Method in class ij.plugin.frame.RoiManager
rename(String) - Method in class ij.text.TextWindow
RENAME - Static variable in interface ij.macro.MacroConstants
renameColumn(String, String) - Method in class ij.measure.ResultsTable
  Changes the name of a column.
renameResults(String) - Static method in class ij.IJ
  Renames a results window.
renameResults(String, String) - Static method in class ij.IJ
  Changes the name of a table window from 'oldTitle' to 'newTitle'.
RenyiEntropy - Enum constant in enum class ij.process.AutoThresholder.Method
RenyiEntropy(int[]) - Static method in class ij.process.AutoThresholder
repaint() - Method in class ij.gui.GenericDialog
repaintImageWindows() - Static method in class ij.WindowManager
  Repaints all open image windows.
repaintOverlay() - Method in class ij.gui.ImageCanvas
repaintTool(int) - Static method in class ij.gui.Toolbar
repaintWindow() - Method in class ij.ImagePlus
  Calls draw to draw the image and also repaints the image window to force the information displayed above the image (dimension, type, size) to be updated.
replace(int, String, double[], double[]) - Method in class ij.gui.Plot
  Replaces the specified plot object (curve or set of points).
REPLACE - Static variable in interface ij.macro.MacroConstants
requireControlKey - Static variable in class ij.Prefs
  Require control or command key for keybaord shortcuts.
REQUIRES - Static variable in interface ij.macro.MacroConstants
resampleArray(double[], int) - Static method in class ij.util.Tools
  Returns an array linearly resampled to a different length.
reset() - Method in class ij.CompositeImage
reset() - Method in class ij.measure.ResultsTable
reset() - Method in class ij.plugin.frame.RoiManager
  Clears this RoiManager so that it contains no ROIs.
reset() - Method in class ij.process.ByteProcessor
  Reset the image from snapshot.
reset() - Method in class ij.process.ColorProcessor
reset() - Method in class ij.process.FloatProcessor
reset() - Method in class ij.process.ImageProcessor
  Restores the pixel data from the snapshot (undo) buffer.
reset() - Method in class ij.process.ShortProcessor
reset() - Static method in class ij.Undo
reset(ImageProcessor) - Method in class ij.process.ByteProcessor
  Restore pixels that are within roi but not part of mask.
reset(ImageProcessor) - Method in class ij.process.ColorProcessor
reset(ImageProcessor) - Method in class ij.process.FloatProcessor
reset(ImageProcessor) - Method in class ij.process.ImageProcessor
  Restores pixels from the snapshot buffer that are within the rectangular roi but not part of the mask.
reset(ImageProcessor) - Method in class ij.process.ShortProcessor
RESET - Static variable in interface ij.macro.MacroConstants
RESET_MIN_MAX - Static variable in interface ij.macro.MacroConstants
RESET_THRESHOLD - Static variable in interface ij.macro.MacroConstants
resetBinaryThreshold() - Method in class ij.process.ImageProcessor
  Resets the threshold if minThreshold=maxThreshold and lutUpdateMode=NO_LUT_UPDATE.
resetBoundingRect() - Method in class ij.gui.PolygonRoi
resetClassLoader() - Static method in class ij.IJ
resetClipboard() - Static method in class ij.ImagePlus
  Clears the internal clipboard.
resetCommandOptions() - Static method in class ij.plugin.frame.Recorder
  Used by GenericDialog.notifyListeners() to clear the command options.
resetCounter - Variable in class ij.plugin.filter.ParticleAnalyzer
resetCounter() - Static method in class ij.plugin.filter.Analyzer
  Sets the measurement counter to zero.
resetCounters() - Method in class ij.gui.GenericDialog
  Reset the counters before reading the dialog parameters
resetCounters() - Method in class ij.gui.PointRoi
resetDefaultHandleSize() - Static method in class ij.gui.Roi
resetDisplayRange() - Method in class ij.CompositeImage
resetDisplayRange() - Method in class ij.ImagePlus
resetDisplayRanges() - Method in class ij.CompositeImage
resetDoubleBuffer() - Method in class ij.gui.ImageCanvas
resetEscape() - Static method in class ij.IJ
  This method sets the `Esc` key to the "up" position.
resetMinAndMax() - Static method in class ij.IJ
  Resets the minimum and maximum displayed pixel values of the current image to be the same as the min and max pixel values.
resetMinAndMax() - Method in class ij.process.ByteProcessor
  Resets this image's LUT.
resetMinAndMax() - Method in class ij.process.FloatProcessor
  Recalculates the min and max values used to scale pixel values to 0-255 for display.
resetMinAndMax() - Method in class ij.process.ImageProcessor
  For short and float images, recalculates the min and max image values needed to correctly display the image.
resetMinAndMax() - Method in class ij.process.IntProcessor
resetMinAndMax() - Method in class ij.process.ShortProcessor
  Recalculates the min and max values used to scale pixel values to 0-255 for display.
resetMinAndMax(ImagePlus) - Static method in class ij.IJ
  Resets the minimum and maximum displayed pixel values of the specified image to be the same as the min and max pixel values.
resetMultiMeasureResults() - Static method in class ij.plugin.frame.RoiManager
resetOutOfRoi(ImageProcessor, int) - Static method in class ij.plugin.filter.GaussianBlur
  Set the processed pixels above and below the roi rectangle back to their previous value (i.e., snapshot buffer).
resetPreferences() - Static method in class ij.Prefs
  Delete the preferences file when ImageJ quits.
resetRoi() - Method in class ij.ImagePlus
  Deletes the current region of interest.
resetRoi() - Method in class ij.process.ImageProcessor
  Sets the ROI (Region of Interest) and clipping rectangle to the entire image.
resetSelection() - Method in class ij.text.TextPanel
  Clears the selection, if any.
resetStack() - Method in class ij.ImagePlus
resetThreshold() - Static method in class ij.IJ
  Disables thresholding on the current image.
resetThreshold() - Method in class ij.process.ImageProcessor
  Disables thresholding.
resetThreshold(ImagePlus) - Static method in class ij.IJ
  Disables thresholding on the specified image.
resize() - Method in class ij.ImageJ
resize(int) - Method in class ij.process.ImageProcessor
  Returns a new ImageProcessor containing a scaled copy of this image or ROI, with the aspect ratio maintained.
resize(int, int) - Method in class ij.process.ByteProcessor
  Creates a new ByteProcessor containing a scaled copy of this image or selection.
resize(int, int) - Method in class ij.process.ColorProcessor
  Creates a new ColorProcessor containing a scaled copy of this image or selection.
resize(int, int) - Method in class ij.process.FloatProcessor
  Creates a new FloatProcessor containing a scaled copy of this image or selection.
resize(int, int) - Method in class ij.process.ImageProcessor
  Returns a new ImageProcessor containing a scaled copy of this image or ROI.
resize(int, int) - Method in class ij.process.ShortProcessor
  Creates a new ShortProcessor containing a scaled copy of this image or selection.
resize(int, int) - Method in class ij.process.StackProcessor
  Creates a new stack with dimensions 'newWidth' x 'newHeight'.
resize(int, int, boolean) - Method in class ij.process.ImageProcessor
  Returns a new ImageProcessor containing a scaled copy of this image or ROI.
resize(int, int, boolean) - Method in class ij.process.StackProcessor
resize(int, int, int, String) - Method in class ij.ImagePlus
  Returns a scaled copy of this image or ROI, where the 'options' string can contain 'none', 'bilinear'.
resize(int, int, String) - Method in class ij.ImagePlus
  Returns a scaled copy of this image or ROI, where the 'options' string can contain 'none', 'bilinear'.
resize(ImagePlus, int, int, int, String) - Static method in class ij.plugin.Scaler
  Returns a scaled copy of this image or ROI, where the 'options' string can contain 'none', 'bilinear'.
resizeLinearly(int, int) - Method in class ij.process.ImageProcessor
  Use linear interpolation to resize images that have a width or height of one.
Resizer - Class in ij.plugin
  This plugin implements the Edit/Crop and Image/Adjust/Size commands.
Resizer() - Constructor for class ij.plugin.Resizer
RESIZING - Static variable in class ij.gui.Roi
reslice(ImagePlus) - Method in class ij.plugin.Slicer
RESOLUTION_UNIT - Static variable in class ij.io.TiffDecoder
RESTORE_PREVIOUS_TOOL - Static variable in interface ij.macro.MacroConstants
RESTORE_SETTINGS - Static variable in interface ij.macro.MacroConstants
restoreCentered(boolean) - Static method in class ij.plugin.frame.RoiManager
restorePlotObjects() - Method in class ij.gui.Plot
  Restores the plot contents (not including axis formats etc) from the snapshot previously created by savePlotObjects().
restorePlotProperties() - Method in class ij.gui.Plot
  Restores the plot properties (formatting, range etc., not PlotObjects such as data and corresponding curves etc.) from a snapshot previously created by savePlotPlotProperties.
restorePreviousTool() - Method in class ij.gui.Toolbar
restoreRoi() - Method in class ij.ImagePlus
restoreTools() - Static method in class ij.gui.Toolbar
ResultsTable - Class in ij.measure
  This is a table for storing measurement results and strings as columns of values.
ResultsTable() - Constructor for class ij.measure.ResultsTable
  Constructs an empty ResultsTable with the counter=0, no columns and the precision set to 3 or the "Decimal places" value in Analyze/Set Measurements if that value is higher than 3.
ResultsTable(Integer) - Constructor for class ij.measure.ResultsTable
  Constructs a ResultsTable with 'nRows' rows.
ResultsTableMacros - Class in ij.measure
  This class implements the Apply Macro command in tables.
ResultsTableMacros(ResultsTable) - Constructor for class ij.measure.ResultsTableMacros
RETURN - Static variable in interface ij.macro.MacroConstants
reverseNextPreviousOrder - Static variable in class ij.Prefs
  Reverse channel-slice-frame priority used by Next Slice and Previous Slice commands.
revert() - Method in class ij.ImagePlus
  Implements the File/Revert command.
revert() - Method in class ij.plugin.frame.Editor
revertSystem() - Static method in class ij.io.LogStream
  Use this method to revert both `System.out` and `System.err` to their original output streams.
revertSystemErr() - Static method in class ij.io.LogStream
  Use this method to revert`System.err` to the original output stream.
revertSystemOut() - Static method in class ij.io.LogStream
  Use this method to revert`System.out` to the original output stream.
revertToSaved(ImagePlus) - Method in class ij.io.FileOpener
  Restores the original version of the specified image.
rgb - Variable in class ij.gui.HistogramWindow
rgb - Variable in class ij.process.FHT
  Used by the FFT class.
RGB - Static variable in class ij.gui.NewImage
RGB - Static variable in class ij.io.FileInfo
  24-bit interleaved RGB.
RGB_DILATE - Static variable in class ij.process.ColorProcessor
RGB_ERODE - Static variable in class ij.process.ColorProcessor
RGB_FIND_EDGES - Static variable in class ij.process.ColorProcessor
RGB_MAX - Static variable in class ij.process.ColorProcessor
RGB_MEDIAN - Static variable in class ij.process.ColorProcessor
RGB_MIN - Static variable in class ij.process.ColorProcessor
RGB_NOISE - Static variable in class ij.process.ColorProcessor
RGB_PLANAR - Static variable in class ij.io.FileInfo
  24-bit planer RGB.
RGB_RESIZE - Static variable in class ij.process.ColorProcessor
RGB_ROTATE - Static variable in class ij.process.ColorProcessor
RGB_SCALE - Static variable in class ij.process.ColorProcessor
RGB_THRESHOLD - Static variable in class ij.process.ColorProcessor
RGB_TRANSLATE - Static variable in class ij.process.ColorProcessor
RGB48 - Static variable in class ij.io.FileInfo
  48-bit interleaved RGB.
RGB48_PLANAR - Static variable in class ij.io.FileInfo
  48-bit planar RGB.
RGBStackConverter - Class in ij.plugin
  Converts a 2 or 3 slice stack, or a hyperstack, to RGB.
RGBStackConverter() - Constructor for class ij.plugin.RGBStackConverter
RGBStackMerge - Class in ij.plugin
  This plugin implements the Image/Color/Merge Channels command.
RGBStackMerge() - Constructor for class ij.plugin.RGBStackMerge
RGBStackSplitter - Class in ij.plugin.filter
  Deprecated; replaced by ij.plugin.ChannelSplitter.
RGBStackSplitter() - Constructor for class ij.plugin.filter.RGBStackSplitter
RGBtoHSB(int[]) - Method in class ij.process.ColorSpaceConverter
RGBtoHSB(int, int, int) - Method in class ij.process.ColorSpaceConverter
RGBtoLab() - Static method in class ij.plugin.frame.ColorThresholder
  Converts the current image from RGB to CIE L*a*b* and stores the results in the same RGB image R=L*, G=a*, B=b*.
RGBtoLAB(int) - Method in class ij.process.ColorSpaceConverter
RGBtoLAB(int[]) - Method in class ij.process.ColorSpaceConverter
RGBToLab(ImagePlus) - Method in class ij.process.ColorSpaceConverter
  Converts an RGB image into a Lab stack.
RGBtoXYZ(int[]) - Method in class ij.process.ColorSpaceConverter
  Convert RGB to XYZ
RGBtoXYZ(int, int, int) - Method in class ij.process.ColorSpaceConverter
  Convert RGB to XYZ
RGBtoYUV() - Static method in class ij.plugin.frame.ColorThresholder
  Converts the current image from RGB to YUV and stores the results in the same RGB image R=Y, G=U, B=V.
rh - Variable in class ij.process.ImageStatistics
RIGHT - Static variable in class ij.gui.Plot
  Text justification.
RIGHT - Static variable in class ij.gui.TextRoi
RIGHT - Static variable in class ij.io.RoiDecoder
RIGHT_JUSTIFY - Static variable in class ij.process.ImageProcessor
  Right justify text.
RIGHT_MARGIN - Static variable in class ij.gui.Plot
  Deprecated.
  Not a fixed value any more, use getDrawingFrame() to get the drawing area
rLUT1 - Variable in class ij.process.ImageProcessor
rLUT2 - Variable in class ij.process.ImageProcessor
rnd - Static variable in class ij.process.ImageProcessor
RODBARD - Static variable in class ij.measure.Calibration
RODBARD - Static variable in class ij.measure.CurveFitter
  Constants for the built-in fit functions
RODBARD2 - Static variable in class ij.measure.Calibration
RODBARD2 - Static variable in class ij.measure.CurveFitter
  Constants for the built-in fit functions
roi - Variable in class ij.ImagePlus
roi - Variable in class ij.io.FileInfo
Roi - Class in ij.gui
  A rectangular region of interest and superclass for the other ROI classes.
Roi(double, double, double, double) - Constructor for class ij.gui.Roi
  Creates a rectangular ROI using double arguments.
Roi(double, double, double, double, int) - Constructor for class ij.gui.Roi
  Creates a rounded rectangular ROI using double arguments.
Roi(int, int, int, int) - Constructor for class ij.gui.Roi
  Creates a rectangular ROI.
Roi(int, int, int, int, int) - Constructor for class ij.gui.Roi
  Creates a new rounded rectangular ROI.
Roi(int, int, int, int, ImagePlus) - Constructor for class ij.gui.Roi
  Deprecated.
Roi(int, int, ImagePlus) - Constructor for class ij.gui.Roi
  Starts the process of creating a user-defined rectangular Roi, where sx and sy are the starting screen coordinates.
Roi(int, int, ImagePlus, int) - Constructor for class ij.gui.Roi
  Starts the process of creating a user-defined rectangular Roi, where sx and sy are the starting screen coordinates.
Roi(Rectangle) - Constructor for class ij.gui.Roi
  Creates a new rectangular Roi.
Roi(double, double, double, double) - Static method in class ij.IJ
  Creates an Roi.
ROI - Static variable in class ij.io.Opener
ROI - Static variable in interface ij.macro.MacroConstants
ROI - Static variable in class ij.Undo
ROI_HEIGHT - Static variable in class ij.measure.ResultsTable
ROI_MANAGER - Static variable in interface ij.macro.MacroConstants
ROI_MANAGER2 - Static variable in interface ij.macro.MacroConstants
ROI_MASKS - Static variable in class ij.plugin.filter.ParticleAnalyzer
ROI_PROPS_LENGTH - Static variable in class ij.io.RoiDecoder
ROI_PROPS_OFFSET - Static variable in class ij.io.RoiDecoder
ROI_REQUIRED - Static variable in interface ij.plugin.filter.PlugInFilter
  Set this flag if the filter requires an ROI.
ROI_WIDTH - Static variable in class ij.measure.ResultsTable
ROI_X - Static variable in class ij.measure.ResultsTable
ROI_Y - Static variable in class ij.measure.ResultsTable
ROIColor - Static variable in class ij.gui.Roi
ROICOLOR - Static variable in class ij.Prefs
RoiDecoder - Class in ij.io
  This class decodes an ImageJ .roi file.
RoiDecoder(byte[], String) - Constructor for class ij.io.RoiDecoder
  Constructs an RoiDecoder using a byte array.
RoiDecoder(String) - Constructor for class ij.io.RoiDecoder
  Constructs an RoiDecoder using a file path.
RoiDefaultsDialog - Class in ij.gui
  This plugin implements the Edit/Options/Roi Defaults command.
RoiDefaultsDialog() - Constructor for class ij.gui.RoiDefaultsDialog
RoiEncoder - Class in ij.io
  Saves an ROI to a file or stream.
RoiEncoder(OutputStream) - Constructor for class ij.io.RoiEncoder
  Creates an RoiEncoder using the specified OutputStream.
RoiEncoder(String) - Constructor for class ij.io.RoiEncoder
  Creates an RoiEncoder using the specified path.
RoiEnlarger - Class in ij.plugin
  This plugin, which enlarges or shrinks selections, implements the Edit/Selection/Enlarge command.
RoiEnlarger() - Constructor for class ij.plugin.RoiEnlarger
roiHeight - Variable in class ij.process.ImageProcessor
roiHeight - Variable in class ij.process.ImageStatistics
RoiInterpolator - Class in ij.plugin
  This class interpolates between ROIs in the ROI Manager.
RoiInterpolator() - Constructor for class ij.plugin.RoiInterpolator
RoiListener - Interface in ij.gui
  Plugins that implement this interface are notified when an ROI is created, modified or deleted.
RoiManager - Class in ij.plugin.frame
  This plugin implements the Analyze/Tools/ROI Manager command.
RoiManager() - Constructor for class ij.plugin.frame.RoiManager
  Opens the "ROI Manager" window, or activates it if it is already open.
RoiManager(boolean) - Constructor for class ij.plugin.frame.RoiManager
  Constructs an ROI Manager without displaying it.
roiManagerSelect(Roi, boolean) - Method in class ij.gui.ImageCanvas
roiModified(ImagePlus, int) - Method in class ij.gui.HistogramWindow
roiModified(ImagePlus, int) - Method in class ij.gui.PlotWindow
  For live plots, update the plot if the ROI of the source image changes
roiModified(ImagePlus, int) - Method in interface ij.gui.RoiListener
roiModified(ImagePlus, int) - Method in class ij.plugin.EventListener
RoiProperties - Class in ij.gui
  Displays a dialog that allows the user to specify ROI properties such as color and line width.
RoiProperties(String, Roi) - Constructor for class ij.gui.RoiProperties
  Constructs a ColorChooser using the specified title and initial color.
RoiReader - Class in ij.plugin
  Opens ImageJ, NIH Image and Scion Image for windows ROI outlines.
RoiReader() - Constructor for class ij.plugin.RoiReader
RoiRotationTool - Class in ij.plugin.tool
RoiRotationTool() - Constructor for class ij.plugin.tool.RoiRotationTool
RoiRotator - Class in ij.plugin
  This plugin implements the Edit/Selection/Rotate command.
RoiRotator() - Constructor for class ij.plugin.RoiRotator
RoiScaler - Class in ij.plugin
  This plugin implements the Edit/Selection/Scale command.
RoiScaler() - Constructor for class ij.plugin.RoiScaler
roiWidth - Variable in class ij.process.ImageProcessor
roiWidth - Variable in class ij.process.ImageStatistics
RoiWriter - Class in ij.plugin.filter
  Saves the current ROI outline to a file.
RoiWriter() - Constructor for class ij.plugin.filter.RoiWriter
roiX - Variable in class ij.process.ImageProcessor
roiX - Variable in class ij.process.ImageStatistics
roiY - Variable in class ij.process.ImageProcessor
roiY - Variable in class ij.process.ImageStatistics
rollingBallBackground(ImageProcessor, double, boolean, boolean, boolean, boolean, boolean) - Method in class ij.plugin.filter.BackgroundSubtracter
  Create or subtract a background, works for all image types.
rollingBallBrightnessBackground(ColorProcessor, double, boolean, boolean, boolean, boolean, boolean) - Method in class ij.plugin.filter.BackgroundSubtracter
  Create or subtract a background, based on the brightness of an RGB image (keeping the hue of each pixel unchanged)
rotate(double) - Method in class ij.gui.ImageRoi
rotate(double) - Method in class ij.plugin.frame.RoiManager
rotate(double) - Method in class ij.process.ByteProcessor
  Rotates the image or ROI 'angle' degrees clockwise.
rotate(double) - Method in class ij.process.ColorProcessor
  Rotates the image or ROI 'angle' degrees clockwise.
rotate(double) - Method in class ij.process.FloatProcessor
  Rotates the image or ROI 'angle' degrees clockwise.
rotate(double) - Method in class ij.process.ImageProcessor
  Rotates the image or selection 'angle' degrees clockwise.
rotate(double) - Method in class ij.process.ShortProcessor
  Rotates the image or ROI 'angle' degrees clockwise.
rotate(double, double, double) - Method in class ij.gui.Overlay
  Returns a rotated version of this Overlay.
rotate(double, double, double) - Method in class ij.plugin.frame.RoiManager
rotate(Roi, double) - Static method in class ij.plugin.RoiRotator
rotate(Roi, double, double, double) - Static method in class ij.plugin.RoiRotator
ROTATED_RECT - Static variable in class ij.io.RoiDecoder
ROTATED_RECT_ROI - Static variable in class ij.gui.Toolbar
RotatedRectRoi - Class in ij.gui
  This class implements the rotated rectangle selection tool.
RotatedRectRoi(double, double, double, double, double) - Constructor for class ij.gui.RotatedRectRoi
RotatedRectRoi(int, int, ImagePlus) - Constructor for class ij.gui.RotatedRectRoi
rotateLeft() - Method in class ij.process.ImageProcessor
  Rotates the entire image 90 degrees counter-clockwise.
rotateLeft() - Method in class ij.process.StackProcessor
rotateLine(ImagePlus, int) - Method in class ij.plugin.Straightener
rotateRight() - Method in class ij.process.ImageProcessor
  Rotates the entire image 90 degrees clockwise.
rotateRight() - Method in class ij.process.StackProcessor
rotateYZ - Static variable in class ij.Prefs
  Rotate YZ orthogonal views 90 degrees
Rotator - Class in ij.plugin.filter
  This plugin implements the Image/Rotate/Arbitrarily command.
Rotator() - Constructor for class ij.plugin.filter.Rotator
ROUND - Static variable in interface ij.macro.MacroConstants
ROUNDED_RECT_ARC_SIZE - Static variable in class ij.io.RoiDecoder
ROUNDED_RECT_ROI - Static variable in class ij.gui.Toolbar
ROUNDNESS - Static variable in class ij.measure.ResultsTable
rowIndex(int) - Method in class ij.text.TextPanel
  Converts a y coordinate in pixels into a row index.
ROWS_PER_STRIP - Static variable in class ij.io.TiffDecoder
rowsPerStrip - Variable in class ij.io.FileInfo
rt - Variable in class ij.plugin.filter.ParticleAnalyzer
run() - Method in class ij.Executer
run() - Method in class ij.gui.HistogramWindow
run() - Method in class ij.gui.PlotWindow
run() - Method in class ij.gui.StackWindow
run() - Method in class ij.ImageJ
  Quit using a separate thread, hopefully avoiding thread deadlocks.
run() - Method in class ij.macro.MacroRunner
  Used to run the macro code in 'macro' on a separate thread.
run() - Method in class ij.macro.StartupRunner
run() - Method in class ij.measure.ResultsTableMacros
run() - Method in class ij.plugin.BatchProcessor
run() - Method in class ij.plugin.Concatenator
  Displays a dialog requiring user to choose images and returns ImagePlus of concatenated images.
run() - Method in class ij.plugin.DragAndDrop
run() - Method in class ij.plugin.filter.PlugInFilterRunner
  The dispatcher for the background threads
run() - Method in class ij.plugin.frame.ColorThresholder
run() - Method in class ij.plugin.frame.ContrastAdjuster
run() - Method in class ij.plugin.frame.Editor
  Downloads BeanShell or Jython interpreter using a separate thread.
run() - Method in class ij.plugin.frame.LineWidthAdjuster
run() - Method in class ij.plugin.frame.ThresholdAdjuster
run() - Method in class ij.plugin.JavaScriptEvaluator
run() - Method in class ij.plugin.Orthogonal_Views
run() - Method in class ij.plugin.tool.BrushTool
run() - Method in class ij.plugin.tool.OverlayBrushTool
run() - Method in class ij.RecentOpener
  Open the file and move the path to top of the submenu.
run() - Method in class ij.text.TextPanel
  For better performance, open double-clicked files on separate thread instead of on event dispatch thread.
run(boolean) - Method in class ij.macro.StartupRunner
  Runs the RunAtStartup and AutoRun macros, on the current thread if 'batchMode' true, otherwise on a separate thread.
run(int) - Method in class ij.macro.Interpreter
  Runs an existing macro starting at the specified program counter location.
run(ImagePlus) - Method in class ij.plugin.Duplicator
  Returns a copy of the image, stack or hyperstack contained in the specified ImagePlus.
run(ImagePlus) - Static method in class ij.plugin.filter.ThresholdToSelection
  Returns a selection created from the thresholded pixels in the specified image, or null if there are no thresholded pixels.
run(ImagePlus[]) - Static method in class ij.plugin.Concatenator
  Concatenates two or more images, stacks or hyperstacks.
run(ImagePlus[]) - Static method in class ij.plugin.ImagesToStack
  Converts the images in 'images' to a stack, using the default settings ("copy center" and "titles as labels").
run(ImagePlus, int[]) - Static method in class ij.plugin.ChannelArranger
  Changes the order of the channels in a hyperstack.
run(ImagePlus, int, int) - Method in class ij.plugin.Duplicator
  Returns a new stack containing a subrange of the specified stack.
run(ImagePlus, int, int, int, int, int, int) - Method in class ij.plugin.Duplicator
  Returns a new hyperstack containing a possibly reduced version of the input image.
run(ImagePlus, Roi[]) - Method in class ij.process.BinaryInterpolator
run(ImagePlus, ImagePlus) - Static method in class ij.plugin.Concatenator
  Concatenates two images, stacks or hyperstacks.
run(ImagePlus, ImagePlus, ImagePlus) - Static method in class ij.plugin.Concatenator
  Concatenates three images, stacks or hyperstacks.
run(ImagePlus, ImagePlus, ImagePlus, ImagePlus) - Static method in class ij.plugin.Concatenator
  Concatenates four images, stacks or hyperstacks.
run(ImagePlus, ImagePlus, ImagePlus, ImagePlus, ImagePlus) - Static method in class ij.plugin.Concatenator
  Concatenates five images, stacks or hyperstacks.
run(ImagePlus, ImagePlus, String) - Static method in class ij.plugin.ImageCalculator
  Performs arithmetic options on two images and returns the result, where 'operation' ("add","subtract", "multiply","divide", "and", "or", "xor", "min", "max", "average", "difference" or "copy") specifies the operation.
run(ImagePlus, String) - Static method in class ij.plugin.SubstackMaker
  Extracts selected slices from a stack to make a new substack.
run(ImagePlus, String) - Static method in class ij.plugin.ZProjector
  Performs projection on the entire stack using the specified method and returns the result, where 'method' is "avg", "min", "max", "sum", "sd" or "median".
run(ImagePlus, String, int, int) - Static method in class ij.plugin.ZProjector
  Performs projection using the specified method and stack range, and returns the result, where 'method' is "avg", "min", "max", "sum", "sd" or "median".
run(ImagePlus, String, String) - Static method in class ij.IJ
  Runs an ImageJ command using the specified image and options.
run(ImageStack) - Method in class ij.process.BinaryInterpolator
run(Interpreter, String, String) - Static method in class ij.IJ
  The macro interpreter uses this method to run commands.
run(Program) - Method in class ij.macro.Interpreter
  Interprets the specified tokenized macro file starting at location 0.
run(Program, int, String) - Method in class ij.macro.MacroRunner
  Runs a tokenized macro on the current thread.
run(ResultsTable) - Method in class ij.plugin.Distribution
run(ImageProcessor) - Method in class ij.plugin.filter.Analyzer
run(ImageProcessor) - Method in class ij.plugin.filter.AVI_Writer
  Asks for the compression type and filename; then saves as AVI file
run(ImageProcessor) - Method in class ij.plugin.filter.BackgroundSubtracter
  Background for any image type
run(ImageProcessor) - Method in class ij.plugin.filter.Benchmark
run(ImageProcessor) - Method in class ij.plugin.filter.Binary
run(ImageProcessor) - Method in class ij.plugin.filter.Calibrator
run(ImageProcessor) - Method in class ij.plugin.filter.Convolver
run(ImageProcessor) - Method in class ij.plugin.filter.Duplicater
  Deprecated.
run(ImageProcessor) - Method in class ij.plugin.filter.EDM
  Called by the PlugInFilterRunner to process the image or one frame of a stack
run(ImageProcessor) - Method in class ij.plugin.filter.FFTCustomFilter
run(ImageProcessor) - Method in class ij.plugin.filter.FFTFilter
run(ImageProcessor) - Method in class ij.plugin.filter.Filler
run(ImageProcessor) - Method in class ij.plugin.filter.Filters
run(ImageProcessor) - Method in class ij.plugin.filter.FractalBoxCounter
run(ImageProcessor) - Method in class ij.plugin.filter.GaussianBlur
  This method is invoked for each slice during execution
run(ImageProcessor) - Method in class ij.plugin.filter.ImageMath
run(ImageProcessor) - Method in class ij.plugin.filter.ImageProperties
run(ImageProcessor) - Method in class ij.plugin.filter.Info
  Deprecated.
run(ImageProcessor) - Method in class ij.plugin.filter.LineGraphAnalyzer
run(ImageProcessor) - Method in class ij.plugin.filter.LutApplier
run(ImageProcessor) - Method in class ij.plugin.filter.LutViewer
run(ImageProcessor) - Method in class ij.plugin.filter.MaximumFinder
  The plugin is inferred from ImageJ by this method
run(ImageProcessor) - Method in class ij.plugin.filter.ParticleAnalyzer
run(ImageProcessor) - Method in interface ij.plugin.filter.PlugInFilter
  Filters use this method to process the image.
run(ImageProcessor) - Method in class ij.plugin.filter.Printer
run(ImageProcessor) - Method in class ij.plugin.filter.RankFilters
run(ImageProcessor) - Method in class ij.plugin.filter.RGBStackSplitter
run(ImageProcessor) - Method in class ij.plugin.filter.RoiWriter
run(ImageProcessor) - Method in class ij.plugin.filter.Rotator
run(ImageProcessor) - Method in class ij.plugin.filter.SaltAndPepper
run(ImageProcessor) - Method in class ij.plugin.filter.ScaleDialog
run(ImageProcessor) - Method in class ij.plugin.filter.Shadows
run(ImageProcessor) - Method in class ij.plugin.filter.StackLabeler
run(ImageProcessor) - Method in class ij.plugin.filter.ThresholdToSelection
run(ImageProcessor) - Method in class ij.plugin.filter.Transformer
run(ImageProcessor) - Method in class ij.plugin.filter.Translator
run(ImageProcessor) - Method in class ij.plugin.filter.UnsharpMask
  This method is invoked for each slice or color channel.
run(ImageProcessor) - Method in class ij.plugin.filter.Writer
  Deprecated.
run(ImageProcessor) - Method in class ij.plugin.filter.XYWriter
run(String) - Method in class ij.gui.RoiDefaultsDialog
run(String) - Static method in class ij.IJ
  Runs an ImageJ command.
run(String) - Method in class ij.macro.Interpreter
  Interprets the specified string.
run(String) - Method in class ij.macro.MacroRunner
  Runs the specified macro code.
run(String) - Method in class ij.plugin.AboutBox
run(String) - Method in class ij.plugin.Animator
  Set 'arg' to "set" to display a dialog that allows the user to specify the animation speed.
run(String) - Method in class ij.plugin.AppearanceOptions
run(String) - Method in class ij.plugin.ArrowToolOptions
run(String) - Method in class ij.plugin.AVI_Reader
  The plugin is invoked by ImageJ using this method.
run(String) - Method in class ij.plugin.BatchConverter
run(String) - Method in class ij.plugin.BatchMeasure
run(String) - Method in class ij.plugin.BatchProcessor
run(String) - Method in class ij.plugin.Benchmark
run(String) - Method in class ij.plugin.Binner
run(String) - Method in class ij.plugin.BMP_Reader
run(String) - Method in class ij.plugin.BMP_Writer
run(String) - Method in class ij.plugin.BrowserLauncher
  Opens the specified URL (default is the ImageJ home page).
run(String) - Method in class ij.plugin.CalibrationBar
run(String) - Method in class ij.plugin.CanvasResizer
run(String) - Method in class ij.plugin.ChannelArranger
run(String) - Method in class ij.plugin.ChannelSplitter
run(String) - Method in class ij.plugin.CircularRoiMaker
run(String) - Method in class ij.plugin.ClassChecker
run(String) - Method in class ij.plugin.Clipboard
run(String) - Method in class ij.plugin.Colors
run(String) - Method in class ij.plugin.CommandFinder
  Displays the Command Finder dialog.
run(String) - Method in class ij.plugin.CommandLister
run(String) - Method in class ij.plugin.Commands
run(String) - Method in class ij.plugin.Compiler
run(String) - Method in class ij.plugin.CompositeConverter
run(String) - Method in class ij.plugin.Concatenator
  Optional string argument sets the name dialog boxes if called from another plugin.
run(String) - Method in class ij.plugin.ContrastEnhancer
run(String) - Method in class ij.plugin.ControlPanel
  Creates a panel with the hierarchical tree structure of ImageJ's commands.
run(String) - Method in class ij.plugin.Converter
run(String) - Method in class ij.plugin.Coordinates
run(String) - Method in class ij.plugin.DICOM
run(String) - Method in class ij.plugin.Distribution
run(String) - Method in class ij.plugin.DragAndDrop
run(String) - Method in class ij.plugin.Duplicator
run(String) - Method in class ij.plugin.EventListener
run(String) - Method in class ij.plugin.FFT
run(String) - Method in class ij.plugin.FFTMath
run(String) - Method in class ij.plugin.FileInfoVirtualStack
run(String) - Method in class ij.plugin.Filters3D
run(String) - Method in class ij.plugin.FITS_Reader
run(String) - Method in class ij.plugin.FITS_Writer
run(String) - Method in class ij.plugin.FolderOpener
run(String) - Method in class ij.plugin.frame.ContrastAdjuster
run(String) - Method in class ij.plugin.frame.PlugInDialog
run(String) - Method in class ij.plugin.frame.PlugInFrame
run(String) - Method in class ij.plugin.GaussianBlur3D
run(String) - Method in class ij.plugin.GelAnalyzer
run(String) - Method in class ij.plugin.GIF_Reader
run(String) - Method in class ij.plugin.GifWriter
run(String) - Method in class ij.plugin.Grid
run(String) - Method in class ij.plugin.GroupedZProjector
run(String) - Method in class ij.plugin.Histogram
run(String) - Method in class ij.plugin.Hotkeys
run(String) - Method in class ij.plugin.HyperStackConverter
run(String) - Method in class ij.plugin.HyperStackMaker
run(String) - Method in class ij.plugin.HyperStackReducer
run(String) - Method in class ij.plugin.ImageCalculator
run(String) - Method in class ij.plugin.ImageInfo
run(String) - Method in class ij.plugin.ImageJ_Updater
run(String) - Method in class ij.plugin.ImagesToStack
run(String) - Method in class ij.plugin.JavaProperties
run(String) - Method in class ij.plugin.JavaScriptEvaluator
run(String) - Method in class ij.plugin.JpegWriter
run(String) - Method in class ij.plugin.ListVirtualStack
run(String) - Method in class ij.plugin.LUT_Editor
run(String) - Method in class ij.plugin.LutLoader
  If 'arg'="", displays a file open dialog and opens the specified LUT.
run(String) - Method in class ij.plugin.Macro_Runner
  Opens and runs the specified macro file (.txt or .ijm) or script file (.js, .bsh or .py) on the current thread.
run(String) - Method in class ij.plugin.MacroInstaller
run(String) - Method in class ij.plugin.MeasurementsWriter
run(String) - Method in class ij.plugin.Memory
run(String) - Method in class ij.plugin.MontageMaker
run(String) - Method in class ij.plugin.NewPlugin
run(String) - Method in class ij.plugin.NextImageOpener
run(String) - Method in class ij.plugin.Options
run(String) - Method in class ij.plugin.Orthogonal_Views
run(String) - Method in class ij.plugin.OverlayCommands
run(String) - Method in class ij.plugin.OverlayLabels
run(String) - Method in class ij.plugin.PGM_Reader
run(String) - Method in interface ij.plugin.PlugIn
  This method is called when the plugin is loaded.
run(String) - Method in class ij.plugin.PluginInstaller
run(String) - Method in class ij.plugin.PlugInInterpreter
  Run script on separate thread.
run(String) - Method in class ij.plugin.PNG_Writer
run(String) - Method in class ij.plugin.PNM_Writer
run(String) - Method in class ij.plugin.PointToolOptions
run(String) - Method in class ij.plugin.Profiler
run(String) - Method in class ij.plugin.Projector
run(String) - Method in class ij.plugin.ProxySettings
run(String) - Method in class ij.plugin.Raw
run(String) - Method in class ij.plugin.RectToolOptions
run(String) - Method in class ij.plugin.Resizer
run(String) - Method in class ij.plugin.RGBStackConverter
run(String) - Method in class ij.plugin.RGBStackMerge
run(String) - Method in class ij.plugin.RoiEnlarger
run(String) - Method in class ij.plugin.RoiInterpolator
run(String) - Method in class ij.plugin.RoiReader
run(String) - Method in class ij.plugin.RoiRotator
run(String) - Method in class ij.plugin.RoiScaler
run(String) - Method in class ij.plugin.ScaleBar
  This method is called when the plugin is loaded.
run(String) - Method in class ij.plugin.Scaler
run(String) - Method in class ij.plugin.ScreenGrabber
run(String) - Method in class ij.plugin.Selection
run(String) - Method in class ij.plugin.SimpleCommands
run(String) - Method in class ij.plugin.Slicer
run(String) - Method in class ij.plugin.SpecifyROI
run(String) - Method in class ij.plugin.Stack_Statistics
run(String) - Method in class ij.plugin.StackCombiner
run(String) - Method in class ij.plugin.StackEditor
run(String) - Method in class ij.plugin.StackInserter
run(String) - Method in class ij.plugin.StackMaker
run(String) - Method in class ij.plugin.StackPlotter
run(String) - Method in class ij.plugin.StackReducer
run(String) - Method in class ij.plugin.StackReverser
run(String) - Method in class ij.plugin.StackWriter
run(String) - Method in class ij.plugin.Startup
run(String) - Method in class ij.plugin.Straightener
run(String) - Method in class ij.plugin.SubHyperstackMaker
run(String) - Method in class ij.plugin.SubstackMaker
run(String) - Method in class ij.plugin.SurfacePlotter
run(String) - Method in class ij.plugin.Text
run(String) - Method in class ij.plugin.TextFileReader
run(String) - Method in class ij.plugin.TextReader
run(String) - Method in class ij.plugin.TextWriter
run(String) - Method in class ij.plugin.ThreadLister
run(String) - Method in class ij.plugin.Thresholder
run(String) - Method in class ij.plugin.tool.BrushTool
run(String) - Method in class ij.plugin.tool.PlugInTool
run(String) - Method in class ij.plugin.URLOpener
  If 'urlOrName' is a URL, opens the image at that URL.
run(String) - Method in class ij.plugin.WandToolOptions
run(String) - Method in class ij.plugin.WindowOrganizer
run(String) - Method in class ij.plugin.XY_Reader
run(String) - Method in class ij.plugin.XYCoordinates
run(String) - Method in class ij.plugin.ZAxisProfiler
run(String) - Method in class ij.plugin.Zoom
run(String) - Method in class ij.plugin.ZProjector
run(String, ImagePlus, ImagePlus) - Method in class ij.plugin.ImageCalculator
run(String, String) - Static method in class ij.IJ
  Runs an ImageJ command, with options that are passed to the GenericDialog and OpenDialog classes.
run(String, String) - Method in class ij.macro.Interpreter
  Runs the specified macro, passing it a string argument and returning a string value.
run(String, String) - Method in class ij.plugin.JavaScriptEvaluator
run(String, String) - Method in class ij.plugin.PlugInInterpreter
  Run script on current thread.
RUN - Static variable in interface ij.macro.MacroConstants
RUN_BAR - Static variable in class ij.plugin.frame.Editor
RUN_MACRO - Static variable in interface ij.macro.MacroConstants
RUN_TO_CARET - Static variable in interface ij.macro.Debugger
RUN_TO_COMPLETION - Static variable in interface ij.macro.Debugger
run2(ImagePlus, String) - Method in class ij.plugin.ZProjector
runBatchMacro(String, ImagePlus) - Method in class ij.macro.Interpreter
  Runs Process/Batch/ macros.
runBeanShell(String, String) - Static method in class ij.plugin.Macro_Runner
  Runs a BeanShell script on the current thread, passing a string argument, which the script can retrieve using the getArgument() function.
runCommand(ImagePlus, String) - Method in class ij.plugin.frame.RoiManager
  Using the specified image, runs the ROI Manager "Add", "Add invalid input: '&' Draw", "Update", "Delete", "Measure", "Draw", "Show All", "Show None", "Fill", "Deselect", "Select All", "Combine", "AND", "XOR", "Split", "Sort" or "Multi Measure" command.
runCommand(String) - Method in class ij.plugin.CommandFinder
runCommand(String) - Method in class ij.plugin.frame.RoiManager
  Executes the ROI Manager "Add", "Add invalid input: '&' Draw", "Update", "Delete", "Measure", "Draw", "Show All", "Show None", "Fill", "Deselect", "Select All", "Combine", "AND", "XOR", "Split", "Sort" or "Multi Measure" command.
runCommand(String, String) - Method in class ij.plugin.frame.RoiManager
  Executes the ROI Manager "Open", "Save" or "Rename" command.
runCommand(String, String, double) - Method in class ij.plugin.frame.RoiManager
  Adds the current selection to the ROI Manager, using the specified color (a 6 digit hex string) and line width.
runFilterPlugIn(Object, String, String) - Method in class ij.ImageJ
runFromLabel(String) - Method in class ij.macro.FunctionFinder
runJavaScript(String, String) - Method in class ij.plugin.Macro_Runner
  Runs a JavaScript script on the current thread, passing a string argument, which the script can retrieve using the getArgument() function.
runMacro(Program, int, String) - Method in class ij.macro.Interpreter
  Interprets the specified tokenized macro starting at the specified location.
runMacro(String) - Static method in class ij.IJ
  Runs the macro contained in the string `macro` on the current thread.
runMacro(String) - Method in class ij.plugin.MacroInstaller
runMacro(String, Editor) - Method in class ij.plugin.MacroInstaller
runMacro(String, String) - Static method in class ij.IJ
  Runs the macro contained in the string `macro` on the current thread.
runMacro(String, String) - Method in class ij.plugin.Macro_Runner
  Runs the specified macro on the current thread.
runMacroCommand(String) - Static method in class ij.plugin.MacroInstaller
  Runs a command in the Plugins/Macros submenu on the current thread.
runMacroFile(String) - Static method in class ij.IJ
  Runs the specified macro file.
runMacroFile(String, String) - Static method in class ij.IJ
  Runs the specified macro or script file in the current thread.
runMacroFile(String, String) - Method in class ij.plugin.Macro_Runner
  Opens and runs the specified macro or script on the current thread.
runMacroFromIJJar(String, String) - Method in class ij.plugin.Macro_Runner
runMacroFromJar(String, String) - Static method in class ij.plugin.Macro_Runner
  Runs the specified macro from a JAR file in the plugins folder, passing it the specified argument.
runMacroShortcut(String) - Static method in class ij.plugin.MacroInstaller
runMacroTool(String) - Method in class ij.plugin.MacroInstaller
runMacroTool(String) - Method in class ij.plugin.tool.MacroToolRunner
runMacroTool(String) - Method in class ij.plugin.tool.PlugInTool
  These methods are overridden by MacroToolRunner.
runMenuTool(String, String) - Method in class ij.plugin.MacroInstaller
runMenuTool(String, String) - Method in class ij.plugin.tool.MacroToolRunner
runMenuTool(String, String) - Method in class ij.plugin.tool.PlugInTool
running - Variable in class ij.gui.ImageWindow
  This variable is set false if the user presses the escape key or closes the window.
running2 - Variable in class ij.gui.ImageWindow
  This variable is set false if the user clicks in this window, presses the escape key, or closes the window.
runPlugIn(ImagePlus, String, String) - Static method in class ij.IJ
  Runs the specified plugin using the specified image.
runPlugIn(String, String) - Static method in class ij.IJ
  Runs the specified plugin and returns a reference to it.
runPlugIn(String, String, String) - Static method in class ij.IJ
  Runs the specified plugin and returns a reference to it.
runPython(String, String) - Static method in class ij.plugin.Macro_Runner
  Runs a Python script on the current thread, passing a string argument, which the script can retrieve using the getArgument() function.
runShortcut(Program, int, String) - Method in class ij.macro.MacroRunner
  Runs tokenized macro on current thread if pgm.queueCommands is true.
runSocketListener - Static variable in class ij.Prefs
  Run the SocketListener.
runUserPlugIn(String, String, String, boolean) - Method in class ij.ImageJ
rw - Variable in class ij.process.ImageStatistics
rx - Variable in class ij.process.ImageStatistics
ry - Variable in class ij.process.ImageStatistics

## S

s2ints(String) - Method in class ij.plugin.ControlPanel
  Breaks the specified string into an array of ints.
s2ints(String) - Method in class ij.plugin.filter.FractalBoxCounter
  Breaks the specified string into an array of ints.
SaltAndPepper - Class in ij.plugin.filter
  Implements ImageJ's Process/Noise/Salt and Pepper command.
SaltAndPepper() - Constructor for class ij.plugin.filter.SaltAndPepper
SAMPLE_FORMAT - Static variable in class ij.io.TiffDecoder
sampleModel - Variable in class ij.process.ImageProcessor
SAMPLES_PER_PIXEL - Static variable in class ij.io.TiffDecoder
samplesPerPixel - Variable in class ij.io.FileInfo
SansSerif12 - Static variable in class ij.ImageJ
  SansSerif, 12-point, plain font.
SansSerif14 - Static variable in class ij.ImageJ
  SansSerif, 14-point, plain font.
save - Variable in class ij.gui.HistogramWindow
save() - Method in class ij.io.FileSaver
  Resaves the image.
save(Roi, String) - Static method in class ij.io.RoiEncoder
  Saves the specified ROI as a file, returning 'true' if successful.
save(ImagePlus, String) - Static method in class ij.IJ
  Saves the specified image, lookup table or selection to the specified file path.
save(ImagePlus, String) - Static method in class ij.plugin.GifWriter
  Saves the specified image in GIF format or as an animated GIF if the image is a stack.
save(ImagePlus, String, int) - Static method in class ij.plugin.JpegWriter
  Thread-safe method.
save(ImagePlus, String, String) - Static method in class ij.plugin.StackWriter
  Saves the specified image as a sequence of images.
save(PrintWriter) - Method in class ij.text.TextPanel
  Writes all the text in this TextPanel to a file.
save(String) - Static method in class ij.IJ
  Saves the current image, lookup table, selection or text window to the specified file path.
save(String) - Method in class ij.measure.ResultsTable
  Saves this ResultsTable as a tab or comma delimited text file.
save(String) - Method in class ij.plugin.frame.RoiManager
  If one ROI is selected, it is saved as a .roi file, if multiple (or no) ROIs are selected, they are saved as a .zip ROI set.
save(String) - Method in class ij.plugin.MeasurementsWriter
SAVE - Static variable in interface ij.macro.MacroConstants
SAVE_AS - Static variable in interface ij.macro.MacroConstants
SAVE_AS_MENU - Static variable in class ij.Menus
SAVE_SETTINGS - Static variable in interface ij.macro.MacroConstants
saveAndRename(String) - Method in class ij.measure.ResultsTable
saveAs() - Method in class ij.plugin.frame.Editor
saveAs(ImagePlus, String, String) - Static method in class ij.IJ
saveAs(String) - Static method in class ij.Macro
saveAs(String) - Method in class ij.measure.ResultsTable
saveAs(String) - Method in class ij.text.TextPanel
  Saves the text in this TextPanel to a file.
saveAs(String, String) - Static method in class ij.IJ
saveAsBmp() - Method in class ij.io.FileSaver
  Save the image in BMP format using a save file dialog.
saveAsBmp(String) - Method in class ij.io.FileSaver
  Save the image in BMP format using the specified path.
saveAsByteArray(Roi) - Static method in class ij.io.RoiEncoder
  Saves the specified ROI as a byte array.
saveAsFits() - Method in class ij.io.FileSaver
  Save the image in FITS format using a save file dialog.
saveAsFits(String) - Method in class ij.io.FileSaver
  Save the image in FITS format using the specified path.
saveAsGif() - Method in class ij.io.FileSaver
  Save the image in GIF format using a save file dialog.
saveAsGif(String) - Method in class ij.io.FileSaver
  Save the image in Gif format using the specified path.
saveAsJpeg() - Method in class ij.io.FileSaver
  Save the image in JPEG format using a save file dialog.
saveAsJpeg(String) - Method in class ij.io.FileSaver
  Save the image in JPEG format using the specified path.
saveAsLut() - Method in class ij.io.FileSaver
  Save the current LUT using a save file dialog.
saveAsLut(String) - Method in class ij.io.FileSaver
  Save the current LUT using the specified path.
saveAsPgm() - Method in class ij.io.FileSaver
  Saves grayscale images in PGM (portable graymap) format and RGB images in PPM (portable pixmap) format, using a save file dialog.
saveAsPgm(String) - Method in class ij.io.FileSaver
  Saves grayscale images in PGM (portable graymap) format and RGB images in PPM (portable pixmap) format, using the specified path.
saveAsPng() - Method in class ij.io.FileSaver
  Save the image in PNG format using a save file dialog.
saveAsPng(String) - Method in class ij.io.FileSaver
  Save the image in PNG format using the specified path.
saveAsRaw() - Method in class ij.io.FileSaver
  Save the image or stack as raw data using a save file dialog.
saveAsRaw(String) - Method in class ij.io.FileSaver
  Save the image as raw data using the specified path.
saveAsRawStack(String) - Method in class ij.io.FileSaver
  Save the stack as raw data using the specified path.
saveAsText() - Method in class ij.io.FileSaver
  Save the image as tab-delimited text using a save file dialog.
saveAsText(String) - Method in class ij.io.FileSaver
  Save the image as tab-delimited text using the specified path.
saveAsTiff() - Method in class ij.io.FileSaver
  Saves the image or stack in TIFF format using a save file dialog.
saveAsTiff(ImagePlus, String) - Static method in class ij.IJ
  Saves the specified image in TIFF format.
saveAsTiff(String) - Method in class ij.io.FileSaver
  Saves the image in TIFF format using the specified path.
saveAsTiffStack(String) - Method in class ij.io.FileSaver
  Saves the stack as a multi-image TIFF using the specified path.
saveAsZip() - Method in class ij.io.FileSaver
  Uses a save file dialog to save the image or stack as a TIFF in a ZIP archive.
saveAsZip(String) - Method in class ij.io.FileSaver
  Save the image or stack in TIFF/ZIP format using the specified path.
saveBitmap(String, Image, int, int) - Method in class ij.plugin.BMP_Writer
saveChanges(int) - Method in class ij.VirtualStack
  Currently not implemented
SaveChangesDialog - Class in ij.gui
  A modal dialog box with a one line message and "Don't Save", "Cancel" and "Save" buttons.
SaveChangesDialog(Frame, String) - Constructor for class ij.gui.SaveChangesDialog
saveColumnHeaders(boolean) - Method in class ij.measure.ResultsTable
saveCommand() - Static method in class ij.plugin.frame.Recorder
  Writes the current command and options to the Recorder window.
SAVED - Static variable in class ij.ImagePlus
SaveDialog - Class in ij.io
  This class displays a dialog window from which the user can save a file.
SaveDialog(String, String, String) - Constructor for class ij.io.SaveDialog
  Displays a file save dialog with 'title' as the title, 'defaultName' as the initial file name, and 'extension' (e.g.
SaveDialog(String, String, String, String) - Constructor for class ij.io.SaveDialog
  Displays a file save dialog, using the specified default directory and file name and extension.
saveDisplayRangesAndLuts(ImagePlus, FileInfo) - Method in class ij.io.FileSaver
savedPoints - Static variable in class ij.gui.PointRoi
saveGlobals(Program) - Method in class ij.macro.Interpreter
  Saves global variables.
saveGroupNames() - Static method in class ij.gui.Roi
saveImageDescription(byte[], FileInfo) - Method in class ij.io.TiffDecoder
  Save the image description in the specified FileInfo.
saveLocation(String, Point) - Static method in class ij.Prefs
  Saves the Point `loc` in the preferences file as a string using the keyword `key`.
saveMetadata(String, String) - Method in class ij.io.TiffDecoder
saveOutput(boolean) - Static method in class ij.plugin.BatchProcessor
saveOverlay(ImagePlus) - Static method in class ij.Undo
savePlotObjects() - Method in class ij.gui.Plot
  Creates a snapshot of the plot contents (not including axis formats etc), for later undo by restorePlotObjects.
savePlotPlotProperties() - Method in class ij.gui.Plot
  Creates a snapshot of the plot properties (formatting, range etc., not PlotObjects such as data and corresponding curves etc.), for later undo by restorePlotProperties.
savePreferences() - Static method in class ij.Prefs
  Saves user preferences in the IJ_Prefs.txt properties file.
savePreferences(Properties) - Static method in class ij.gui.NewImage
  Called when ImageJ quits.
savePreferences(Properties) - Static method in class ij.gui.PlotWindow
  Called once when ImageJ quits.
savePreferences(Properties) - Method in class ij.ImageJ
  Called once when ImageJ quits.
savePreferences(Properties) - Static method in class ij.io.ImportDialog
  Called once when ImageJ quits.
savePreferences(Properties) - Static method in class ij.Menus
  Called once when ImageJ quits.
savePreferences(Properties) - Static method in class ij.plugin.filter.Analyzer
  Called once when ImageJ quits.
savePreferences(Properties) - Static method in class ij.plugin.filter.ParticleAnalyzer
  Called once when ImageJ quits.
savePrefs(Properties, String) - Static method in class ij.Prefs
savePressed() - Method in class ij.gui.SaveChangesDialog
  Returns true if the user dismissed dialog by pressing "Save".
saveResults(ImageStatistics, Roi) - Method in class ij.plugin.filter.Analyzer
  Saves the measurements specified in the "Set Measurements" dialog, or by calling setMeasurements(), in the default results table.
saveResults(ImageStatistics, Roi) - Method in class ij.plugin.filter.ParticleAnalyzer
  Saves statistics for one particle in a results table.
saveRoi() - Method in class ij.ImagePlus
saveRoi(ImagePlus) - Method in class ij.plugin.filter.RoiWriter
saveString(String, String) - Static method in class ij.IJ
  Saves a string as a file.
saveThreshold(double, double, Calibration) - Method in class ij.process.ImageStatistics
saveXValues - Static variable in class ij.gui.PlotWindow
  Write first X column when listing or saving.
saveXYCoordinates(ImagePlus) - Method in class ij.plugin.filter.XYWriter
scalableLabels() - Method in class ij.gui.Overlay
scale(double, double) - Method in class ij.gui.Overlay
  Returns a scaled version of this Overlay.
scale(double, double) - Method in class ij.process.ByteProcessor
  Scales the image or selection using the specified scale factors.
scale(double, double) - Method in class ij.process.ColorProcessor
  Scales the image or selection using the specified scale factors.
scale(double, double) - Method in class ij.process.FloatProcessor
  Scales the image or selection using the specified scale factors.
scale(double, double) - Method in class ij.process.ImageProcessor
  Scales the image by the specified factors.
scale(double, double) - Method in class ij.process.ShortProcessor
  Scales the image or selection using the specified scale factors.
scale(double, double) - Method in class ij.process.StackProcessor
scale(double, double, boolean) - Method in class ij.plugin.frame.RoiManager
scale(double, double, double) - Method in class ij.process.StackProcessor
scale(Roi, double, double, boolean) - Static method in class ij.plugin.RoiScaler
scale(Component) - Static method in class ij.gui.GUI
  Scales an AWT component according to `Prefs.getGuiScale()`.
scale(JComponent) - Static method in class ij.gui.GUI
  Tries to detect if a Swing component is unscaled and scales it it according to
  invalid reference

      #getGuiScale()

  .
SCALE_LABELS - Static variable in class ij.io.RoiDecoder
SCALE_STROKE_WIDTH - Static variable in class ij.io.RoiDecoder
SCALE_T - Static variable in class ij.plugin.Resizer
scaleAndSetThreshold(double, double, int) - Method in class ij.process.ImageProcessor
  Set the threshold using a 0-255 range.
ScaleBar - Class in ij.plugin
  This plugin implements the Analyze/Tools/Scale Bar command.
ScaleBar() - Constructor for class ij.plugin.ScaleBar
scaled() - Method in class ij.measure.Calibration
  Returns 'true' if this image is spatially calibrated.
ScaleDialog - Class in ij.plugin.filter
  Implements the Analyze/Set Scale command.
ScaleDialog() - Constructor for class ij.plugin.filter.ScaleDialog
scaledOrOffset() - Method in class ij.measure.Calibration
  Returns 'true' if this image is spatially calibrated or has offsets.
scalePopupMenu(PopupMenu) - Static method in class ij.gui.GUI
Scaler - Class in ij.plugin
  This plugin implements the Image/Scale command.
Scaler() - Constructor for class ij.plugin.Scaler
scaleXtoPxl(double) - Method in class ij.gui.Plot
  Converts calibrated coordinates to pixel coordinates.
scaleYtoPxl(double) - Method in class ij.gui.Plot
  Converts calibrated coordinates to pixel coordinates.
SCIENTIFIC_NOTATION - Static variable in interface ij.measure.Measurements
SCREEN_HEIGHT - Static variable in interface ij.macro.MacroConstants
SCREEN_WIDTH - Static variable in interface ij.macro.MacroConstants
ScreenGrabber - Class in ij.plugin
  This plugin implements the Plugins/Utilities/Capture Screen and Plugins/Utilities/Capture Image commands.
ScreenGrabber() - Constructor for class ij.plugin.ScreenGrabber
screenX(int) - Method in class ij.gui.ImageCanvas
  Converts an offscreen x-coordinate to a screen x-coordinate.
screenX(int) - Method in class ij.gui.Roi
screenXD(double) - Method in class ij.gui.ImageCanvas
  Converts a floating-point offscreen x-coordinate to a screen x-coordinate.
screenXD(double) - Method in class ij.gui.Roi
  Converts an image pixel x (offscreen)coordinate to a screen x coordinate, taking the the line or area convention for coordinates into account
screenY(int) - Method in class ij.gui.ImageCanvas
  Converts an offscreen y-coordinate to a screen y-coordinate.
screenY(int) - Method in class ij.gui.Roi
screenYD(double) - Method in class ij.gui.ImageCanvas
  Converts a floating-point offscreen x-coordinate to a screen x-coordinate.
screenYD(double) - Method in class ij.gui.Roi
  Converts an image pixel y (offscreen)coordinate to a screen y coordinate, taking the the line or area convention for coordinates into account
scriptMode() - Static method in class ij.plugin.frame.Recorder
scroll(int, int) - Method in class ij.gui.ImageCanvas
scroll(int, int) - Method in class ij.gui.PlotCanvas
  overrides ImageCanvas.scroll; if plot is not frozen, scrolling modifies the plot data range
ScrollbarWithLabel - Class in ij.gui
  This class, based on Joachim Walter's Image5D package, adds "c", "z" labels and play-pause icons (T) to the stack and hyperstacks dimension sliders.
ScrollbarWithLabel() - Constructor for class ij.gui.ScrollbarWithLabel
ScrollbarWithLabel(StackWindow, int, int, int, int, char) - Constructor for class ij.gui.ScrollbarWithLabel
scrollToTop() - Method in class ij.text.TextPanel
SD_METHOD - Static variable in class ij.plugin.ZProjector
seed - Static variable in class ij.process.ImageProcessor
seek(int) - Method in class ij.io.RandomAccessStream
seek(long) - Method in class ij.io.RandomAccessStream
SEGMENTED - Static variable in class ij.plugin.filter.MaximumFinder
  Output type watershed-segmented image
select(int) - Method in class ij.plugin.frame.RoiManager
  Assigns the ROI at the specified index to the current image.
select(int, boolean, boolean) - Method in class ij.plugin.frame.RoiManager
select(ImagePlus, int) - Method in class ij.plugin.frame.RoiManager
  Assigns the ROI at the specified index to 'imp'.
SELECT - Static variable in interface ij.macro.MacroConstants
SELECT_IMAGE - Static variable in interface ij.macro.MacroConstants
selectable(boolean) - Method in class ij.gui.Overlay
  Set 'false' to prevent ROIs in this overlay from being activated by clicking on their labels or by a long clicking.
selectAll() - Method in class ij.text.TextPanel
  Selects all the lines in this TextPanel.
selectAndMakeVisible(ImagePlus, int) - Method in class ij.plugin.frame.RoiManager
selected() - Method in class ij.plugin.frame.RoiManager
  Returns the count of selected ROIs.
selectGroup(int) - Method in class ij.plugin.frame.RoiManager
  Selects all ROIs of a given group.
selectGroup(String) - Static method in class ij.plugin.frame.RoiManager
  Obsolete; replaced by RoiManager.selectGroup() macro function.
Selection - Class in ij.plugin
  This plugin implements the commands in the Edit/Selection submenu.
Selection() - Constructor for class ij.plugin.Selection
SELECTION_CONTAINS - Static variable in interface ij.macro.MacroConstants
SELECTION_NAME - Static variable in interface ij.macro.MacroConstants
SELECTION_TYPE - Static variable in interface ij.macro.MacroConstants
selectPosition(int, int, int) - Method in class ij.plugin.frame.RoiManager
  Selects all ROIs at the specified position.
selectRow(Roi) - Static method in class ij.measure.ResultsTable
  Selects the row in the "Results" table assocuiated with the specified Roi.
selectWindow(int) - Static method in class ij.IJ
  For IDs less than zero, activates the image with the specified ID.
selectWindow(String) - Static method in class ij.IJ
  Activates the window with the specified title.
sendArguments(String[]) - Static method in class ij.OtherInstance
SEPARATED_BAR - Static variable in class ij.gui.Plot
  Draw a free-standing bar for each point.
separator - Static variable in class ij.Prefs
  file.separator system property
serialize() - Method in class ij.io.FileSaver
  Converts this image to a TIFF encoded array of bytes, which can be decoded using Opener.deserialize().
set(double) - Method in class ij.process.FloatProcessor
set(double) - Method in class ij.process.ImageProcessor
  Assigns 'value' to each pixel in the image or ROI.
set(double) - Method in class ij.process.ShortProcessor
set(int, float) - Method in class ij.util.FloatArray
  Replaces the element at the specified position with the value given.
set(int, int) - Method in class ij.process.ByteProcessor
set(int, int) - Method in class ij.process.ColorProcessor
set(int, int) - Method in class ij.process.FloatProcessor
set(int, int) - Method in class ij.process.ImageProcessor
set(int, int) - Method in class ij.process.ShortProcessor
set(int, int, int) - Method in class ij.process.ByteProcessor
set(int, int, int) - Method in class ij.process.ColorProcessor
set(int, int, int) - Method in class ij.process.FloatProcessor
set(int, int, int) - Method in class ij.process.ImageProcessor
  This is a faster version of putPixel() that does not clip out of range values and does not do bounds checking.
set(int, int, int) - Method in class ij.process.ShortProcessor
set(Roi, int) - Method in class ij.gui.Overlay
  Replaces the ROI at the specified index.
set(ImagePlus, double) - Static method in class ij.plugin.Zoom
set(ImagePlus, double, int, int) - Static method in class ij.plugin.Zoom
set(String, boolean) - Static method in class ij.Prefs
  Saves the value of the boolean `value` in the preferences file using the keyword `key`.
set(String, double) - Static method in class ij.Prefs
  Saves the value of the double `value` in the preferences file using the keyword `key`.
set(String, int) - Static method in class ij.Prefs
  Saves the value of the integer `value` in the preferences file using the keyword `key`.
set(String, String) - Static method in class ij.Prefs
  Saves the value of the string `text` in the preferences file using the keyword `key`.
SET_AUTO_THRESHOLD - Static variable in interface ij.macro.MacroConstants
SET_BACKGROUND - Static variable in interface ij.macro.MacroConstants
SET_BATCH_MODE - Static variable in interface ij.macro.MacroConstants
SET_COLOR - Static variable in interface ij.macro.MacroConstants
SET_FIRST_CHANNEL - Static variable in class ij.process.ImageProcessor
  Composite image projection modes.
SET_FONT - Static variable in interface ij.macro.MacroConstants
SET_FOREGROUND - Static variable in interface ij.macro.MacroConstants
SET_JUSTIFICATION - Static variable in interface ij.macro.MacroConstants
SET_KEY_DOWN - Static variable in interface ij.macro.MacroConstants
SET_LINE_WIDTH - Static variable in interface ij.macro.MacroConstants
SET_LOCATION - Static variable in interface ij.macro.MacroConstants
SET_LUT - Static variable in interface ij.macro.MacroConstants
SET_METADATA - Static variable in interface ij.macro.MacroConstants
SET_MIN_MAX - Static variable in interface ij.macro.MacroConstants
SET_OPTION - Static variable in interface ij.macro.MacroConstants
SET_PASTE_MODE - Static variable in interface ij.macro.MacroConstants
SET_PIXEL - Static variable in interface ij.macro.MacroConstants
SET_RANGE - Static variable in class ij.gui.PlotDialog
  Types of dialog.
SET_RESULT - Static variable in interface ij.macro.MacroConstants
SET_RGB_WEIGHTS - Static variable in interface ij.macro.MacroConstants
SET_SELECTION_LOC - Static variable in interface ij.macro.MacroConstants
SET_SELECTION_NAME - Static variable in interface ij.macro.MacroConstants
SET_SLICE - Static variable in interface ij.macro.MacroConstants
SET_THRESHOLD - Static variable in interface ij.macro.MacroConstants
SET_TOOL - Static variable in interface ij.macro.MacroConstants
SET_VOXEL_SIZE - Static variable in interface ij.macro.MacroConstants
SET_Z_COORDINATE - Static variable in interface ij.macro.MacroConstants
set16bitRange(int) - Static method in class ij.plugin.frame.ContrastAdjuster
setActivated() - Method in class ij.ImagePlus
  Called by ImageWindow.windowActivated(); to end waiting in waitTillActivated.
setActiveChannels(String) - Method in class ij.ImagePlus
  Controls which channels in a composite color image are displayed, where 'channels' is a list of ones and zeros that specify the channels to display.
setAdditionalFunctions(String) - Static method in class ij.macro.Interpreter
  Obsolete; replaced by the #include statement.
setAllPoints(boolean) - Static method in class ij.gui.Wand
  Set 'true' and output will contain intermediate points for straight lines longer than one pixel.
setAngle(double) - Method in class ij.gui.ImageRoi
setAngle(double) - Method in class ij.gui.TextRoi
setAnimate(boolean) - Method in class ij.gui.StackWindow
setAntiAlias(boolean) - Method in class ij.gui.Roi
setAntialiased(boolean) - Method in class ij.gui.TextRoi
  Sets the 'antiAlias' instance variable.
setAntialiased(boolean) - Static method in class ij.text.TextWindow
setAntialiased(Graphics, boolean) - Static method in class ij.util.Java2
setAntialiasedText(boolean) - Method in class ij.gui.Plot
  Determines whether to use antialiased text (default true)
setAntialiasedText(boolean) - Static method in class ij.gui.TextRoi
  Sets the state of the global 'antialiasedText' variable.
setAntialiasedText(boolean) - Method in class ij.process.ImageProcessor
  Specifies whether or not text is drawn using antialiasing, which is enabled by default on macOS or when the font size is 14 or greater.
setAntialiasedText(Graphics, boolean) - Static method in class ij.util.Java2
setAntialiasRendering(boolean) - Method in class ij.ImagePlus
  Enable/disable use of antialiasing by the flatten() method.
setApplyMacroTable(ResultsTable) - Method in class ij.macro.Interpreter
setAsRepeatCommand(String) - Static method in class ij.Executer
setAutoThreshold(int, int) - Method in class ij.process.ImageProcessor
  Automatically sets the lower and upper threshold levels, where 'method' must be ISODATA or ISODATA2 and 'lutUpdate' must be RED_LUT, BLACK_AND_WHITE_LUT, OVER_UNDER_LUT or NO_LUT_UPDATE.
setAutoThreshold(ImagePlus, String) - Static method in class ij.IJ
  Replaced by ImagePlus.setAutoThreshold().
setAutoThreshold(AutoThresholder.Method, boolean) - Method in class ij.process.ImageProcessor
setAutoThreshold(AutoThresholder.Method, boolean, int) - Method in class ij.process.ImageProcessor
setAutoThreshold(String) - Method in class ij.ImagePlus
  Uses the specified method to set the threshold levels of this image.
setAutoThreshold(String) - Method in class ij.process.ImageProcessor
  Automatically sets the lower and upper threshold levels, where 'method' must be "Default", "Huang", "Intermodes", "IsoData", "IJ_IsoData", "Li", "MaxEntropy", "Mean", "MinError", "Minimum", "Moments", "Otsu", "Percentile", "RenyiEntropy", "Shanbhag", "Triangle" or "Yen".
setAutoThreshold(String, boolean, int) - Method in class ij.process.ImageProcessor
setAverageWhenDownsizing(boolean) - Method in class ij.plugin.Resizer
setAxes(boolean, boolean, boolean, boolean, boolean, boolean, int, int) - Method in class ij.gui.Plot
  Sets the properties of the axes.
setAxisLabelFont(int, float) - Method in class ij.gui.Plot
  Sets the x and y label font size and style.
setAxisXLog(boolean) - Method in class ij.gui.Plot
  Sets the X Axis format to Log or Linear.
setAxisYLog(boolean) - Method in class ij.gui.Plot
  Sets the Y Axis format to Log or Linear.
setBackground(String) - Static method in class ij.plugin.Thresholder
setBackgroundColor(int, int, int) - Static method in class ij.IJ
  Sets the background color.
setBackgroundColor(Color) - Method in class ij.gui.Plot
  Set the plot frame background color.
setBackgroundColor(Color) - Static method in class ij.gui.Toolbar
setBackgroundColor(Color) - Static method in class ij.plugin.frame.Recorder
setBackgroundColor(Color) - Method in class ij.process.ByteProcessor
  Sets the background fill/draw color.
setBackgroundColor(Color) - Method in class ij.process.ColorProcessor
  Sets the background fill/draw color.
setBackgroundColor(Color) - Method in class ij.process.FloatProcessor
  Sets the background fill/draw color.
setBackgroundColor(Color) - Method in class ij.process.ImageProcessor
  Sets the background fill/draw color.
setBackgroundColor(Color) - Method in class ij.process.ShortProcessor
  Sets the background fill/draw color.
setBackgroundColor(String) - Method in class ij.gui.Plot
  Set the plot frame background color.
setBackgroundValue(double) - Static method in class ij.gui.Toolbar
  Sets the background color to grayscale, where value is between 0 (black) and 255 (white).
setBackgroundValue(double) - Method in class ij.process.ByteProcessor
  Sets the background fill value, where 0invalid input: '<'=valueinvalid input: '<'=255.
setBackgroundValue(double) - Method in class ij.process.ColorProcessor
  Sets the background fill value, where `value` is interpreted as an RGB int.
setBackgroundValue(double) - Method in class ij.process.FloatProcessor
setBackgroundValue(double) - Method in class ij.process.ImageProcessor
  Sets the background fill value used by the rotate() and scale() methods.
setBackgroundValue(double) - Method in class ij.process.ShortProcessor
setBatchMode(boolean) - Method in class ij.gui.ProgressBar
setBilevelSubractOne(boolean) - Method in class ij.process.AutoThresholder
setBilinearInterpolation(Graphics, boolean) - Static method in class ij.util.Java2
setBinaryThreshold() - Method in class ij.process.ImageProcessor
setBitDepth(int) - Method in class ij.gui.PlotVirtualStack
setBitDepth(int) - Method in class ij.ImageStack
  Sets the bit depth (8=byte, 16=short, 24=RGB, 32=float).
setBitDepth(int) - Method in class ij.VirtualStack
  Sets the bit depth (8, 16, 24 or 32).
setBlackBackground() - Static method in class ij.plugin.frame.Recorder
setBlockIncrement(int) - Method in class ij.gui.ScrollbarWithLabel
setBorderColor(Color) - Method in class ij.ImagePlus
setBounds(Rectangle2D.Double) - Method in class ij.gui.Roi
  Sets the bounds of rectangular, oval or text selections.
setBrightness(FloatProcessor) - Method in class ij.process.ColorProcessor
  Updates the brightness using the pixels in the specified FloatProcessor).
setBrushSize(int) - Static method in class ij.gui.Toolbar
  Set the size of the selection brush tool, in pixels.
setBrushWidth(int) - Static method in class ij.plugin.tool.BrushTool
setBufferSize(int) - Static method in class ij.io.FileSaver
  Sets the BufferedOutputStream buffer size in bytes (default is 32K).
setC(int) - Method in class ij.ImagePlus
  Sets the hyperstack channel position (one based).
setC(ImageWindow, int) - Static method in class ij.plugin.frame.SyncWindows
setCalibration(Calibration) - Method in class ij.ImagePlus
  Sets this image's calibration.
setCalibrationTable(float[]) - Method in class ij.process.ImageProcessor
  Set a lookup table used by getPixelValue(), getLine() and convertToFloat() to calibrate pixel values.
setCancelLabel(String) - Method in class ij.gui.GenericDialog
  Sets a replacement label for the "Cancel" button.
setCaseSensitive(boolean) - Method in class ij.util.WildcardMatch
  Makes pattern matching case insensitive.
setChannel(int, ByteProcessor) - Method in class ij.process.ColorProcessor
  Sets the pixels of one color channel from a ByteProcessor.
setChannelColorModel(IndexColorModel) - Method in class ij.CompositeImage
setChannelLut(LUT) - Method in class ij.CompositeImage
setChannelLut(LUT, int) - Method in class ij.CompositeImage
setChannelsUpdated() - Method in class ij.CompositeImage
  Deprecated
setClipRect(Rectangle) - Method in class ij.process.ImageProcessor
  Updates the clipping rectangle used by lineTo(), drawLine(), drawDot() and drawPixel().
setColor(double) - Method in class ij.process.ImageProcessor
  Sets the default fill/draw value.
setColor(int) - Method in class ij.process.ColorProcessor
  Sets the fill/draw color, where `color` is an RGB int.
setColor(int) - Method in class ij.process.ImageProcessor
  Sets the default fill/draw value.
setColor(Color) - Method in class ij.gui.Plot
  Changes the drawing color for the next objects that will be added to the plot.
setColor(Color) - Method in class ij.gui.PlotWindow
  Deprecated.
  use the corresponding method of the Plot class
setColor(Color) - Static method in class ij.gui.Roi
  Sets the default (global) color used for ROI outlines.
setColor(Color) - Method in class ij.gui.Toolbar
  Deprecated.
  replaced by setForegroundColor()
setColor(Color) - Method in class ij.ImagePlus
  Sets current foreground color.
setColor(Color) - Method in class ij.process.ByteProcessor
  Sets the foreground drawing color.
setColor(Color) - Method in class ij.process.ColorProcessor
  Sets the foreground color.
setColor(Color) - Method in class ij.process.FloatProcessor
  Sets the foreground fill/draw color.
setColor(Color) - Method in class ij.process.ImageProcessor
  Sets the default fill/draw value to the pixel value closest to the specified color.
setColor(Color) - Method in class ij.process.ShortProcessor
  Sets the foreground fill/draw color.
setColor(Color, Color) - Method in class ij.gui.Plot
  Changes the drawing color for the next objects that will be added to the plot.
setColor(String) - Method in class ij.gui.Plot
setColor(String) - Method in class ij.process.ImageProcessor
  Sets the fill/draw color, where 'color' is "white", "black", "blue", etc., or a hex value like "#ff0000".
setColor(String, String) - Method in class ij.gui.Plot
  Sets the drawing colors for the next objects that will be added to the plot.
setColorModel(ColorModel) - Method in class ij.ImageStack
  Assigns a new color model to this stack.
setColorModel(ColorModel) - Method in class ij.process.ColorProcessor
setColorModel(ColorModel) - Method in class ij.process.ImageProcessor
  Sets the color model.
setColorModel(ColorModel) - Method in class ij.process.IntProcessor
setColumn(String, Variable[]) - Method in class ij.measure.ResultsTable
  Implements the Table.setColumn() macro function.
setColumnHeadings(String) - Static method in class ij.IJ
  Clears the "Results" window and sets the column headings to those in the tab-delimited 'headings' String.
setColumnHeadings(String) - Method in class ij.text.TextPanel
  Clears this TextPanel and sets the column headings to those in the tab-delimited 'headings' String.
setCommand(String) - Static method in class ij.plugin.frame.Recorder
  Starts recording a command.
setCommandName(String) - Static method in class ij.ImageJ
setComposite(Composite) - Method in class ij.gui.ImageRoi
  Sets the composite mode.
setCornerDiameter(int) - Method in class ij.gui.Roi
  Sets the rounded rectangle corner diameter (pixels).
setCounter(int) - Method in class ij.gui.PointRoi
setCounterInfo(int[]) - Method in class ij.gui.PointRoi
setCounters(int[]) - Method in class ij.gui.PointRoi
  Sets the counter number and slice number for each point from an array, where the lower 8 bits are the counter number and the higher 24 bits contain the slice position of each point.
setCrossLoc(int, int, int) - Method in class ij.plugin.Orthogonal_Views
setCTable(float[], String) - Method in class ij.measure.Calibration
  Sets the calibration table.
setCurrentFont(Font) - Method in class ij.gui.TextRoi
  Deprecated.
  Replaced by setFont(font)
setCurrentWindow(ImageWindow) - Static method in class ij.WindowManager
  Makes the image contained in the specified window the active image.
setCursor(int, int, int, int) - Method in class ij.gui.ImageCanvas
  Sets the cursor based on the current tool and cursor location.
setCursor(ImagePlus, Roi) - Method in class ij.plugin.frame.SyncWindows
setCursor(Cursor, int) - Static method in class ij.gui.ImageCanvas
  Experimental
setCustomRoi(boolean) - Method in class ij.gui.ImageCanvas
  Allows plugins (e.g., Orthogonal_Views) to create a custom ROI using a display list.
setDeactivated() - Method in class ij.ImagePlus
  Called by `new StackWindow(ImagePlus)` before showing the StackWindow, to prepare for waitTillActivated().
setDebugger(Debugger) - Method in class ij.macro.Interpreter
setDebugMode(boolean) - Static method in class ij.IJ
  Enable/disable debug mode.
setDebugMode(int) - Method in class ij.macro.Interpreter
setDecimalPlaces(int, int) - Method in class ij.measure.ResultsTable
setDefault16bitRange(int) - Static method in class ij.ImagePlus
  Set the default 16-bit display range, where 'bitDepth' must be 0 (auto-scaling), 8 (0-255), 10 (0-1023), 12 (0-4095, 14 (0-16383), 15 (0-32767) or 16 (0-65535).
setDefaultAngle(double) - Static method in class ij.gui.TextRoi
  Sets the default angle.
setDefaultColor(Color) - Static method in class ij.gui.Roi
  Sets the default stroke color.
setDefaultCounter(int) - Static method in class ij.gui.PointRoi
setDefaultCrossColor(Color) - Static method in class ij.gui.PointRoi
  Deprecated
setDefaultDirectory(String) - Static method in class ij.io.DirectoryChooser
  Sets the default directory presented in the dialog.
setDefaultDirectory(String) - Static method in class ij.io.OpenDialog
  Sets the default directory.
setDefaultDirectory(String) - Static method in class ij.plugin.frame.Editor
setDefaultDisplayRange(double, double) - Method in class ij.ImagePlus
setDefaultDoubleHeaded(boolean) - Static method in class ij.gui.Arrow
setDefaultFillColor(Color) - Static method in class ij.gui.Roi
setDefaultFillColor(Color) - Static method in class ij.gui.TextRoi
  Sets the default fill (background) color.
setDefaultFont(Font) - Static method in class ij.gui.TextRoi
  Sets the default font.
setDefaultFontSize(int) - Static method in class ij.gui.PlotWindow
setDefaultFontSize(int) - Static method in class ij.gui.TextRoi
  Sets the default font size.
setDefaultGroup(int) - Static method in class ij.gui.Roi
  Sets the group value assigned to newly created ROIs, and also sets the default ROI color to the group color.
setDefaultHeadings() - Method in class ij.measure.ResultsTable
  Sets the headings used by the Measure command ("Area", "Mean", etc.).
setDefaultHeadings() - Static method in class ij.plugin.filter.Analyzer
  Sets the default headings ("Area", "Mean", etc.).
setDefaultHeadSize(double) - Static method in class ij.gui.Arrow
setDefaultMarkerSize(String) - Static method in class ij.gui.PointRoi
  Deprecated.
setDefaultOutline(boolean) - Static method in class ij.gui.Arrow
setDefaultSize(int) - Static method in class ij.gui.PointRoi
  Sets the default point size, where 'size' is 0-6 (Tiny-XXXL).
setDefaultString(int, String) - Method in class ij.gui.GenericDialog
setDefaultStrokeWidth(double) - Static method in class ij.gui.Roi
  Sets the default stroke width.
setDefaultStyle(int) - Static method in class ij.gui.Arrow
setDefaultType(int) - Static method in class ij.gui.PointRoi
setDefaultWidth(double) - Static method in class ij.gui.Arrow
setDialog(GenericDialog) - Method in class ij.plugin.filter.PlugInFilterRunner
setDimensions(int, int, int) - Method in class ij.ImagePlus
  Sets the 3rd, 4th and 5th dimensions, where `nChannels`*`nSlices`*`nFrames` must be equal to the stack size.
setDirectory(String) - Method in class ij.plugin.FolderOpener
  Used by DragAndDrop when a directory is dragged onto the ImageJ window.
setDisplayList(Roi, Color) - Method in class ij.gui.ImageCanvas
  Deprecated.
  replaced by ImagePlus.setOverlay(Roi, Color, int, Color)
setDisplayList(Shape, Color, BasicStroke) - Method in class ij.gui.ImageCanvas
  Deprecated.
  replaced by ImagePlus.setOverlay(Shape, Color, BasicStroke)
setDisplayList(Vector) - Method in class ij.gui.ImageCanvas
  Deprecated.
  replaced by ImagePlus.setOverlay(ij.gui.Overlay)
setDisplayMode(int) - Method in class ij.ImagePlus
  Sets the display mode of composite color images, where 'mode' should be IJ.COMPOSITE, IJ.COLOR or IJ.GRAYSCALE.
setDisplayRange(double, double) - Method in class ij.CompositeImage
setDisplayRange(double, double) - Method in class ij.ImagePlus
  Sets the display range of the current channel.
setDisplayRange(double, double, int) - Method in class ij.ImagePlus
  Sets the display range of specified channels in an RGB image, where 4=red, 2=green, 1=blue, 6=red+green, etc.
setDoScaling(boolean) - Static method in class ij.process.ImageConverter
  Set true to scale to 0-255 when converting short to byte or float to byte and to 0-65535 when converting float to short.
setDoubleHeaded(boolean) - Method in class ij.gui.Arrow
setDraggable(boolean) - Method in class ij.gui.Overlay
  Set 'false' to prevent ROIs in this overlay from being dragged by their labels.
setDrawingColor(int, int, boolean) - Method in class ij.gui.ImageCanvas
  Sets the foreground drawing color (or background color if 'setBackground' is true) to the color of the pixel at (ox,oy).
setDrawingSize(int, int) - Method in class ij.gui.ImageCanvas
  Obsolete; replaced by setSize()
setDrawOffset(boolean) - Method in class ij.gui.Roi
  Deprecated.
  This method was previously used to draw lines and polylines shifted by 0.5 pixels top the bottom and right, for better agreement with the position used by ProfilePlot, with the default taken from Prefs.subPixelResolution. Now the shift is independent of this setting and only depends on the ROI type (area or line/point ROI).
setDrawStringMode(boolean) - Method in class ij.gui.TextRoi
setEchoChar(char) - Method in class ij.gui.GenericDialog
  Sets the echo character for the next string field.
setEditMode(ImagePlus, boolean) - Method in class ij.plugin.frame.RoiManager
setEditor(Editor) - Method in class ij.macro.MacroRunner
  Use the specified Editor to run the macro in debug mode.
setEscapeChar(char) - Method in class ij.util.WildcardMatch
  Sets the new character to be used as an escape character, overriding the the default of '\'.
setExceptionHandler(IJ.ExceptionHandler) - Static method in class ij.IJ
  Installs a custom exception handler that overrides the handleException() method.
setExtension(String, String) - Static method in class ij.io.SaveDialog
setExtraArrayElements(int) - Method in class ij.measure.Minimizer
  Add a given number of extra elements to array of parameters (independent vaiables) for private use in the user function.
setf(int, float) - Method in class ij.process.ByteProcessor
setf(int, float) - Method in class ij.process.ColorProcessor
setf(int, float) - Method in class ij.process.FloatProcessor
setf(int, float) - Method in class ij.process.ImageProcessor
setf(int, float) - Method in class ij.process.ShortProcessor
setf(int, int, float) - Method in class ij.process.ByteProcessor
setf(int, int, float) - Method in class ij.process.ColorProcessor
setf(int, int, float) - Method in class ij.process.FloatProcessor
setf(int, int, float) - Method in class ij.process.ImageProcessor
  Sets the value of the pixel at (x,y) to 'value'.
setf(int, int, float) - Method in class ij.process.ShortProcessor
setFileInfo(FileInfo) - Method in class ij.ImagePlus
  Saves this image's FileInfo so it can be later retieved using getOriginalFileInfo().
setFileName(String) - Method in class ij.plugin.MacroInstaller
setFilePath(String) - Static method in class ij.plugin.Macro_Runner
setFillColor(Color) - Method in class ij.gui.Overlay
  Sets the fill color of all the ROIs in this overlay.
setFillColor(Color) - Method in class ij.gui.Roi
  Sets the fill color used to display this ROI, or set to null to display it transparently.
setFlattenScale(double) - Method in class ij.gui.Roi
setFloatArray(float[][]) - Method in class ij.process.ImageProcessor
  Replaces the pixel data with contents of the specified 2D float array.
setFocusable(boolean) - Method in class ij.gui.ScrollbarWithLabel
setFont(char, Font) - Method in class ij.gui.Plot
  Sets the font for xLabel ('x'), yLabel('y'), numbers ('f' for 'frame') or the legend ('l')
setFont(int, float) - Method in class ij.gui.Plot
  Sets the font size and style for all following addLabel() etc.
setFont(Font) - Method in class ij.gui.GenericDialog
setFont(Font) - Method in class ij.gui.MultiLineLabel
setFont(Font) - Method in class ij.gui.Plot
  Sets the font for all following addLabel() etc.
setFont(Font) - Method in class ij.gui.TextRoi
  Sets the current font.
setFont(Font) - Method in class ij.plugin.frame.Editor
setFont(Font) - Method in class ij.process.ImageProcessor
  Sets the font used by drawString().
setFont(Font, boolean) - Method in class ij.text.TextPanel
setFont(String, int, int) - Static method in class ij.gui.TextRoi
  Sets the global font face, size and style that will be used by TextROIs interactively created using the text tool.
setFont(String, int, int) - Static method in class ij.text.TextWindow
setFont(String, int, int, boolean) - Static method in class ij.gui.TextRoi
  Sets the font face, size, style and antialiasing mode that will be used by TextROIs interactively created using the text tool.
setFontColor(String) - Static method in class ij.plugin.filter.ParticleAnalyzer
  Sets the color ("blue", "black", etc.) of the font used to label outlines in the next particle analyzer instance.
setFontSize(int) - Method in class ij.gui.Plot
  Sets the font size for all following addLabel() etc.
setFontSize(int) - Method in class ij.gui.TextRoi
  Sets the size of the current font.
setFontSize(int) - Static method in class ij.Menus
  Set the size (in points) used for the fonts in ImageJ menus.
setFontSize(int) - Static method in class ij.plugin.filter.ParticleAnalyzer
  Sets the size of the font used to label outlines in the next particle analyzer instance.
setFontSize(int) - Method in class ij.plugin.MontageMaker
setFontSize(int) - Method in class ij.process.ImageProcessor
  Sets the size of the font used by drawString().
setForegroundColor(int, int, int) - Static method in class ij.IJ
  Sets the foreground color.
setForegroundColor(Color) - Static method in class ij.gui.Toolbar
setForegroundColor(Color) - Static method in class ij.plugin.frame.Recorder
setForegroundValue(double) - Static method in class ij.gui.Toolbar
  Sets the foreground color to grayscale, where value is between 0 (black) and 255 (white).
setFormatFlags(int) - Method in class ij.gui.Plot
  Sets the flags that control the axes format.
setFrameSize(int, int) - Method in class ij.gui.Plot
  Sets the plot frame size in (unscaled) pixels.
setFromFloatArrays(float[][]) - Method in class ij.process.ByteProcessor
setFromFloatProcessors(FloatProcessor[]) - Method in class ij.process.ByteProcessor
setFrozen(boolean) - Method in class ij.gui.Plot
  Freezes or unfreezes the plot.
setFunction(int, double[], String) - Method in class ij.measure.Calibration
  Sets the calibration function, coefficient table and unit (e.g.
setFunction(int, double[], String, boolean) - Method in class ij.measure.Calibration
setFunction(UserFunction, int) - Method in class ij.measure.Minimizer
  Set the the target function, i.e.
setGlobalBackgroundColor() - Method in class ij.process.ImageProcessor
  Sets the global (Color Picker) background color as the fill/draw color.
setGlobalCalibration(Calibration) - Method in class ij.ImagePlus
  Sets the system-wide calibration.
setGlobalForegroundColor() - Method in class ij.process.ImageProcessor
  Sets the global (Color Picker) foreground color as the fill/draw color.
setGlobalJustification(int) - Static method in class ij.gui.TextRoi
  Sets the default text tool justification (LEFT, CENTER or RIGHT).
setGroup(int) - Method in class ij.gui.Roi
  Sets the group of this Roi, and updates stroke color accordingly.
setGroup(int) - Method in class ij.plugin.frame.RoiManager
  Sets the group for the selected ROIs.
setGroup(String) - Static method in class ij.plugin.frame.RoiManager
  Obsolete; replaced by RoiManager.setGroup() macro function.
setGroupName(int, String) - Static method in class ij.gui.Roi
setGroupNames(String) - Static method in class ij.gui.Roi
  Sets the group names from a comma-delimeted string.
setGuiScale(double) - Static method in class ij.Prefs
  Sets the GenericDialog and Command Finder text scale (0.5 to 3.0).
setHandleSize(int) - Method in class ij.gui.Roi
  Sets the current handle size.
setHeading(int, String) - Method in class ij.measure.ResultsTable
  Deprecated.
  Replaced by addValue(String,double) and setValue(String,int,double)
setHeadSize(double) - Method in class ij.gui.Arrow
setHelpLabel(String) - Method in class ij.gui.GenericDialog
  Sets a replacement label for the "Help" button.
setHideLabels(boolean) - Method in class ij.gui.PointRoi
  Deprecated.
setHideOutputImage(boolean) - Method in class ij.plugin.filter.ParticleAnalyzer
  Set 'hideOutputImage' true to not display the "Show:" image.
setHideOverlay(boolean) - Method in class ij.ImagePlus
setHistogramRange(double, double) - Method in class ij.process.ImageProcessor
  Set the range used for histograms of float images.
setHistogramSize(int) - Method in class ij.process.ImageProcessor
  Set the number of bins to be used for histograms of float images.
setHSB(byte[], byte[], byte[]) - Method in class ij.process.ColorProcessor
  Sets the current pixels from 3 byte arrays (hue, saturation and brightness).
setHSB(float[], float[], float[]) - Method in class ij.process.ColorProcessor
  Sets the current pixels from 3 float arrays (hue, saturation and brightness).
setIcon(String, String) - Static method in class ij.gui.Toolbar
  Sets the icon of the specified macro or plugin tool.
  See: Help>Examples>Tool>Animated Icon Tool;
setIgnoreClipRect(boolean) - Method in class ij.gui.Roi
setIgnoreErrors(boolean) - Method in class ij.macro.Interpreter
setIgnoreFlush(boolean) - Method in class ij.ImagePlus
setIgnoreGlobalCalibration(boolean) - Method in class ij.ImagePlus
setIJMenuBar - Variable in class ij.ImagePlus
setIJMenuBar - Static variable in class ij.Prefs
  Set MenuBar on Macs running Java 8.
setIJMenuBar() - Method in class ij.ImagePlus
setIJMenuBar(boolean) - Method in class ij.ImagePlus
setIm5D(boolean) - Method in class ij.plugin.Concatenator
setImage(ImagePlus) - Method in class ij.gui.ImageWindow
setImage(ImagePlus) - Method in class ij.gui.Roi
  Sets the ImagePlus associated with this ROI.
setImage(ImagePlus) - Method in class ij.ImagePlus
  Replaces this image with the specified ImagePlus.
setImage(ImagePlus) - Method in class ij.measure.Calibration
  Disables the density calibation if the specified image has a differenent bit depth.
setImage(ImagePlus) - Method in class ij.plugin.ZProjector
  Explicitly set image to be projected.
setImage(Image) - Method in class ij.ImagePlus
  Replaces the image, if any, with the one specified.
setImageJMenuBar(ImageWindow) - Static method in class ij.gui.ImageWindow
setImagePlus(ImagePlus) - Method in class ij.gui.Plot
  Sets the ImagePlus where the plot will be displayed.
setImagesURL(String) - Static method in class ij.Prefs
  Sets the URL of the directory that contains the ImageJ sample images.
setImageUpdated() - Method in class ij.gui.ImageCanvas
  ImagePlus.updateAndDraw calls this method to force the paint() method to update the image from the ImageProcessor.
setIndexes(int[]) - Method in class ij.VirtualStack
  Sets the table that translates slice numbers of hyperstacks not in default CZT order.
setInitialParameters(double[]) - Method in class ij.measure.CurveFitter
  Sets the initial parameters, which override the default initial parameters.
setInputEvent(InputEvent) - Static method in class ij.IJ
setInsets(int, int, int) - Method in class ij.gui.GenericDialog
  Set the insets (margins), in pixels, that will be used for the next component added to the dialog (except components added to the same row with addToSameRow)
setInstanceColor(Color) - Method in class ij.gui.Roi
  Deprecated.
  replaced by setStrokeColor()
setIntArray(int[][]) - Method in class ij.process.ImageProcessor
  Replaces the pixel data with contents of the specified 2D int array.
setInterpolate(boolean) - Method in class ij.process.ImageProcessor
  This method has been replaced by setInterpolationMethod().
setInterpolationMethod(int) - Method in class ij.process.ImageProcessor
  Use this method to set the interpolation method (NONE, BILINEAR or BICUBIC) used by scale(), resize() and rotate().
setInvertY(boolean) - Method in class ij.measure.Calibration
  Sets the 'invertY' flag.
setIsCalibrationBar(boolean) - Method in class ij.gui.Overlay
setIsCursor(boolean) - Method in class ij.gui.Roi
setIsMacroWindow(boolean) - Method in class ij.plugin.frame.Editor
setIsResultsTable(boolean) - Method in class ij.measure.ResultsTable
setJpegQuality(int) - Static method in class ij.io.FileSaver
  Specifies the image quality (0-100).
setJustification(int) - Method in class ij.gui.Plot
  Sets the justification used by addLabel(), where `justification` is Plot.LEFT, Plot.CENTER or Plot.RIGHT.
setJustification(int) - Method in class ij.gui.TextRoi
  Sets the 'justification' instance variable (LEFT, CENTER or RIGHT)
setJustification(int) - Method in class ij.process.ImageProcessor
  Sets the justification used by drawString(), where `justification` is CENTER_JUSTIFY, RIGHT_JUSTIFY or LEFT_JUSTIFY.
setKeyDown(int) - Static method in class ij.IJ
setKeyUp(int) - Static method in class ij.IJ
setLabel(int, String) - Method in class ij.gui.Plot
  Sets the label for the plot object number 'index' in the sequence they were added.
setLabel(String, int) - Method in class ij.measure.ResultsTable
  Adds a label to the beginning of the specified row, or updates an existing lable, where 0invalid input: '<'=rowinvalid input: '<'size().
setLabelColor(Color) - Method in class ij.gui.Overlay
setLabelFont(Font) - Method in class ij.gui.Overlay
setLabelFont(Font, boolean) - Method in class ij.gui.Overlay
setLabelFontSize(int, String) - Method in class ij.gui.Overlay
  Set the label font size with options.
setLastDirectory(String) - Static method in class ij.io.OpenDialog
  Sets the path to the directory containing the last file opened by the user.
setLastName(String) - Static method in class ij.io.OpenDialog
  Sets the name of the last file opened by the user.
setLegend(String, int) - Method in class ij.gui.Plot
  Adds a legend.
setLimits(double[]) - Method in class ij.gui.Plot
  Sets the current limits from an array xMin, xMax, yMin, yMax The array may be also longer or shorter, but should not contain NaN values.
setLimits(double, double, double, double) - Method in class ij.gui.Plot
  Sets the x-axis and y-axis range.
setLimits(double, double, double, double) - Method in class ij.gui.PlotWindow
  Deprecated.
  use the corresponding method of the Plot class
setLimitsToDefaults(boolean) - Method in class ij.gui.Plot
  Sets the plot range to the initial value determined from minimainvalid input: '&maxima' or given by setLimits.
setLimitsToFit(boolean) - Method in class ij.gui.Plot
  Sets the plot range to encompass all data.
setLine(int, String) - Method in class ij.text.TextPanel
  Replaces the contents of the specified line, where 'index' must be greater than or equal to zero and less than the value returned by getLineCount().
setLineWidth(float) - Method in class ij.gui.Plot
  Changes the line width for the next objects that will be added to the plot.
setLineWidth(int) - Method in class ij.gui.Plot
  Changes the line width for the next objects that will be added to the plot.
setLineWidth(int) - Method in class ij.gui.PlotWindow
  Deprecated.
  use the corresponding method of the Plot class
setLineWidth(int) - Method in class ij.gui.Roi
  Deprecated.
  replaced by setStrokeWidth(int)
setLineWidth(int) - Static method in class ij.plugin.filter.ParticleAnalyzer
  Sets the outline line width for the next ParticleAnalyzer instance.
setLineWidth(int) - Method in class ij.process.ImageProcessor
  Sets the line width used by lineTo() and drawDot().
setLocation(double, double) - Method in class ij.gui.Line
  Sets the x coordinate of the leftmost and y coordinate of the topmost end point
setLocation(double, double) - Method in class ij.gui.PolygonRoi
setLocation(double, double) - Method in class ij.gui.Roi
  Set the location of the ROI in image coordinates.
setLocation(int, int) - Method in class ij.gui.GenericDialog
setLocation(int, int) - Method in class ij.gui.ImageWindow
setLocation(int, int) - Method in class ij.gui.Line
setLocation(int, int) - Method in class ij.gui.Roi
  Set the location of the ROI in image coordinates.
setLocation(int, int) - Method in class ij.gui.TextRoi
setLocationAndSize(int, int, int, int) - Method in class ij.gui.ImageWindow
  Moves and resizes this window.
setLogScaleX() - Method in class ij.gui.Plot
  Sets log scale in x.
setLogScaleY() - Method in class ij.gui.Plot
setLongClickDelay(int) - Static method in class ij.gui.ImageCanvas
  Sets the context menu long click delay in milliseconds (default is 1000).
setLongClickDelay(int) - Static method in class ij.gui.Toolbar
  Sets the tool menu long click delay in milliseconds (default is 600).
setLookAndFeel(LookAndFeel) - Static method in class ij.util.Java2
  Sets the Swing look and feel.
setLoopBackAndForth(boolean) - Static method in class ij.measure.Calibration
  Set the default state of the animation "Loop back and forth" flag
setLut(LUT) - Method in class ij.ImagePlus
  Assigns a LUT (lookup table) to this image.
setLut(LUT) - Method in class ij.process.ImageProcessor
setLutAnimation(boolean) - Method in class ij.process.FloatProcessor
setLutAnimation(boolean) - Method in class ij.process.ImageProcessor
  For 16 and 32 bit processors, set 'lutAnimation' true to have createImage() use the cached 8-bit version of the image.
setLutAnimation(boolean) - Method in class ij.process.ShortProcessor
setLuts(LUT[]) - Method in class ij.CompositeImage
setMagnification(double) - Method in class ij.gui.ImageCanvas
setMagnification(double) - Method in class ij.gui.PlotCanvas
  The image of a PlotCanvas is always shown at 100% magnification unless the plot is frozen
setMask(ImageProcessor) - Method in class ij.process.ImageProcessor
  Defines a byte mask that limits processing to an irregular ROI.
setMaxError(double) - Method in class ij.measure.CurveFitter
  Set the maximum error.
setMaxError(double) - Method in class ij.measure.Minimizer
  Sets the accuracy of convergence.
setMaxError(double, double) - Method in class ij.measure.Minimizer
  Sets the accuracy of convergence.
setMaximum(int) - Method in class ij.gui.ScrollbarWithLabel
setMaximumThreads(int) - Method in class ij.measure.Minimizer
  Call setMaximuThreads(1) to avoid multi-threaded execution (in case the user-provided target function does not allow moultithreading).
setMaxIntervals(int) - Method in class ij.gui.Plot
  Sets the maximum number of intervals in a plot.
setMaxIterations(int) - Method in class ij.measure.CurveFitter
  Set maximum number of iterations allowed (sum of iteration count for all restarts)
setMaxIterations(int) - Method in class ij.measure.Minimizer
  Set maximum number of iterations allowed (including all restarts and all threads).
setMaxRestarts(int) - Method in class ij.measure.Minimizer
  Set maximum number of minimization restarts to do.
setMeasurement(int, boolean) - Static method in class ij.plugin.filter.Analyzer
  Sets the specified system-wide measurement option.
setMeasurements(int) - Static method in class ij.plugin.filter.Analyzer
  Sets the system-wide measurement options.
setMenuBarCount - Static variable in class ij.Menus
setMenuBarTime - Static variable in class ij.gui.ImageWindow
setMethod(int) - Method in class ij.plugin.ZProjector
setMethod(String) - Static method in class ij.plugin.frame.ThresholdAdjuster
  Sets the thresholding method ("Default", "Huang", etc).
setMethod(String) - Static method in class ij.plugin.Thresholder
setMinAndMax(double, double) - Static method in class ij.gui.ProfilePlot
  Sets the y-axis min and max.
setMinAndMax(double, double) - Static method in class ij.IJ
  Sets the display range (minimum and maximum displayed pixel values) of the current image.
setMinAndMax(double, double) - Method in class ij.process.ByteProcessor
  Maps the entries in this image's LUT from min-max to 0-255.
setMinAndMax(double, double) - Method in class ij.process.ColorProcessor
  Uses a table look-up to map the pixels in this image from min-max to 0-255.
setMinAndMax(double, double) - Method in class ij.process.FloatProcessor
  Sets the min and max variables that control how real pixel values are mapped to 0-255 screen values.
setMinAndMax(double, double) - Method in class ij.process.ImageProcessor
  This image will be displayed by mapping pixel values in the range min-max to screen values in the range 0-255.
setMinAndMax(double, double) - Method in class ij.process.ShortProcessor
  Sets the min and max variables that control how real pixel values are mapped to 0-255 screen values.
setMinAndMax(double, double, int) - Static method in class ij.IJ
  Sets the minimum and maximum displayed pixel values on the specified RGB channels, where 4=red, 2=green and 1=blue.
setMinAndMax(double, double, int) - Method in class ij.process.ColorProcessor
setMinAndMax(double, double, int) - Method in class ij.process.IntProcessor
setMinAndMax(ImagePlus, double, double) - Static method in class ij.IJ
  Sets the display range (minimum and maximum displayed pixel values) of the specified image.
setMinimum(int) - Method in class ij.gui.ScrollbarWithLabel
setMinorTickLength(int) - Method in class ij.gui.Plot
  Sets the length of the minor tick in pixels.
setMode(int) - Method in class ij.CompositeImage
setMode(String) - Static method in class ij.plugin.frame.ThresholdAdjuster
  Sets the current mode ("Red","Binvalid input: '&W'" or"Over/Under").
setMonospaced(boolean) - Static method in class ij.text.TextWindow
setName(String) - Method in class ij.gui.Roi
  Sets the name of this ROI.
setNaNEmptyCells(boolean) - Method in class ij.measure.ResultsTable
  Set 'true' to initially fill data arrays with NaNs instead of zeros.
setNextLocation(int, int) - Static method in class ij.gui.ImageWindow
  Causes the next image to be displayed at the specified location.
setNextLocation(int, int) - Static method in class ij.gui.WaitForUserDialog
  Display the next WaitForUser dialog at the specified location.
setNextLocation(Point) - Static method in class ij.gui.ImageWindow
  Causes the next image to be displayed at the specified location.
setNonScalable(boolean) - Method in class ij.gui.Roi
  Set 'nonScalable' true to have TextRois in a display list drawn at a fixed location and size.
setNormalize(boolean) - Method in class ij.plugin.ContrastEnhancer
setNormalize(boolean) - Method in class ij.plugin.filter.Convolver
  If 'normalize' is true (the default), the convolve(), convolveFloat() and convolveFloat1D() (4 argument version) methods divide each kernel coefficient by the sum of the coefficients, preserving image brightness.
setNPasses(int) - Method in class ij.plugin.filter.BackgroundSubtracter
setNPasses(int) - Method in class ij.plugin.filter.Binary
setNPasses(int) - Method in class ij.plugin.filter.Convolver
setNPasses(int) - Method in class ij.plugin.filter.EDM
  Prepare the progress bar.
setNPasses(int) - Method in interface ij.plugin.filter.ExtendedPlugInFilter
  This method is called by ImageJ to inform the plugin-filter about the passes to its run method.
setNPasses(int) - Method in class ij.plugin.filter.GaussianBlur
  Set the number of passes of the blur1Direction method.
setNPasses(int) - Method in class ij.plugin.filter.ImageMath
setNPasses(int) - Method in class ij.plugin.filter.MaximumFinder
  Set his to the number of images to process (for the watershed progress bar only).
setNPasses(int) - Method in class ij.plugin.filter.RankFilters
  This method is called by ImageJ to set the number of calls to run(ip) corresponding to 100% of the progress bar.
setNPasses(int) - Method in class ij.plugin.filter.Rotator
setNPasses(int) - Method in class ij.plugin.filter.StackLabeler
setNPasses(int) - Method in class ij.plugin.filter.Translator
setNPasses(int) - Method in class ij.plugin.filter.UnsharpMask
  Since most computing time is spent in GaussianBlur, forward the information about the number of passes to Gaussian Blur.
setOffsetMultiplySlopeParams(int, int, int) - Method in class ij.measure.CurveFitter
  For improved fitting performance when using a custom fit formula, one may specify parameters that can be calculated directly by linear regression.
setOKLabel(String) - Method in class ij.gui.GenericDialog
  Sets a replacement label for the "OK" button.
setOpacity(double) - Method in class ij.gui.ImageRoi
  Sets the composite mode using the specified opacity (alpha), in the range 0.0-1.0, where 0.0 is fully transparent and 1.0 is fully opaque.
setOpenAsHyperStack(boolean) - Method in class ij.ImagePlus
setOpenUsingPlugins(boolean) - Static method in class ij.io.Opener
  Open all images using HandleExtraFileTypes.
setOption(String, boolean) - Static method in class ij.plugin.filter.Analyzer
setOptions(String) - Method in class ij.gui.Plot
  Sets options for the plot.
setOptions(String) - Method in class ij.gui.PointRoi
setOptions(String) - Method in class ij.ImageStack
setOptions(String) - Static method in class ij.Macro
  Define a set of Macro options for the current Thread.
setOptions(Thread, String) - Static method in class ij.Macro
  Define a set of Macro options for a Thread.
setOutline(boolean) - Method in class ij.gui.Arrow
setOutputType(int) - Static method in class ij.plugin.filter.EDM
  Sets the output type (BYTE_OVERWRITE, BYTE, SHORT or FLOAT)
setOverColor(int, int, int) - Static method in class ij.process.ImageProcessor
  Sets the upper Over/Under threshold color.
setOverlay(Overlay) - Method in class ij.gui.ImageCanvas
  Use ImagePlus.setOverlay(ij.gui.Overlay).
setOverlay(Overlay) - Method in class ij.ImagePlus
  Installs a list of ROIs that will be drawn on this image as a non-destructive overlay.
setOverlay(Overlay) - Method in class ij.plugin.frame.RoiManager
setOverlay(Overlay) - Method in class ij.process.ImageProcessor
  This method is used to display virtual stack overlays.
setOverlay(Roi, Color, int, Color) - Method in class ij.ImagePlus
  Creates an Overlay from the specified ROI, and assigns it to this image.
setOverlay(Shape, Color, BasicStroke) - Method in class ij.ImagePlus
  Creates an Overlay from the specified Shape, Color and BasicStroke, and assigns it to this image.
setPaintPending(boolean) - Method in class ij.gui.ImageCanvas
setParamResolutions(double[]) - Method in class ij.measure.Minimizer
  Set the resolution of the parameters, for problems where the target function is not smooth but suffers from numerical noise.
setPasteMode(int) - Static method in class ij.gui.Roi
  Sets the Paste transfer mode.
setPasteMode(String) - Static method in class ij.IJ
  Sets the transfer mode used by the Edit/Paste command, where mode is "Copy", "Blend", "Average", "Difference", "Transparent", "Transparent2", "AND", "OR", "XOR", "Add", "Subtract", "Multiply", or "Divide".
setPixels(int, FloatProcessor) - Method in class ij.process.ByteProcessor
  Sets the pixels from a FloatProcessor, no scaling.
setPixels(int, FloatProcessor) - Method in class ij.process.ColorProcessor
  Sets the pixels of one color channel from a FloatProcessor.
setPixels(int, FloatProcessor) - Method in class ij.process.FloatProcessor
  Sets the pixels, and mininvalid input: '&max' values from a FloatProcessor.
setPixels(int, FloatProcessor) - Method in class ij.process.ImageProcessor
  Sets the pixels (of one color channel for RGB images) from a FloatProcessor.
setPixels(int, FloatProcessor) - Method in class ij.process.ShortProcessor
  Sets the pixels from a FloatProcessor, no scaling.
setPixels(Object) - Method in class ij.process.ByteProcessor
setPixels(Object) - Method in class ij.process.ColorProcessor
setPixels(Object) - Method in class ij.process.FloatProcessor
setPixels(Object) - Method in class ij.process.ImageProcessor
  Sets a new pixel array for the image.
setPixels(Object) - Method in class ij.process.ShortProcessor
setPixels(Object, int) - Method in class ij.gui.PlotVirtualStack
setPixels(Object, int) - Method in class ij.ImageStack
  Assigns a pixel array to the specified slice, where 1<=n<=nslices.
setPixels(Object, int) - Method in class ij.VirtualStack
  Assigns a pixel array to the specified slice, where 1<=n<=nslices.
setPlot(Plot) - Method in class ij.gui.PlotCanvas
  Tells the PlotCanvas which plot to use for zooming etc.
setPlot(Plot) - Method in class ij.gui.PlotWindow
  Sets the Plot object shown in this PlotWindow.
setPlot(Plot) - Method in class ij.ImagePlus
setPlotMaker(PlotMaker) - Method in class ij.gui.Plot
setPlotObjectLabel(int, String) - Method in class ij.gui.Plot
  Set the label the i-th PlotObject (in the sequence how they were added, including hidden ones) PlotObjects here refers to curves, arrows, labels etc.
setPlotObjectStyle(int, String) - Method in class ij.gui.Plot
setPointType(int) - Method in class ij.gui.PointRoi
  Sets the point type (0=hybrid, 1=cross, 2=dot, 3=circle).
setPolygon(float[], float[], int, double, double) - Method in class ij.process.PolygonFiller
  Specifies the polygon to be filled in case of float coordinates.
setPolygon(int[], int[], int) - Method in class ij.process.PolygonFiller
  Specifies the polygon to be filled.
setPosition(int) - Method in class ij.gui.Roi
  Sets the stack position (image number) of this ROI.
setPosition(int) - Method in class ij.ImagePlus
  Set the current hyperstack position based on the stack index 'n' (one-based).
setPosition(int) - Method in class ij.plugin.frame.RoiManager
  Sets the position of the selected ROIs.
setPosition(int, int, int) - Method in class ij.gui.Roi
  Sets the hyperstack position of this ROI.
setPosition(int, int, int) - Method in class ij.gui.StackWindow
setPosition(int, int, int) - Method in class ij.ImagePlus
  Sets the current hyperstack position and updates the display, where 'channel', 'slice' and 'frame' are one-based indexes.
setPosition(int, int, int) - Method in class ij.plugin.frame.RoiManager
  Sets the c,z,t position of the selected ROIs.
setPosition(ImagePlus) - Method in class ij.gui.Roi
  Sets the position of this ROI based on the stack position of the specified image.
setPositionWithoutUpdate(int, int, int) - Method in class ij.ImagePlus
  Sets the current hyperstack position without updating the display, where 'channel', 'slice' and 'frame' are one-based indexes.
setPrecision(int) - Method in class ij.measure.ResultsTable
  Sets the decimal places (digits to the right of decimal point) that are used when this table is displayed.
setPrecision(int) - Static method in class ij.plugin.filter.Analyzer
  Sets the number of digits displayed to the right of decimal point.
setPreviousMinMax() - Method in class ij.gui.Plot
  reverts plot range to previous values and updates the image
setPreviousRoi(Roi) - Static method in class ij.gui.Roi
  Saves 'roi' so it can be restored later using Edit/Selection/Restore Selection.
setPreviousTextRoi(Roi) - Method in class ij.gui.TextRoi
setProcessor(ImageProcessor) - Method in class ij.gui.ImageRoi
setProcessor(ImageProcessor) - Method in class ij.ImagePlus
  Replaces the ImageProcessor with the one specified and updates the display.
setProcessor(ImageProcessor, int) - Method in class ij.ImageStack
  Assigns the pixel array of an ImageProcessor to the specified slice, where 1<=n<=nslices.
setProcessor(String, ImageProcessor) - Method in class ij.ImagePlus
  Replaces the ImageProcessor with the one specified and updates the display.
setProcessStack(boolean) - Method in class ij.plugin.ContrastEnhancer
setProgressBar(ProgressBar) - Method in class ij.process.ImageProcessor
  Assigns a progress bar to this processor.
setProp(String, double) - Method in class ij.ImagePlus
  Saves a persistent numeric propery.
setProp(String, String) - Method in class ij.ImagePlus
  Adds a key-value pair to this image's string properties.
setProperties(String) - Method in class ij.gui.Roi
setProperties(String[]) - Method in class ij.ImagePlus
  Creates a set of image properties from an array of strings.
setProperty(String, Object) - Static method in class ij.IJ
  Adds a key-value pair to IJ.properties.
setProperty(String, Object) - Method in class ij.ImagePlus
  Adds a key-value pair to this image's properties.
setProperty(String, String) - Method in class ij.gui.Roi
setPrototypeOverlay(Overlay) - Method in class ij.gui.Roi
setQuality(int) - Static method in class ij.plugin.JpegWriter
setRandomSeed(double) - Static method in class ij.process.ImageProcessor
setRandomSeed(int) - Method in class ij.measure.Minimizer
  Set a seed to initialize the random number generator, which is used for initialization of the simplex.
setRawThreshold(ImagePlus, double, double) - Static method in class ij.IJ
  This is a version of setThreshold() that uses raw (uncalibrated) values in the range 0-255 for 8-bit images and 0-65535 for 16-bit images and the "Red" LUT display mode.
setRawThreshold(ImagePlus, double, double, String) - Static method in class ij.IJ
  This is a version of setThreshold() that always uses raw (uncalibrated) values in the range 0-255 for 8-bit images and 0-65535 for 16-bit images.
setRedirectImage(ImagePlus) - Static method in class ij.plugin.filter.Analyzer
  Set the "Redirect To" image.
setRejectMacrosMsg(String) - Method in class ij.plugin.frame.Editor
setRenderingHint(Graphics2D) - Method in class ij.gui.Roi
setRestarts(int) - Method in class ij.measure.CurveFitter
  Set maximum number of simplex restarts to do.
setResultsTable(ResultsTable) - Static method in class ij.plugin.filter.Analyzer
setResultsTable(ResultsTable) - Static method in class ij.plugin.filter.ParticleAnalyzer
  Sets the ResultsTable to be used by the next ParticleAnalyzer instance.
setResultsTable(ResultsTable) - Method in class ij.text.TextPanel
  Sets the ResultsTable associated with this TextPanel.
setRGB(byte[], byte[], byte[]) - Method in class ij.process.ColorProcessor
  Sets the current pixels from 3 byte arrays (reg, green, blue).
setRGBWeights(double[]) - Method in class ij.process.ColorProcessor
  This is a thread-safe (non-static) version of setWeightingFactors().
setRGBWeights(double, double, double) - Method in class ij.process.ColorProcessor
  This is a thread-safe (non-static) version of setWeightingFactors().
setRoi(int, int, int, int) - Method in class ij.ImagePlus
  Creates a rectangular selection.
setRoi(int, int, int, int) - Method in class ij.process.ImageProcessor
  Defines a rectangular region of interest and sets the mask to null if this ROI is not the same size as the previous one.
setRoi(Roi) - Method in class ij.ImagePlus
  Assigns the specified ROI to this image and displays it.
setRoi(Roi) - Method in class ij.process.ImageProcessor
  Defines a non-rectangular region of interest that will consist of a rectangular ROI and a mask.
setRoi(Roi, boolean) - Method in class ij.ImagePlus
  Assigns 'newRoi' to this image and displays it if 'updateDisplay' is true.
setRoi(Roi, int) - Method in class ij.plugin.frame.RoiManager
  Replaces the ROI at the specified index.
setRoi(Polygon) - Method in class ij.process.ImageProcessor
  Defines a polygonal region of interest that will consist of a rectangular ROI and a mask.
setRoi(Rectangle) - Method in class ij.ImagePlus
  Creates a rectangular selection.
setRoi(Rectangle) - Method in class ij.ImageStack
setRoi(Rectangle) - Method in class ij.process.ImageProcessor
  Defines a rectangular region of interest and sets the mask to null if this ROI is not the same size as the previous one.
setRoiManager(RoiManager) - Static method in class ij.plugin.filter.ParticleAnalyzer
  Sets the RoiManager to be used by the next ParticleAnalyzer instance.
setRotationCenter(double, double) - Method in class ij.gui.Roi
setRoundRectArcSize(int) - Method in class ij.gui.Roi
  Obsolete; replaced by setCornerDiameter().
setRoundRectArcSize(int) - Static method in class ij.gui.Toolbar
  Sets the rounded rectangle corner diameter (pixels).
setScale(float) - Method in class ij.gui.Plot
  Sets the scale.
setScaleToFit(boolean) - Method in class ij.gui.ImageCanvas
setScaleWhenConverting(boolean) - Method in class ij.plugin.RGBStackMerge
setSelectedIndexes(int[]) - Method in class ij.plugin.frame.RoiManager
  Selects multiple ROIs, where 'indexes' is an array of integers, each greater than or equal to 0 and less than the value returned by getCount().
setSelection(int, int) - Method in class ij.text.TextPanel
  Creates a selection and insures it is visible.
setShowAllColor(Color) - Static method in class ij.gui.ImageCanvas
  Obsolete
setShowAllList(Overlay) - Method in class ij.gui.ImageCanvas
setShowAllROIs(boolean) - Method in class ij.gui.ImageCanvas
  Obsolete
setShowConflictMessage(boolean) - Static method in class ij.io.FileOpener
setShowCursorStatus(boolean) - Method in class ij.gui.ImageCanvas
  Called by IJ.showStatus() to prevent status bar text from being overwritten until the cursor moves at least 12 pixels.
setShowLabels(boolean) - Method in class ij.gui.PointRoi
setShowProgress(boolean) - Method in class ij.process.FHT
  Enables/disables display of the progress bar during transforms.
setSigned16BitCalibration() - Method in class ij.measure.Calibration
  Sets up a calibration function that subtracts 32,768 from pixel values.
setSilentMode(boolean) - Method in class ij.io.Opener
  The "Opening: path" status message is not displayed in silent mode.
setSize(int) - Method in class ij.gui.PointRoi
  Sets the point size, where 'size' is 0-6 (Tiny-XXXL).
setSize(int) - Method in class ij.util.ArrayUtil
setSize(int, int) - Method in class ij.gui.ImageCanvas
setSize(int, int) - Method in class ij.gui.Plot
  Sets the canvas size in (unscaled) pixels and sets the scale to 1.0.
setSlice(int) - Static method in class ij.IJ
  Switches to the specified stack slice, where 1invalid input: '<'='slice'invalid input: '<'=stack-size.
setSlice(int) - Method in class ij.ImagePlus
  Displays the specified stack image, where 1<=n<=stackSize.
setSliceLabel(String, int) - Method in class ij.ImageStack
  Sets the label of the specified slice, where 1<=n<=nslices.
setSliceLabel(String, int) - Method in class ij.VirtualStack
  Does nothing.
setSliceNumber(int) - Method in class ij.process.ImageProcessor
  ImagePlus.setStack(n), ImageStack.getProcessor(n), VirtualStack.getProcessor(n) and the PlugInFilterRunner set the stack position using this method.
setSliceWithoutUpdate(int) - Method in class ij.ImagePlus
  Displays the specified stack image (1<=n<=stackSize) without updating the display.
setSliderHeight(int) - Method in class ij.gui.ImageWindow
setSlidersEnabled(boolean) - Method in class ij.gui.StackWindow
  Enables or disables the sliders.
setSmartRecording(boolean) - Method in class ij.gui.GenericDialog
  Unchanged parameters are not recorder in 'smart recording' mode.
setSnapshotCopyMode(boolean) - Method in class ij.process.ImageProcessor
  The getPixelsCopy() method returns a reference to the snapshot buffer if it is not null and 'snapshotCopyMode' is true.
setSnapshotPixels(Object) - Method in class ij.process.ByteProcessor
setSnapshotPixels(Object) - Method in class ij.process.ColorProcessor
setSnapshotPixels(Object) - Method in class ij.process.FloatProcessor
setSnapshotPixels(Object) - Method in class ij.process.ImageProcessor
  Sets a new pixel array for the snapshot (undo) buffer.
setSnapshotPixels(Object) - Method in class ij.process.ShortProcessor
setSourceRect(Rectangle) - Method in class ij.gui.ImageCanvas
  Sets the region of the image (in pixels) to be displayed.
setSourceRect(Rectangle) - Method in class ij.gui.PlotCanvas
  Scrolling a PlotCanvas is updating the plot, not viewing part of the plot, unless the plot is frozen
setStack(ImageStack) - Method in class ij.ImagePlus
  Replaces the image with the specified stack and updates the display.
setStack(ImageStack, int, int, int) - Method in class ij.ImagePlus
setStack(String, ImageStack) - Method in class ij.ImagePlus
  Replaces the image with the specified stack and updates the display.
setStart(int, int) - Static method in class ij.plugin.WandToolOptions
setStartSlice(int) - Method in class ij.plugin.ZProjector
setStatusAndEsc(String, boolean) - Method in class ij.measure.CurveFitter
  Create output on the number of iterations in the ImageJ Status line, e.g.
setStatusAndEsc(String, boolean) - Method in class ij.measure.Minimizer
  Create output on the number of iterations in the ImageJ Status line, e.g.
setStopSlice(int) - Method in class ij.plugin.ZProjector
setStroke(BasicStroke) - Method in class ij.gui.Roi
  Sets the Stroke used to draw this ROI.
setStrokeColor(Color) - Method in class ij.gui.Overlay
  Sets the stroke color of all the ROIs in this overlay.
setStrokeColor(Color) - Method in class ij.gui.Roi
  Sets the color used by this ROI to draw its outline.
setStrokeWidth(double) - Method in class ij.gui.Roi
  This is a version of setStrokeWidth() that accepts a double argument.
setStrokeWidth(float) - Method in class ij.gui.Line
setStrokeWidth(float) - Method in class ij.gui.Roi
  Sets the width of the line used to draw this ROI.
setStrokeWidth(Double) - Method in class ij.gui.Overlay
  Sets the stroke width of all the ROIs in this overlay.
setStyle(int) - Method in class ij.gui.Arrow
setStyle(int, String) - Method in class ij.gui.Plot
  Sets the style of the specified PlotObject (curve, label, etc.) from a comma-delimited string ("color1,color2,lineWidth[,symbol][,hidden]"), where "color2" can be "none" and "symbol" and "hidden" are optional.
setStyle(String) - Method in class ij.gui.Arrow
setSummaryTable(ResultsTable) - Static method in class ij.plugin.filter.ParticleAnalyzer
  Sets the ResultsTable to be used by the next ParticleAnalyzer instance for the summary.
setSystemLookAndFeel() - Static method in class ij.util.Java2
  Sets the Swing look and feel to the system look and feel (Windows only).
setT(int) - Method in class ij.ImagePlus
  Sets the hyperstack frame position (one based).
setT(ImageWindow, int) - Static method in class ij.plugin.frame.SyncWindows
setTempCurrentImage(ImagePlus) - Static method in class ij.WindowManager
  Makes the specified image temporarily the active image for this thread.
setTempCurrentImage(Thread, ImagePlus) - Static method in class ij.WindowManager
  Sets a temporary image for the specified thread.
setTemporary() - Method in class ij.ImagePlus
setText(String) - Method in class ij.gui.MultiLineLabel
setText(String) - Method in class ij.gui.TextRoi
setTextPanel(TextPanel) - Static method in class ij.IJ
  TextWindow calls this method with a null argument when the "Results" window is closed.
setThreads(int) - Static method in class ij.Prefs
  Sets the number of threads (1-32) used by PlugInFilters to process stacks.
setThreshold(double, double) - Static method in class ij.IJ
  Sets the lower and upper threshold levels and displays the image using red to highlight thresholded pixels.
setThreshold(double, double) - Method in class ij.process.ImageProcessor
  Sets the lower and upper threshold levels using NO_LUT_UPDATE.
setThreshold(double, double, int) - Method in class ij.process.ByteProcessor
setThreshold(double, double, int) - Method in class ij.process.FloatProcessor
setThreshold(double, double, int) - Method in class ij.process.ImageProcessor
  Sets the lower and upper threshold levels.
setThreshold(double, double, int) - Method in class ij.process.ShortProcessor
setThreshold(double, double, String) - Static method in class ij.IJ
  Sets the lower and upper threshold levels and displays the image using the specified `displayMode` ("Red", "Black invalid input: '&' White", "Over/Under" or "No Update").
setThreshold(ImagePlus, double, double) - Static method in class ij.IJ
  Sets the lower and upper threshold levels of the specified image.
setThreshold(ImagePlus, double, double, String) - Static method in class ij.IJ
  Sets the lower and upper threshold levels of the specified image and updates the display using the specified `displayMode` ("Red", "Black invalid input: '&' White", "Over/Under" or "No Update").
setTickLength(int) - Method in class ij.gui.Plot
  Sets the length of the major tick in pixels.
setTimeUnit(String) - Method in class ij.measure.Calibration
  Sets the time unit (e.g.
setTitle(String) - Method in class ij.ImagePlus
  Sets the image name.
setTitle(String) - Method in class ij.text.TextPanel
setTool(int) - Method in class ij.gui.Toolbar
setTool(int) - Static method in class ij.IJ
  Switches to the specified tool, where id = Toolbar.RECTANGLE (0), Toolbar.OVAL (1), etc.
setTool(String) - Method in class ij.gui.Toolbar
setTool(String) - Static method in class ij.IJ
  Switches to the specified tool, where 'name' is "rect", "elliptical", "brush", etc.
setTransparentColor(Color) - Method in interface ij.process.Blitter
  Sets the transparent color used in the COPY_TRANSPARENT mode (default is Color.white).
setTransparentColor(Color) - Method in class ij.process.ByteBlitter
setTransparentColor(Color) - Method in class ij.process.ColorBlitter
setTransparentColor(Color) - Method in class ij.process.FloatBlitter
setTransparentColor(Color) - Method in class ij.process.ShortBlitter
setTransparentIndex(int) - Static method in class ij.Prefs
  Sets the transparent index (0-255), or set to -1 to disable transparency.
setType(int) - Method in class ij.ImagePlus
setTypeToColor256() - Method in class ij.ImagePlus
setUnderColor(int, int, int) - Static method in class ij.process.ImageProcessor
  Set the lower Over/Under thresholding color.
setUnit(String) - Method in class ij.measure.Calibration
  Sets the default length unit (e.g.
setUnitIncrement(int) - Method in class ij.gui.ScrollbarWithLabel
setUnsavedMeasurements(boolean) - Static method in class ij.plugin.filter.Analyzer
setUnscalableStrokeWidth(double) - Method in class ij.gui.Roi
  Sets the width of the line used to draw this ROI and prevents the width from increasing when the image is zoomed.
setup() - Method in class ij.gui.GenericDialog
setup() - Method in class ij.gui.HistogramWindow
setup(int, ImagePlus) - Static method in class ij.Undo
setup(String, ImagePlus) - Method in class ij.plugin.filter.Analyzer
setup(String, ImagePlus) - Method in class ij.plugin.filter.AVI_Writer
setup(String, ImagePlus) - Method in class ij.plugin.filter.BackgroundSubtracter
setup(String, ImagePlus) - Method in class ij.plugin.filter.Benchmark
setup(String, ImagePlus) - Method in class ij.plugin.filter.Binary
setup(String, ImagePlus) - Method in class ij.plugin.filter.Calibrator
setup(String, ImagePlus) - Method in class ij.plugin.filter.Convolver
setup(String, ImagePlus) - Method in class ij.plugin.filter.Duplicater
  Deprecated.
setup(String, ImagePlus) - Method in class ij.plugin.filter.EDM
  Prepare for processing; also called at the very end with argument 'final' to show any newly created output image.
setup(String, ImagePlus) - Method in class ij.plugin.filter.FFTCustomFilter
setup(String, ImagePlus) - Method in class ij.plugin.filter.FFTFilter
setup(String, ImagePlus) - Method in class ij.plugin.filter.Filler
setup(String, ImagePlus) - Method in class ij.plugin.filter.Filters
setup(String, ImagePlus) - Method in class ij.plugin.filter.FractalBoxCounter
setup(String, ImagePlus) - Method in class ij.plugin.filter.GaussianBlur
  Method to return types supported
setup(String, ImagePlus) - Method in class ij.plugin.filter.ImageMath
setup(String, ImagePlus) - Method in class ij.plugin.filter.ImageProperties
setup(String, ImagePlus) - Method in class ij.plugin.filter.Info
  Deprecated.
setup(String, ImagePlus) - Method in class ij.plugin.filter.LineGraphAnalyzer
setup(String, ImagePlus) - Method in class ij.plugin.filter.LutApplier
setup(String, ImagePlus) - Method in class ij.plugin.filter.LutViewer
setup(String, ImagePlus) - Method in class ij.plugin.filter.MaximumFinder
  Method to return types supported
setup(String, ImagePlus) - Method in class ij.plugin.filter.ParticleAnalyzer
setup(String, ImagePlus) - Method in interface ij.plugin.filter.PlugInFilter
  This method is called once when the filter is loaded.
setup(String, ImagePlus) - Method in class ij.plugin.filter.Printer
setup(String, ImagePlus) - Method in class ij.plugin.filter.RankFilters
  Setup of the PlugInFilter.
setup(String, ImagePlus) - Method in class ij.plugin.filter.RGBStackSplitter
setup(String, ImagePlus) - Method in class ij.plugin.filter.RoiWriter
setup(String, ImagePlus) - Method in class ij.plugin.filter.Rotator
setup(String, ImagePlus) - Method in class ij.plugin.filter.SaltAndPepper
setup(String, ImagePlus) - Method in class ij.plugin.filter.ScaleDialog
setup(String, ImagePlus) - Method in class ij.plugin.filter.Shadows
setup(String, ImagePlus) - Method in class ij.plugin.filter.StackLabeler
setup(String, ImagePlus) - Method in class ij.plugin.filter.ThresholdToSelection
setup(String, ImagePlus) - Method in class ij.plugin.filter.Transformer
setup(String, ImagePlus) - Method in class ij.plugin.filter.Translator
setup(String, ImagePlus) - Method in class ij.plugin.filter.UnsharpMask
  Method to return types supported
setup(String, ImagePlus) - Method in class ij.plugin.filter.Writer
  Deprecated.
setup(String, ImagePlus) - Method in class ij.plugin.filter.XYWriter
SETUP_UNDO - Static variable in interface ij.macro.MacroConstants
setupDialog(ImagePlus, int) - Static method in class ij.IJ
  Displays a "Process all images?" dialog.
setupScroll(int, int) - Method in class ij.gui.ImageCanvas
setupScroll(int, int) - Method in class ij.gui.PlotCanvas
  overrides ImageCanvas.setupScroll; if plot is not frozen, scrolling modifies the plot data range
setUseBicubic(boolean) - Static method in class ij.process.ImageProcessor
setUseStackHistogram(boolean) - Method in class ij.plugin.ContrastEnhancer
setValue(double) - Method in class ij.process.ByteProcessor
  Sets the default fill/draw value, where 0invalid input: '<'=valueinvalid input: '<'=255.
setValue(double) - Method in class ij.process.ColorProcessor
  Sets the default fill/draw value, where `value` is interpreted as an RGB int.
setValue(double) - Method in class ij.process.FloatProcessor
  Sets the default fill/draw value.
setValue(double) - Method in class ij.process.ImageProcessor
  Sets the default fill/draw value.
setValue(double) - Method in class ij.process.ShortProcessor
  Sets the default fill/draw value, where 0invalid input: '<'=valueinvalid input: '<'=65535).
setValue(int) - Method in class ij.gui.ScrollbarWithLabel
setValue(int, int, double) - Method in class ij.measure.ResultsTable
  Sets the value of the given column and row, where where 0<=column<=(lastRow+1 and 0<=row<=size().
setValue(int, int, String) - Method in class ij.measure.ResultsTable
  Sets the string value of the given column and row, where where 0<=column<=(lastRow+1 and 0<=row<=size().
setValue(String, int, double) - Method in class ij.measure.ResultsTable
  Sets the value of the given column and row, where where 0<=row<size().
setValue(String, int, String) - Method in class ij.measure.ResultsTable
  Sets the string value of the given column and row, where where 0<=row<size().
setValues(String, double[]) - Method in class ij.measure.ResultsTable
  Sets the values of the given column to the values in the array.
setValueUnit(String) - Method in class ij.measure.Calibration
  Sets the value unit.
setVariable(String, double) - Method in class ij.macro.Interpreter
setVariable(String, String) - Method in class ij.macro.Interpreter
setVirtual(boolean) - Method in class ij.plugin.AVI_Reader
  Open as virtual stack?
setVisibleAmount(int) - Method in class ij.gui.ScrollbarWithLabel
setVoxel(int, int, int, double) - Method in class ij.ImageStack
setVoxels(int, int, int, int, int, int, float[]) - Method in class ij.ImageStack
  Experimental
setVoxels(int, int, int, int, int, int, float[], int) - Method in class ij.ImageStack
  Experimental
setWeightingFactors(double, double, double) - Static method in class ij.process.ColorProcessor
  Sets the weighting factors used by getPixelValue(), getHistogram() and convertToByte() to do color conversions.
setWeights(double[]) - Method in class ij.measure.CurveFitter
  Sets weights of the data points.
setWidth(double) - Static method in class ij.plugin.tool.OverlayBrushTool
setWidth(int) - Static method in class ij.gui.Line
  Sets the default line width.
setWildcardChars(char, char) - Method in class ij.util.WildcardMatch
  Sets new characters to be used as wildcard characters, overriding the the default of '?' for any single character match and '*' for any amount of characters, including 0 characters.
setWindow(ImageWindow) - Method in class ij.ImagePlus
  This method should only be called from an ImageWindow.
setWindow(Frame) - Static method in class ij.WindowManager
  The specified frame becomes the front window, the one returnd by getFrontWindow().
setWindow(Window) - Static method in class ij.WindowManager
  The specified Window becomes the front window.
setWindowSize(int, int) - Method in class ij.gui.Plot
  Sets the plot window size in pixels.
setXLabelFont(Font) - Method in class ij.gui.Plot
  Sets the xLabelFont; must not be null.
setXMinorTicks(boolean) - Method in class ij.gui.Plot
  Sets whether to show minor ticks on the x axis (if linear).
setXTicks(boolean) - Method in class ij.gui.Plot
  Sets whether to show major ticks at the x axis.
setXUnit(String) - Method in class ij.measure.Calibration
  Sets the X length unit.
setXYLabels(String, String) - Method in class ij.gui.Plot
  Sets the labels of the x and y axes.
setYLabelFont(Font) - Method in class ij.gui.Plot
  Sets the yLabelFont; must not be null.
setYMinorTicks(boolean) - Method in class ij.gui.Plot
  Sets whether to show minor ticks on the y axis (if linear).
setYTicks(boolean) - Method in class ij.gui.Plot
  Sets whether to show major ticks at the y axis.
setYUnit(String) - Method in class ij.measure.Calibration
  Sets the Y length unit.
setZ(int) - Method in class ij.ImagePlus
  Sets the hyperstack slice position (one based).
setZ(ImageWindow, int) - Static method in class ij.plugin.frame.SyncWindows
setZeroTransparent(boolean) - Method in class ij.gui.ImageRoi
setZUnit(String) - Method in class ij.measure.Calibration
  Sets the Z length unit.
Shadows - Class in ij.plugin.filter
  Implements the commands in the Process/Shadows submenu.
Shadows() - Constructor for class ij.plugin.filter.Shadows
Shanbhag - Enum constant in enum class ij.process.AutoThresholder.Method
Shanbhag(int[]) - Static method in class ij.process.AutoThresholder
SHAPE_DESCRIPTORS - Static variable in interface ij.measure.Measurements
SHAPE_ROI_SIZE - Static variable in class ij.io.RoiDecoder
ShapeRoi - Class in ij.gui
  A subclass of `ij.gui.Roi` (2D Regions Of Interest) implemented in terms of java.awt.Shape.
ShapeRoi(float[]) - Constructor for class ij.gui.ShapeRoi
  Constructs a ShapeRoi from an array of variable length path segments.
ShapeRoi(int, int, Shape) - Constructor for class ij.gui.ShapeRoi
  Constructs a ShapeRoi from a Shape.
ShapeRoi(Roi) - Constructor for class ij.gui.ShapeRoi
  Constructs a ShapeRoi from an Roi.
ShapeRoi(Shape) - Constructor for class ij.gui.ShapeRoi
  Constructs a ShapeRoi from a Shape.
shapeToRoi() - Method in class ij.gui.ShapeRoi
  Attempts to convert this ShapeRoi into a single non-composite Roi.
sharpen() - Method in class ij.process.ImageProcessor
  Sharpens the image or ROI using a 3x3 convolution kernel.
sharpenFloat(FloatProcessor, double, float) - Method in class ij.plugin.filter.UnsharpMask
  Unsharp Mask filtering of a float image.
SHIFT_LEFT - Static variable in interface ij.macro.MacroConstants
SHIFT_RIGHT - Static variable in interface ij.macro.MacroConstants
shiftKeyDown() - Static method in class ij.IJ
  Returns true if the shift key is down.
SHORT - Static variable in class ij.plugin.filter.EDM
  Output type: new 16-bit image
ShortBlitter - Class in ij.process
  This class does bit blitting of 16-bit images.
ShortBlitter(ShortProcessor) - Constructor for class ij.process.ShortBlitter
  Constructs a ShortBlitter from a ShortProcessor.
SHORTCUT_IN_USE - Static variable in class ij.Menus
shortcutInUse(String) - Static method in class ij.Menus
  Returns 'true' if this keyboard shortcut is in use.
SHORTCUTS_MENU - Static variable in class ij.Menus
ShortProcessor - Class in ij.process
  ShortProcessors contain a 16-bit unsigned image and methods that operate on that image.
ShortProcessor(int, int) - Constructor for class ij.process.ShortProcessor
  Creates a blank ShortProcessor using the default grayscale LUT that displays zero as black.
ShortProcessor(int, int, boolean) - Constructor for class ij.process.ShortProcessor
  Obsolete.
ShortProcessor(int, int, short[], ColorModel) - Constructor for class ij.process.ShortProcessor
  Creates a new ShortProcessor using the specified pixel array and ColorModel.
ShortProcessor(int, int, short[], ColorModel, boolean) - Constructor for class ij.process.ShortProcessor
  Deprecated.
  16 bit images are normally unsigned but signed images can be simulated by subtracting 32768 and using a calibration function to restore the original values.
ShortProcessor(BufferedImage) - Constructor for class ij.process.ShortProcessor
  Creates a ShortProcessor from a TYPE_USHORT_GRAY BufferedImage.
ShortStatistics - Class in ij.process
  16-bit image statistics, including histogram.
ShortStatistics(ImageProcessor) - Constructor for class ij.process.ShortStatistics
  Construct an ImageStatistics object from a ShortProcessor using the standard measurement options (area, mean, mode, min and max).
ShortStatistics(ImageProcessor, int, Calibration) - Constructor for class ij.process.ShortStatistics
  Constructs a ShortStatistics object from a ShortProcessor using the specified measurement options.
show() - Method in class ij.gui.HistogramPlot
show() - Method in class ij.gui.Plot
  Displays the plot in a PlotWindow.
show() - Method in class ij.gui.WaitForUserDialog
show() - Method in class ij.ImagePlus
  Opens a window to display this image and clears the status bar.
show(double) - Method in class ij.gui.ProgressBar
  Updates the progress bar, where abs(progress) should run from 0 to 1.
show(double, boolean) - Method in class ij.gui.ProgressBar
  Updates the progress bar, where abs(progress) should run from 0 to 1.
show(int, int) - Method in class ij.gui.ProgressBar
  Updates the progress bar, where the length of the bar is set to (`(abs(currentIndex)+1)/abs(finalIndex)` of the maximum bar length.
show(String) - Method in class ij.ImagePlus
  Opens a window to display this image and displays 'statusMessage' in the status bar.
show(String) - Method in class ij.measure.ResultsTable
  Displays the contents of this ResultsTable in a window with the specified title, or updates an existing results window.
SHOW_ALL_COLOR - Static variable in class ij.Prefs
SHOW_LABELS - Static variable in class ij.io.RoiDecoder
SHOW_MASKS - Static variable in class ij.plugin.filter.ParticleAnalyzer
  Display image containing binary masks of measured particles.
SHOW_MESSAGE - Static variable in interface ij.macro.MacroConstants
SHOW_MESSAGE_WITH_CANCEL - Static variable in interface ij.macro.MacroConstants
SHOW_NONE - Static variable in class ij.plugin.filter.ParticleAnalyzer
  Do not display particle outline image.
SHOW_OUTLINES - Static variable in class ij.plugin.filter.ParticleAnalyzer
  Display image containing outlines of measured particles.
SHOW_OVERLAY_MASKS - Static variable in class ij.plugin.filter.ParticleAnalyzer
  Display filled particle as an overlay.
SHOW_OVERLAY_OUTLINES - Static variable in class ij.plugin.filter.ParticleAnalyzer
  Display particle outlines as an overlay.
SHOW_PROGRESS - Static variable in interface ij.macro.MacroConstants
SHOW_PROGRESS - Static variable in class ij.plugin.filter.ParticleAnalyzer
  Display a progress bar.
SHOW_RESULTS - Static variable in class ij.plugin.filter.ParticleAnalyzer
  Display results in the ImageJ console.
SHOW_ROI_MASKS - Static variable in class ij.plugin.filter.ParticleAnalyzer
  Display image containing grayscales masks that identify measured particles.
SHOW_STATUS - Static variable in interface ij.macro.MacroConstants
SHOW_SUMMARY - Static variable in class ij.plugin.filter.ParticleAnalyzer
  Obsolete, replaced by DISPLAY_SUMMARY
SHOW_TEXT - Static variable in interface ij.macro.MacroConstants
showAllPoints - Static variable in class ij.Prefs
  Ignore stack positions when displaying points.
showAllSliceOnly - Static variable in class ij.Prefs
  Only show ROIs associated with current slice in Roi Manager "Show All" mode.
showArrayInspector(int) - Method in class ij.macro.Interpreter
  Shows array elements after clicking an array variable in Debug window N.
showCell(int, String) - Method in class ij.text.TextPanel
  Updates the scroll bars so that the specified cell is visible.
showCode(String, String) - Static method in class ij.gui.Toolbar
showCompositeAdvisory(ImagePlus, String) - Static method in class ij.gui.GUI
showDialog() - Method in class ij.gui.GenericDialog
  Displays this dialog box.
showDialog() - Method in class ij.gui.NonBlockingGenericDialog
showDialog() - Method in class ij.gui.RoiProperties
  Displays the dialog box and returns 'false' if the user cancels it.
showDialog() - Method in class ij.plugin.Compiler
showDialog() - Method in class ij.plugin.FFTMath
showDialog() - Method in class ij.plugin.filter.ParticleAnalyzer
  Displays a modal options dialog.
showDialog() - Method in class ij.plugin.NewPlugin
showDialog() - Method in class ij.plugin.OverlayLabels
showDialog() - Method in class ij.plugin.RoiScaler
showDialog(double) - Method in class ij.plugin.RoiRotator
showDialog(ImagePlus) - Method in class ij.plugin.filter.Calibrator
showDialog(ImagePlus, double) - Method in class ij.plugin.RoiEnlarger
showDialog(ImagePlus, String, PlugInFilterRunner) - Method in class ij.plugin.filter.BackgroundSubtracter
showDialog(ImagePlus, String, PlugInFilterRunner) - Method in class ij.plugin.filter.Binary
showDialog(ImagePlus, String, PlugInFilterRunner) - Method in class ij.plugin.filter.Convolver
showDialog(ImagePlus, String, PlugInFilterRunner) - Method in class ij.plugin.filter.EDM
  Called by the PlugInFilterRunner after setup.
showDialog(ImagePlus, String, PlugInFilterRunner) - Method in interface ij.plugin.filter.ExtendedPlugInFilter
  This method is called after `setup(arg, imp)` unless the `DONE` flag has been set.
showDialog(ImagePlus, String, PlugInFilterRunner) - Method in class ij.plugin.filter.GaussianBlur
  Ask the user for the parameters
showDialog(ImagePlus, String, PlugInFilterRunner) - Method in class ij.plugin.filter.ImageMath
showDialog(ImagePlus, String, PlugInFilterRunner) - Method in class ij.plugin.filter.MaximumFinder
showDialog(ImagePlus, String, PlugInFilterRunner) - Method in class ij.plugin.filter.RankFilters
showDialog(ImagePlus, String, PlugInFilterRunner) - Method in class ij.plugin.filter.Rotator
showDialog(ImagePlus, String, PlugInFilterRunner) - Method in class ij.plugin.filter.StackLabeler
showDialog(ImagePlus, String, PlugInFilterRunner) - Method in class ij.plugin.filter.Translator
showDialog(ImagePlus, String, PlugInFilterRunner) - Method in class ij.plugin.filter.UnsharpMask
  Ask the user for the parameters
showDialog(ImageStack) - Method in class ij.plugin.StackReducer
showDialog(Frame) - Method in class ij.gui.PlotContentsDialog
  Shows the dialog, with a given parent Frame (may be null)
showDialog(Frame) - Method in class ij.gui.PlotDialog
  Asks the user for axis scaling; then replot with new scale on the same ImageProcessor.
showHistogram(ImagePlus, int) - Method in class ij.gui.HistogramWindow
  Draws the histogram using the specified title and number of bins.
showHistogram(ImagePlus, int, double, double) - Method in class ij.gui.HistogramWindow
  Draws the histogram using the specified title, number of bins and histogram range.
showHistogram(ImagePlus, ImageStatistics) - Method in class ij.gui.HistogramWindow
  Draws the histogram using the specified title and ImageStatistics.
showImageDialog(String) - Method in class ij.gui.RoiProperties
showList() - Method in class ij.gui.HistogramWindow
showList() - Static method in class ij.WindowManager
showLogWindow() - Method in class ij.plugin.frame.Editor
showMacroFunctions() - Method in class ij.plugin.frame.Editor
showMessage(String) - Static method in class ij.IJ
  Displays a message in a dialog box titled "Message".
showMessage(String, String) - Static method in class ij.IJ
  Displays a message in a dialog box with the specified title.
showMessageWithCancel(String, String) - Static method in class ij.IJ
  Displays a message in a dialog box with the specified title.
showOptionsDialog() - Method in class ij.plugin.tool.ArrowTool
showOptionsDialog() - Method in class ij.plugin.tool.BrushTool
showOptionsDialog() - Method in class ij.plugin.tool.OverlayBrushTool
showOptionsDialog() - Method in class ij.plugin.tool.PixelInspectionTool
showOptionsDialog() - Method in class ij.plugin.tool.PlugInTool
showOptionsDialog() - Method in class ij.plugin.tool.RoiRotationTool
showOverlay - Variable in class ij.plugin.filter.ParticleAnalyzer
showPopupMenu(MouseEvent, Toolbar) - Method in class ij.plugin.tool.PlugInTool
showProgress - Variable in class ij.plugin.filter.ParticleAnalyzer
showProgress(boolean) - Method in class ij.plugin.filter.GaussianBlur
showProgress(double) - Static method in class ij.IJ
  Updates the progress bar, where 0invalid input: '<'=progressinvalid input: '<'=1.0.
showProgress(double) - Method in class ij.process.ImageProcessor
showProgress(int, int) - Static method in class ij.IJ
  Updates the progress bar, where the length of the bar is set to (`currentValue+1)/finalValue` of the maximum bar length.
showResults - Variable in class ij.plugin.filter.ParticleAnalyzer
showRow(int) - Method in class ij.text.TextPanel
  Updates the vertical scroll bar so that the specified row is visible.
showRowIndexes(boolean) - Method in class ij.measure.ResultsTable
showRowNumbers() - Method in class ij.measure.ResultsTable
showRowNumbers(boolean) - Method in class ij.measure.ResultsTable
showSizeDistribution - Variable in class ij.plugin.filter.ParticleAnalyzer
showSlice(int) - Method in class ij.gui.StackWindow
  Displays the specified slice and updates the stack scrollbar.
showStatus() - Method in class ij.gui.EllipseRoi
showStatus() - Method in class ij.gui.Line
showStatus() - Method in class ij.gui.Roi
showStatus() - Method in class ij.gui.RotatedRectRoi
showStatus(boolean) - Method in class ij.plugin.filter.ThresholdToSelection
  Determines whether to show status messages and a progress bar
showStatus(String) - Method in class ij.gui.PlotWindow
  Shows the text in the coordinateinvalid input: '&status' readout field at the bottom.
showStatus(String) - Static method in class ij.IJ
  Displays a message in the ImageJ status bar.
showStatus(String, String) - Static method in class ij.IJ
  Displays a message in the status bar and flashes either the status bar or the active image.
  See: http://wsr.imagej.net/macros/FlashingStatusMessages.txt
showTime(ImagePlus, long, String) - Static method in class ij.IJ
showTime(ImagePlus, long, String, int) - Static method in class ij.IJ
shrink(ImagePlus, int, int, int, int) - Method in class ij.plugin.Binner
shrink(ImageProcessor, int, int, int) - Method in class ij.plugin.Binner
shuffle(ImagePlus, int) - Method in class ij.plugin.HyperStackConverter
  Changes the dimension order of a 4D or 5D stack from the specified order (CTZ, ZCT, ZTC, TCZ or TZC) to the XYCZT order used by ImageJ.
SIGNED_INT - Static variable in class ij.gui.NewImage
SignedShortProcessor - Class in ij.process
  An extended ShortProcessor that supports signed 16-bit images (experimental).
SignedShortProcessor(int, int) - Constructor for class ij.process.SignedShortProcessor
  Creates a blank SignedShortProcessor with the specified dimensions.
SignedShortProcessor(ShortProcessor) - Constructor for class ij.process.SignedShortProcessor
SimpleCommands - Class in ij.plugin
  This plugin implements the Plugins/Utilities/Unlock, Image/Rename and Plugins/Utilities/Search commands.
SimpleCommands() - Constructor for class ij.plugin.SimpleCommands
SIN - Static variable in interface ij.macro.MacroConstants
SINGLE_POINTS - Static variable in class ij.plugin.filter.MaximumFinder
  Output type single points
SIXTEEN_BIT - Static variable in class ij.plugin.frame.ThresholdAdjuster
sixteenBitRanges - Static variable in class ij.plugin.frame.ContrastAdjuster
size() - Method in class ij.gui.Line
  Returns the number of points in this selection; equivalent to getPolygon().npoints.
size() - Method in class ij.gui.OvalRoi
  Returns the number of corner points in the mask of this selection; equivalent to getPolygon().npoints.
size() - Method in class ij.gui.Overlay
  Returns the number of ROIs in this Overlay.
size() - Method in class ij.gui.PolygonRoi
  Returns the number of points in this selection; equivalent to getPolygon().npoints.
size() - Method in class ij.gui.Roi
  Returns the number of points in this selection; equivalent to getFloatPolygon().npoints.
size() - Method in class ij.gui.ShapeRoi
  Retuns the number of vertices, of this shape as approximated by straight lines.
size() - Method in class ij.ImageStack
  Returns the number of slices in this stack.
size() - Method in class ij.measure.ResultsTable
  Returns the size of this ResultsTable.
size() - Method in class ij.plugin.FileInfoVirtualStack
  Returns the number of slices in this stack.
size() - Method in class ij.util.FloatArray
  Returns the number of elements in the array.
size() - Method in class ij.VirtualStack
  Returns the number of slices in this stack.
SIZE - Static variable in class ij.io.RoiDecoder
SIZE_KEY - Static variable in class ij.gui.Arrow
sizes - Static variable in class ij.gui.PointRoi
skeletonize() - Method in class ij.process.BinaryProcessor
  Converts black objects in a binary image to single pixel skeletons.
skeletonize() - Method in class ij.process.ByteProcessor
  Converts black objects in a binary image to single pixel skeletons.
skeletonize(int) - Method in class ij.process.BinaryProcessor
  Converts objects in a binary image with pixel values of 'forground' (255 or 0) to single pixel skeletons.
skeletonize(int) - Method in class ij.process.ByteProcessor
  Converts objects with pixel values of 'forground' (255 or 0) in a binary imager to single pixel skeletons.
skewness - Variable in class ij.process.ImageStatistics
SKEWNESS - Static variable in interface ij.measure.Measurements
SKEWNESS - Static variable in class ij.measure.ResultsTable
skipRawDialog - Static variable in class ij.Prefs
  Do not display dialog when opening .raw files
slice - Variable in class ij.gui.StackWindow
slice - Variable in class ij.plugin.filter.ParticleAnalyzer
SLICE - Static variable in interface ij.measure.Measurements
SLICE - Static variable in class ij.measure.ResultsTable
sliceLabels - Variable in class ij.io.FileInfo
sliceNumber - Variable in class ij.io.FileInfo
Slicer - Class in ij.plugin
  Implements the Image/Stacks/Reslice command.
Slicer() - Constructor for class ij.plugin.Slicer
sliceSelector - Variable in class ij.gui.StackWindow
slider - Variable in class ij.gui.GenericDialog
smooth() - Method in class ij.process.ImageProcessor
  Replaces each pixel with the 3x3 neighborhood mean.
smoothWand - Static variable in class ij.Prefs
  Wand tool "Smooth if thresholded" option
snapshot() - Method in class ij.process.ByteProcessor
  Make a snapshot of the current image.
snapshot() - Method in class ij.process.ColorProcessor
snapshot() - Method in class ij.process.FloatProcessor
snapshot() - Method in class ij.process.ImageProcessor
  Makes a copy of this image's pixel data that can be later restored using reset() or reset(mask).
snapshot() - Method in class ij.process.ShortProcessor
SNAPSHOT - Static variable in interface ij.macro.MacroConstants
SNAPSHOT - Static variable in interface ij.plugin.filter.PlugInFilter
  Set this flag if the filter requires a snapshot (copy of the pixels array).
snapshotHeight - Variable in class ij.process.ImageProcessor
snapshotMax - Variable in class ij.process.ShortProcessor
snapshotMin - Variable in class ij.process.ShortProcessor
snapshotPixels - Variable in class ij.process.ByteProcessor
snapshotPixels - Variable in class ij.process.ColorProcessor
snapshotWidth - Variable in class ij.process.ImageProcessor
SOFTWARE - Static variable in class ij.io.TiffDecoder
SOLIDITY - Static variable in class ij.measure.ResultsTable
sort() - Method in class ij.util.ArrayUtil
sort(ImageStack) - Static method in class ij.util.DicomTools
  Sorts a DICOM stack by image number.
sort(String) - Method in class ij.measure.ResultsTable
  Sorts this table on the specified column, with string support.
sort(String[]) - Static method in class ij.util.StringSorter
  Sorts the array.
sortByMetaData(boolean) - Method in class ij.plugin.FolderOpener
sortDicom(String[], String[], int) - Method in class ij.VirtualStack
sortedTypes - Static variable in class ij.measure.CurveFitter
  Nicer sequence of the built-in function types
sortFileList(String[]) - Method in class ij.plugin.FolderOpener
  Sorts file names containing numerical components.
sortFileNames(boolean) - Method in class ij.plugin.FolderOpener
sortNumerically(String[]) - Static method in class ij.util.StringSorter
  Sorts file names containing numerical components.
source - Variable in class ij.process.ImageProcessor
south(ImageProcessor) - Method in class ij.plugin.filter.Shadows
southeast(ImageProcessor) - Method in class ij.plugin.filter.Shadows
southwest(ImageProcessor) - Method in class ij.plugin.filter.Shadows
spaceBarDown() - Static method in class ij.IJ
  Returns true if the space bar is down.
SPARE1 - Static variable in class ij.gui.Toolbar
  Obsolete public constants
SPARE2 - Static variable in class ij.gui.Toolbar
  Obsolete public constants
SPARE3 - Static variable in class ij.gui.Toolbar
  Obsolete public constants
SPARE4 - Static variable in class ij.gui.Toolbar
  Obsolete public constants
SPARE5 - Static variable in class ij.gui.Toolbar
  Obsolete public constants
SPARE6 - Static variable in class ij.gui.Toolbar
  Obsolete public constants
SPARE7 - Static variable in class ij.gui.Toolbar
  Obsolete public constants
SPARE8 - Static variable in class ij.gui.Toolbar
  Obsolete public constants
SPARE9 - Static variable in class ij.gui.Toolbar
  Obsolete public constants
SpecifyROI - Class in ij.plugin
  This plugin implements the Edit/Selection/Specify command.
SpecifyROI() - Constructor for class ij.plugin.SpecifyROI
SPLINE_FIT - Static variable in class ij.io.RoiDecoder
splineFitLines - Static variable in class ij.Prefs
  Automatically spline fit line selections
SplineFitter - Class in ij.measure
  This class interpolates a set of points using natural cubic splines (assuming zero second derivatives at end points).
SplineFitter(float[], float[], int) - Constructor for class ij.measure.SplineFitter
SplineFitter(float[], float[], int, boolean) - Constructor for class ij.measure.SplineFitter
  For closed curves: the first and last y value should be identical; internally, a periodic continuation with a few will be used at both ends
SplineFitter(int[], int[], int) - Constructor for class ij.measure.SplineFitter
splinePoints - Variable in class ij.gui.PolygonRoi
split(ImagePlus) - Static method in class ij.plugin.ChannelSplitter
  Splits the specified image into separate channels.
split(ImagePlus) - Method in class ij.plugin.filter.RGBStackSplitter
  Deprecated; replaced by ij.plugin.ChannelSplitter.
split(ImageStack, boolean) - Method in class ij.plugin.filter.RGBStackSplitter
  Deprecated; replaced by ChannelSplitter.splitRGB().
split(String) - Static method in class ij.util.Tools
  Splits a string into substrings using the default delimiter set, which is " \t\n\r" (space, tab, newline and carriage-return).
split(String, String) - Static method in class ij.util.Tools
  Splits a string into substring using the characters contained in the second argument as the delimiter set.
SPLIT - Static variable in interface ij.macro.MacroConstants
splitRGB(ImageStack, boolean) - Static method in class ij.plugin.ChannelSplitter
  Splits the specified RGB stack into three 8-bit grayscale stacks.
sqr() - Method in class ij.process.FloatProcessor
sqr() - Method in class ij.process.ImageProcessor
  Performs a square transform on the image or ROI.
sqr() - Method in class ij.process.ShortProcessor
sqrt() - Method in class ij.process.FloatProcessor
sqrt() - Method in class ij.process.ImageProcessor
  Performs a square root transform on the image or ROI.
sqrt() - Method in class ij.process.ShortProcessor
SQRT - Static variable in interface ij.macro.MacroConstants
SQRT2 - Static variable in class ij.plugin.filter.EDM
  In old make16bitEDM this pixel value corresponds to a pixel distance of sqrt(2)
SQRT5 - Static variable in class ij.plugin.filter.EDM
  In old make16bitEDM this pixel value corresponds to a pixel distance of sqrt(5)
srcEnd - Variable in class ij.process.DownsizeTable
  index of the last point of the source data that should be accessed
srcRect - Variable in class ij.gui.ImageCanvas
srcStart - Variable in class ij.process.DownsizeTable
  index of the first point of the source data that should be accessed
STACK - Static variable in interface ij.macro.MacroConstants
STACK_POSITION - Static variable in interface ij.measure.Measurements
STACK_REQUIRED - Static variable in interface ij.plugin.filter.PlugInFilter
  Set this flag if the filter requires a stack.
Stack_Statistics - Class in ij.plugin
  This plugin implements the Image/Stacks/Statistics command.
Stack_Statistics() - Constructor for class ij.plugin.Stack_Statistics
StackCombiner - Class in ij.plugin
  This plugin implements the Image/Stacks/Combine command.
StackCombiner() - Constructor for class ij.plugin.StackCombiner
StackConverter - Class in ij.process
  This class does stack type conversions.
StackConverter(ImagePlus) - Constructor for class ij.process.StackConverter
StackEditor - Class in ij.plugin
  Implements the AddSlice, DeleteSlice and "Stack to Images" commands.
StackEditor() - Constructor for class ij.plugin.StackEditor
StackInserter - Class in ij.plugin
  This plugin, which implements the Image/Stacks/Tools/Insert command, inserts an image or stack into another image or stack.
StackInserter() - Constructor for class ij.plugin.StackInserter
StackLabeler - Class in ij.plugin.filter
  This plugin implements the Image/Stacks/Label command.
StackLabeler() - Constructor for class ij.plugin.filter.StackLabeler
StackMaker - Class in ij.plugin
  The plugin implements the Image/Stacks/Tools/Montage to Stack command.
StackMaker() - Constructor for class ij.plugin.StackMaker
StackPlotter - Class in ij.plugin
StackPlotter() - Constructor for class ij.plugin.StackPlotter
StackProcessor - Class in ij.process
  This class processes stacks.
StackProcessor(ImageStack) - Constructor for class ij.process.StackProcessor
  Constructs a StackProcessor from a stack.
StackProcessor(ImageStack, ImageProcessor) - Constructor for class ij.process.StackProcessor
  Constructs a StackProcessor from a stack.
StackReducer - Class in ij.plugin
  This plugin implements the Image/Stacks/Tools/Reduce command.
StackReducer() - Constructor for class ij.plugin.StackReducer
StackReverser - Class in ij.plugin
  This plugin implements the Image/Transform/Flip Z and Image/Stacks/Tools/Reverse commands.
StackReverser() - Constructor for class ij.plugin.StackReverser
stackStatistics - Variable in class ij.process.ImageStatistics
  Used by HistogramWindow
StackStatistics - Class in ij.process
  Statistics, including the histogram, of a stack.
StackStatistics(ImagePlus) - Constructor for class ij.process.StackStatistics
  Creates a StackStatistics object from a stack, using 256 histogram bins and the entire stack pixel value range.
StackStatistics(ImagePlus, int, double, double) - Constructor for class ij.process.StackStatistics
  Creates a StackStatistics object from a stack, using the specified histogram bin count and x-axis range (pixel value tange).
StackWindow - Class in ij.gui
  This class is an extended ImageWindow that displays stacks and hyperstacks.
StackWindow(ImagePlus) - Constructor for class ij.gui.StackWindow
StackWindow(ImagePlus, ImageCanvas) - Constructor for class ij.gui.StackWindow
StackWriter - Class in ij.plugin
  This plugin, which saves the images in a stack as separate files, implements the File/Save As/Image Sequence command.
StackWriter() - Constructor for class ij.plugin.StackWriter
STANDALONE - Static variable in class ij.ImageJ
  Run as normal application.
start(Callable[]) - Static method in class ij.util.ThreadUtil
  Starts all callables for parallel execution (using a ThreadPoolExecutor) without waiting for the results.
startAndJoin(Thread[]) - Static method in class ij.util.ThreadUtil
  Start all given threads and wait on each of them until all are done.
startAndJoin(Callable[]) - Static method in class ij.util.ThreadUtil
  Starts all callables for parallel execution (using a ThreadPoolExecutor) and waits until each of them has finished.
startPaste(ImagePlus) - Method in class ij.gui.Roi
STARTS_WITH - Static variable in interface ij.macro.MacroConstants
startServer() - Static method in class ij.OtherInstance
startTiming() - Method in class ij.ImagePlus
  Calls System.currentTimeMillis() to save the current time so it can be retrieved later using getStartTime() to calculate the elapsed time of an operation.
Startup - Class in ij.plugin
  This plugin implements the Edit/Options/Startup command.
Startup() - Constructor for class ij.plugin.Startup
StartupRunner - Class in ij.macro
  Runs the RunAtStartup (created by Edit/Options/Startup) and AutoRun (in StartupMacros) macros.
StartupRunner() - Constructor for class ij.macro.StartupRunner
startxd - Variable in class ij.gui.Line
startyd - Variable in class ij.gui.Line
staticShowChoice - Static variable in class ij.plugin.filter.ParticleAnalyzer
stats - Variable in class ij.gui.HistogramWindow
STATUS_STRING - Static variable in class ij.measure.Minimizer
  Strings describing the status codes
statusBarProtected() - Static method in class ij.IJ
STD_DEV - Static variable in interface ij.measure.Measurements
STD_DEV - Static variable in class ij.measure.ResultsTable
stdDev - Variable in class ij.process.ImageStatistics
STEP - Static variable in interface ij.macro.Debugger
stop() - Static method in class ij.plugin.Orthogonal_Views
str - Variable in class ij.macro.Symbol
STRAIGHT_LINE - Static variable in class ij.measure.Calibration
STRAIGHT_LINE - Static variable in class ij.measure.CurveFitter
  Constants for the built-in fit functions
straighten(ImagePlus, Roi, int) - Method in class ij.plugin.Straightener
Straightener - Class in ij.plugin
  This plugin implements the Edit/Selection/Straighten command.
Straightener() - Constructor for class ij.plugin.Straightener
straightenLine(ImagePlus, int) - Method in class ij.plugin.Straightener
straightenLine(ImagePlus, Line, int) - Method in class ij.plugin.Straightener
straightenStack(ImagePlus, Roi, int) - Method in class ij.plugin.Straightener
stretchHistogram(ImagePlus, double) - Method in class ij.plugin.ContrastEnhancer
stretchHistogram(ImageProcessor, double) - Method in class ij.plugin.ContrastEnhancer
stretchHistogram(ImageProcessor, double, ImageStatistics) - Method in class ij.plugin.ContrastEnhancer
STRING - Static variable in interface ij.macro.MacroConstants
STRING_CONSTANT - Static variable in interface ij.macro.MacroConstants
STRING_FUNCTION - Static variable in interface ij.macro.MacroConstants
stringField - Variable in class ij.gui.GenericDialog
stringFunctionIDs - Static variable in interface ij.macro.MacroConstants
stringFunctions - Static variable in interface ij.macro.MacroConstants
StringSorter - Class in ij.util
  A simple QuickSort for String arrays.
StringSorter() - Constructor for class ij.util.StringSorter
stringToPasteMode(String) - Static method in class ij.IJ
STRIP_BYTE_COUNT - Static variable in class ij.io.TiffDecoder
STRIP_OFFSETS - Static variable in class ij.io.TiffDecoder
stripLengths - Variable in class ij.io.FileInfo
stripOffsets - Variable in class ij.io.FileInfo
stroke - Variable in class ij.gui.Roi
STROKE_COLOR - Static variable in class ij.io.RoiDecoder
STROKE_WIDTH - Static variable in class ij.io.RoiDecoder
STROKE_WIDTH - Static variable in class ij.plugin.CalibrationBar
strokeColor - Variable in class ij.gui.Roi
STYLE - Static variable in class ij.gui.PlotContentsDialog
  Types of dialog (ERROR suppresses the dialog after an invalid call of a constructor)
STYLE_KEY - Static variable in class ij.gui.Arrow
styles - Static variable in class ij.gui.Arrow
SUB_PIXEL_RESOLUTION - Static variable in class ij.io.RoiDecoder
SubHyperstackMaker - Class in ij.plugin
  This plugin is used by the Image/Stacks/Tools/Make Substack command to create substacks of hyperstacks.
SubHyperstackMaker() - Constructor for class ij.plugin.SubHyperstackMaker
subPixelResolution - Static variable in class ij.Prefs
  Use sub-pixel resolution with line selections
subPixelResolution() - Method in class ij.gui.EllipseRoi
  Always returns true.
subPixelResolution() - Method in class ij.gui.Line
  Always returns true.
subPixelResolution() - Method in class ij.gui.PointRoi
  Always returns true.
subPixelResolution() - Method in class ij.gui.Roi
  Returns true if this is a slection that supports sub-pixel resolution.
subPixelResolution() - Method in class ij.gui.RotatedRectRoi
  Always returns true.
SubstackMaker - Class in ij.plugin
  This plugin implements the Image/Stacks/Tools/Make Substack command.
SubstackMaker() - Constructor for class ij.plugin.SubstackMaker
SUBSTRING - Static variable in interface ij.macro.MacroConstants
subtract(double) - Method in class ij.process.ImageProcessor
  Subtracts 'value' from each pixel in the image or ROI.
SUBTRACT - Static variable in interface ij.process.Blitter
  dst=dst-src
subtractBackround(ImageProcessor, int) - Method in class ij.plugin.filter.BackgroundSubtracter
  Depracated.
subtractPoints(Roi) - Method in class ij.gui.PointRoi
  Returns the points of this Roi that are not contained in the specified area ROI.
subtractRGBBackround(ColorProcessor, int) - Method in class ij.plugin.filter.BackgroundSubtracter
  Depracated.
SUBTYPE - Static variable in class ij.io.RoiDecoder
SUCCESS - Static variable in class ij.measure.Minimizer
  Status returned: successful completion
SUM - Static variable in class ij.plugin.Binner
SUM_METHOD - Static variable in class ij.plugin.ZProjector
SUM_PROJECTION - Static variable in class ij.process.ImageProcessor
  Composite image projection modes.
summarize() - Method in class ij.plugin.filter.Analyzer
supportMacroUndo - Static variable in class ij.Prefs
  Support TRANSFORM Undo in macros
SUPPORTS_MASKING - Static variable in interface ij.plugin.filter.PlugInFilter
  Set this flag if the filter wants ImageJ, for non-rectangular ROIs, to restore that part of the image that's inside the bounding rectangle but outside of the ROI.
suppressPluginNotFoundError() - Static method in class ij.IJ
  Temporarily suppress "plugin not found" errors.
SurfacePlotter - Class in ij.plugin
SurfacePlotter() - Constructor for class ij.plugin.SurfacePlotter
swapPixelArrays() - Method in class ij.process.ByteProcessor
  Swaps the pixel and snapshot (undo) arrays.
swapPixelArrays() - Method in class ij.process.ColorProcessor
  Swaps the pixel and snapshot (undo) arrays.
swapPixelArrays() - Method in class ij.process.FloatProcessor
  Swaps the pixel and snapshot (undo) arrays.
swapPixelArrays() - Method in class ij.process.ImageProcessor
  Swaps the pixel and snapshot (undo) buffers.
swapPixelArrays() - Method in class ij.process.ShortProcessor
  Swaps the pixel and snapshot (undo) arrays.
swapQuadrants() - Method in class ij.process.FHT
  Swap quadrants 1 and 3 and 2 and 4 of the image contained in this FHT.
swapQuadrants(ImageProcessor) - Static method in class ij.plugin.FFT
swapQuadrants(ImageProcessor) - Method in class ij.process.FHT
  Swap quadrants 1 and 3 and 2 and 4 of the specified ImageProcessor so the power spectrum origin is at the center of the image.
Symbol - Class in ij.macro
  Objects of this class are used as entries in the macro language symbol table.
SyncWindows - Class in ij.plugin.frame
  This class "synchronizes" mouse input in multiple windows.
SyncWindows() - Constructor for class ij.plugin.frame.SyncWindows
  Create window sync frame.
SyncWindows(String) - Constructor for class ij.plugin.frame.SyncWindows

## T

T_POSITION - Static variable in class ij.io.RoiDecoder
TABLE - Static variable in class ij.io.Opener
TABLE - Static variable in interface ij.macro.MacroConstants
TABLE - Static variable in class ij.plugin.NewPlugin
TABLE_FULL - Static variable in class ij.measure.ResultsTable
TableListener - Interface in ij.text
  Plugins that implement this interface are notified when a table is opened, closed or updated.
TableUpdated(TextPanel, String, int) - Method in interface ij.text.TableListener
tableWindowExists() - Static method in class ij.gui.PlotContentsDialog
  Returns whether there is at least one table that can be used for "Add from Table"
TAN - Static variable in interface ij.macro.MacroConstants
TCZ - Static variable in class ij.plugin.HyperStackConverter
TEMPLATE - Static variable in class ij.gui.PlotDialog
  Types of dialog.
TEMPLATE - Static variable in class ij.plugin.NewPlugin
temporarilyHide() - Method in class ij.gui.Roi
  Deprecated
tempOverlay() - Method in class ij.ImagePlus
Text - Class in ij.plugin
  This plugin implements the Edit/Options/Fonts command and the dialog displayed when you double click on the text tool.
Text() - Constructor for class ij.plugin.Text
TEXT - Static variable in class ij.gui.Toolbar
TEXT - Static variable in class ij.io.Opener
TEXT - Static variable in class ij.io.RoiDecoder
TEXT_FILE - Static variable in class ij.plugin.NewPlugin
textArea1 - Variable in class ij.gui.GenericDialog
textArea2 - Variable in class ij.gui.GenericDialog
TextEncoder - Class in ij.io
  Saves an image described by an ImageProcessor object as a tab-delimited text file.
TextEncoder(ImageProcessor, Calibration, int) - Constructor for class ij.io.TextEncoder
  Constructs a TextEncoder from an ImageProcessor and optional Calibration.
TextFileReader - Class in ij.plugin
  This plugin displays the contents of a text file in a window.
TextFileReader() - Constructor for class ij.plugin.TextFileReader
TextPanel - Class in ij.text
  This is an unlimited size text panel with tab-delimited, labeled and resizable columns.
TextPanel() - Constructor for class ij.text.TextPanel
  Constructs a new TextPanel.
TextPanel(String) - Constructor for class ij.text.TextPanel
  Constructs a new TextPanel.
TextReader - Class in ij.plugin
  This plugin opens a tab or comma delimeted text file as an image.
TextReader() - Constructor for class ij.plugin.TextReader
TextRoi - Class in ij.gui
  This class is a rectangular ROI containing text.
TextRoi(double, double, double, double, String, Font) - Constructor for class ij.gui.TextRoi
  Creates a TextRoi using the specified sub-pixel location, size and Font.
TextRoi(double, double, String) - Constructor for class ij.gui.TextRoi
  Creates a TextRoi using sub-pixel coordinates.
TextRoi(double, double, String, Font) - Constructor for class ij.gui.TextRoi
  Creates a TextRoi using the specified sub-pixel location and Font.
TextRoi(int, int, ImagePlus) - Constructor for class ij.gui.TextRoi
TextRoi(int, int, String) - Constructor for class ij.gui.TextRoi
  Creates a TextRoi using the defaultFont.
TextRoi(int, int, String, Font) - Constructor for class ij.gui.TextRoi
  Creates a TextRoi using the specified location and Font.
TextRoi(int, int, String, Font, Color) - Constructor for class ij.gui.TextRoi
  Deprecated.
TextRoi(String, double, double, Font) - Constructor for class ij.gui.TextRoi
  Use this constructor as a drop-in replacement for ImageProcessor.drawString().
textValueChanged(TextEvent) - Method in class ij.gui.ColorChooser
textValueChanged(TextEvent) - Method in class ij.gui.GenericDialog
textValueChanged(TextEvent) - Method in class ij.gui.RoiProperties
textValueChanged(TextEvent) - Method in class ij.macro.FunctionFinder
textValueChanged(TextEvent) - Method in class ij.plugin.ChannelArranger
textValueChanged(TextEvent) - Method in class ij.plugin.Distribution
textValueChanged(TextEvent) - Method in class ij.plugin.Duplicator
textValueChanged(TextEvent) - Method in class ij.plugin.filter.ImageProperties
textValueChanged(TextEvent) - Method in class ij.plugin.FolderOpener
textValueChanged(TextEvent) - Method in class ij.plugin.frame.Editor
textValueChanged(TextEvent) - Method in class ij.plugin.frame.LineWidthAdjuster
textValueChanged(TextEvent) - Method in class ij.plugin.Histogram
textValueChanged(TextEvent) - Method in class ij.plugin.Resizer
textValueChanged(TextEvent) - Method in class ij.plugin.Scaler
textValueChanged(TextEvent) - Method in class ij.plugin.Slicer
TextWindow - Class in ij.text
  Uses a TextPanel to displays text in a window.
TextWindow(String, int, int) - Constructor for class ij.text.TextWindow
  Opens a new text window containing the contents of a text file.
TextWindow(String, String, int, int) - Constructor for class ij.text.TextWindow
  Opens a new single-column text window.
TextWindow(String, String, String, int, int) - Constructor for class ij.text.TextWindow
  Opens a new multi-column text window.
TextWindow(String, String, ArrayList, int, int) - Constructor for class ij.text.TextWindow
  Opens a new multi-column text window.
TextWriter - Class in ij.plugin
  This plugin implements the File/Save As/Text command, which saves the contents of Editor windows and TextWindows (e.g., "Log" and "Results").
TextWriter() - Constructor for class ij.plugin.TextWriter
theLabel - Variable in class ij.gui.GenericDialog
theta - Variable in class ij.process.EllipseFitter
  Angle in radians
thread - Variable in class ij.gui.StackWindow
ThreadLister - Class in ij.plugin
  Displays thread information in a text window.
ThreadLister() - Constructor for class ij.plugin.ThreadLister
threadPoolExecutor - Static variable in class ij.util.ThreadUtil
  The threadPoolExecutor holds at least as many threads for parallel execution as the number of processors; additional threads are added as required.
THREADS - Static variable in class ij.Prefs
ThreadUtil - Class in ij.util
ThreadUtil() - Constructor for class ij.util.ThreadUtil
threshold(int) - Method in class ij.process.ByteProcessor
  Sets pixels less than or equal to 'level' to 0 and all other pixels to 255.
threshold(int) - Method in class ij.process.ColorProcessor
  Not implemented.
threshold(int) - Method in class ij.process.FloatProcessor
  Not implemented.
threshold(int) - Method in class ij.process.ImageProcessor
  Sets pixels less than or equal to level to 0 and all other pixels to 255.
threshold(int) - Method in class ij.process.ShortProcessor
threshold(int, int) - Method in class ij.process.ByteProcessor
  Sets pixels less than 'level1' or greater than 'level2' to 0 and all other pixels to 255.
threshold(int, int) - Method in class ij.process.ImageProcessor
  Sets pixels less than 'level1' or greater than 'level2' to 0 and all other pixels to 255.
ThresholdAdjuster - Class in ij.plugin.frame
  Adjusts the lower and upper threshold levels of the active image.
ThresholdAdjuster() - Constructor for class ij.plugin.frame.ThresholdAdjuster
Thresholder - Class in ij.plugin
  This plugin implements the Process/Binary/Make Binary and Convert to Mask commands.
Thresholder() - Constructor for class ij.plugin.Thresholder
ThresholdToSelection - Class in ij.plugin.filter
ThresholdToSelection() - Constructor for class ij.plugin.filter.ThresholdToSelection
TIFF - Static variable in class ij.io.FileInfo
TIFF - Static variable in class ij.io.Opener
TIFF_AND_DICOM - Static variable in class ij.io.Opener
TiffDecoder - Class in ij.io
  Decodes single and multi-image TIFF files.
TiffDecoder(InputStream, String) - Constructor for class ij.io.TiffDecoder
TiffDecoder(String, String) - Constructor for class ij.io.TiffDecoder
TiffEncoder - Class in ij.io
  Saves an image described by a FileInfo object as an uncompressed TIFF file.
TiffEncoder(FileInfo) - Constructor for class ij.io.TiffEncoder
TILE_WIDTH - Static variable in class ij.io.TiffDecoder
tileMirror(ImageProcessor, int, int, int, int) - Method in class ij.plugin.filter.FFTFilter
  Puts ImageProcessor (ROI) into a new ImageProcessor of size width x height y at position (x,y).
time(ImagePlus, long) - Static method in class ij.IJ
  Experimental
TO_BINARY - Static variable in interface ij.macro.MacroConstants
TO_HEX - Static variable in interface ij.macro.MacroConstants
TO_LOWER_CASE - Static variable in interface ij.macro.MacroConstants
TO_SCALED - Static variable in interface ij.macro.MacroConstants
TO_STRING - Static variable in interface ij.macro.MacroConstants
TO_UNSCALED - Static variable in interface ij.macro.MacroConstants
TO_UPPER_CASE - Static variable in interface ij.macro.MacroConstants
toArray() - Method in class ij.gui.Overlay
  Returns on array containing the ROIs in this Overlay.
toArray() - Method in class ij.util.FloatArray
  Returns a float array containing all elements of this FloatArray.
toArray(int[]) - Method in class ij.gui.Overlay
  Returns on array containing the ROIs with the specified indexes.
toByteArray() - Method in class ij.gui.Plot
  Writes this plot into a byte array containing (1) the serialized PlotProperties and (2) the serialized Vector of all 'added' PlotObjects.
toColor(int, int, int) - Static method in class ij.plugin.Colors
  Returns an opaque color with the specified red, green, and blue values.
toDouble(float[]) - Static method in class ij.util.Tools
  Converts the float array 'a' to a double array.
toEDM(ImageProcessor) - Method in class ij.plugin.filter.EDM
  Converts a binary image into a 8-bit grayscale Euclidean Distance Map (EDM).
toFloat(double[]) - Static method in class ij.util.Tools
  Converts the double array 'a' to a float array.
toFloat(int[]) - Static method in class ij.gui.Roi
  Converts an int array to a float array.
toFloat(int, FloatProcessor) - Method in class ij.process.ByteProcessor
  Returns a FloatProcessor with the same image, no scaling or calibration (pixel values 0 to 255).
toFloat(int, FloatProcessor) - Method in class ij.process.ColorProcessor
  Returns a FloatProcessor with one color channel of the image.
toFloat(int, FloatProcessor) - Method in class ij.process.FloatProcessor
  Returns this FloatProcessor.
toFloat(int, FloatProcessor) - Method in class ij.process.ImageProcessor
  Returns a FloatProcessor with the image or one color channel thereof.
toFloat(int, FloatProcessor) - Method in class ij.process.ShortProcessor
  Returns a FloatProcessor with the same image, no scaling or calibration (pixel values 0 to 65535).
toFloatArrays() - Method in class ij.process.ByteProcessor
toFloatProcessors() - Method in class ij.process.ByteProcessor
toFront(Frame) - Static method in class ij.WindowManager
toFront(Window) - Static method in class ij.WindowManager
toggleOverlay() - Method in class ij.ImagePlus
toHyperStack(ImagePlus, int, int, int) - Static method in class ij.plugin.HyperStackConverter
  Converts the specified stack into a hyperstack with 'c' channels, 'z' slices and 't' frames using the default ordering ("xyczt") and display mode ("Composite").
toHyperStack(ImagePlus, int, int, int, String) - Static method in class ij.plugin.HyperStackConverter
  Converts the specified stack into a hyperstack with 'c' channels, 'z' slices and 't' frames using the default ordering ("xyczt") and the specified display mode ("composite", "color" or "grayscale").
toHyperStack(ImagePlus, int, int, int, String, String) - Static method in class ij.plugin.HyperStackConverter
  Converts the specified stack into a hyperstack with 'c' channels, 'z' slices and 't' frames.
toInt(float[]) - Static method in class ij.gui.Roi
  Converts a float array to an int array using truncation.
toInt(float[], int[], int) - Static method in class ij.gui.Roi
toIntR(float[]) - Static method in class ij.gui.Roi
  Converts a float array to an int array using rounding.
TOK_MASK - Static variable in interface ij.macro.MacroConstants
TOK_SHIFT - Static variable in interface ij.macro.MacroConstants
tokenize(String) - Method in class ij.macro.Tokenizer
  Uses a StreamTokenizer to convert an ImageJ macro file into a token stream.
Tokenizer - Class in ij.macro
  This class converts an imageJ macro file file into a token stream.
Tokenizer() - Constructor for class ij.macro.Tokenizer
TOOL_CHANGED - Static variable in interface ij.IJEventListener
TOOL_ID - Static variable in interface ij.macro.MacroConstants
TOOL_KEY - Static variable in class ij.gui.Toolbar
Toolbar - Class in ij.gui
  The ImageJ toolbar.
Toolbar() - Constructor for class ij.gui.Toolbar
Tools - Class in ij.util
  This class contains static utility methods.
Tools() - Constructor for class ij.util.Tools
TOOLS_MENU - Static variable in class ij.Menus
TOP - Static variable in class ij.io.RoiDecoder
TOP_HAT - Static variable in class ij.plugin.filter.RankFilters
TOP_LEFT - Static variable in class ij.gui.Plot
  Legend positions
TOP_MARGIN - Static variable in class ij.gui.Plot
  Deprecated.
  Not a fixed value any more, use getDrawingFrame() to get the drawing area
TOP_RIGHT - Static variable in class ij.gui.Plot
  Legend positions
toSelection(ImagePlus) - Static method in class ij.plugin.Zoom
toShape(String) - Static method in class ij.gui.Plot
  Returns the number for a given plot symbol shape, -1 for xError and -2 for yError (all case-insensitive)
toStack(ImagePlus) - Static method in class ij.plugin.HyperStackConverter
  Converts the specified hyperstack into a stack.
toString() - Method in class ij.gui.ImageWindow
toString() - Method in class ij.gui.Overlay
toString() - Method in class ij.gui.PointRoi
toString() - Method in class ij.gui.Roi
toString() - Method in class ij.ImagePlus
toString() - Method in class ij.ImageStack
toString() - Method in class ij.io.FileInfo
toString() - Method in class ij.macro.Program
toString() - Method in class ij.macro.Symbol
toString() - Method in class ij.macro.Variable
toString() - Method in class ij.measure.Calibration
toString() - Method in class ij.measure.ResultsTable
toString() - Method in class ij.plugin.frame.RoiManager
toString() - Method in class ij.plugin.JavaScriptEvaluator
toString() - Method in class ij.plugin.MacroInstaller
toString() - Method in class ij.process.FHT
  Returns a string containing information about this FHT.
toString() - Method in class ij.process.FloatPolygon
toString() - Method in class ij.process.ImageProcessor
  Returns a string containing information about this ImageProcessor.
toString() - Method in class ij.process.ImageStatistics
toString() - Method in class ij.process.LUT
toString() - Method in class ij.util.ArrayUtil
  information to be displayed
toWatershed(ImageProcessor) - Method in class ij.plugin.filter.EDM
  Do watershed segmentation based on the EDM of the foreground objects (nonzero pixels) in an 8-bit image.
TRACE - Static variable in interface ij.macro.Debugger
TRACED_ROI - Static variable in class ij.gui.Roi
transform() - Method in class ij.process.FHT
  Performs a forward transform, converting this image into the frequency domain.
TRANSFORM - Static variable in class ij.Undo
  Undo using a single image, or composite color stack, copy (limited to 200MB).
transform1D(float[]) - Method in class ij.process.FHT
  Performs an optimized 1D Fast Hartley Transform (FHT) of an array.
Transformer - Class in ij.plugin.filter
  Implements the Flip and Rotate commands in the Image/Transform submenu.
Transformer() - Constructor for class ij.plugin.filter.Transformer
translate(double, double) - Method in class ij.gui.Overlay
  Moves all the ROIs in this overlay.
translate(double, double) - Method in class ij.gui.Roi
translate(double, double) - Method in class ij.plugin.frame.RoiManager
  Moves the selected ROIs or all the ROIs if none are selected.
translate(double, double) - Method in class ij.process.FloatPolygon
translate(double, double) - Method in class ij.process.ImageProcessor
  Moves the image or selection vertically or horizontally by a specified number of pixels.
translate(int) - Method in class ij.VirtualStack
  Translates slice numbers of hyperstacks not in default CZT order.
translate(int, int) - Method in class ij.gui.Overlay
  Moves all the ROIs in this overlay.
translate(int, int, boolean) - Method in class ij.process.ImageProcessor
  Deprecated.
  replaced by translate(x,y)
Translator - Class in ij.plugin.filter
  This plugin implements the Image/Translate command.
Translator() - Constructor for class ij.plugin.filter.Translator
TRANSPARENT - Static variable in class ij.CompositeImage
  Display modes (note: TRANSPARENT mode has not yet been implemented)
Triangle - Enum constant in enum class ij.process.AutoThresholder.Method
Triangle(int[]) - Static method in class ij.process.AutoThresholder
TRIANGLE - Static variable in class ij.gui.Plot
  Display points using an tiangular mark.
TRIANGLE - Static variable in class ij.gui.PlotWindow
  Deprecated.
triggerPopupMenu(int, MouseEvent, boolean, boolean) - Method in class ij.gui.Toolbar
trim() - Method in class ij.ImageStack
  Frees memory by deleting a few slices from the end of the stack.
trim() - Method in class ij.VirtualStack
  Does nothing.
TRIM - Static variable in interface ij.macro.MacroConstants
trimFileList(String[]) - Method in class ij.plugin.FolderOpener
  Removes names that start with "." or end with ".db", ".txt", ".lut", "roi", ".pty", ".hdr", ".py", etc.
trimKey(String) - Static method in class ij.Macro
TrimmedButton - Class in ij.gui
  This is an extended Button class used to reduce the width of the HUGE buttons on Mac OS X.
TrimmedButton(String, int) - Constructor for class ij.gui.TrimmedButton
trimProcessor() - Method in class ij.ImagePlus
  Frees RAM by setting the snapshot (undo) buffer in the current ImageProcessor to null.
trimTitle(String) - Static method in class ij.plugin.FolderOpener
trimToSize() - Method in class ij.util.FloatArray
  Trims the capacity of this FloatArray instance to be its current size, minimizing the storage of the FloatArray instance.
TRUE - Static variable in interface ij.macro.MacroConstants
trySimplify() - Method in class ij.gui.ShapeRoi
  Attempts to convert this ShapeRoi into a single non-composite Roi.
tSelector - Variable in class ij.gui.StackWindow
type - Variable in class ij.gui.Roi
type - Variable in class ij.macro.Symbol
TYPE - Static variable in class ij.io.RoiDecoder
TYPE_CONVERSION - Static variable in class ij.Undo
  Undo using an ImageProcessor copy.
TypeConverter - Class in ij.process
  This class converts an ImageProcessor to another data type.
TypeConverter(ImageProcessor, boolean) - Constructor for class ij.process.TypeConverter
types - Static variable in class ij.gui.PointRoi
types - Static variable in class ij.io.Opener
TZC - Static variable in class ij.plugin.HyperStackConverter

## U

umean - Variable in class ij.process.ImageStatistics
  Uncalibrated mean
UNCALIBRATED_OD - Static variable in class ij.measure.Calibration
uncaughtException(Thread, Throwable) - Method in class ij.ImageJ.ExceptionHandler
undo() - Static method in class ij.Undo
Undo - Class in ij
  This class consists of static methods and fields that implement ImageJ's Undo command.
Undo() - Constructor for class ij.Undo
uninstallPlugin(String) - Static method in class ij.Menus
  Deletes a command installed by Plugins/Shortcuts/Add Shortcut.
unit - Variable in class ij.io.FileInfo
units - Variable in class ij.gui.ProfilePlot
UNKNOWN - Static variable in class ij.io.FileInfo
UNKNOWN - Static variable in class ij.io.Opener
unlock() - Method in class ij.ImagePlus
  Unlocks the image.
UnsharpMask - Class in ij.plugin.filter
  This plugin-filter implements ImageJ's Unsharp Mask command.
UnsharpMask() - Constructor for class ij.plugin.filter.UnsharpMask
UNUSED - Static variable in class ij.gui.Toolbar
unzoom() - Method in class ij.gui.ImageCanvas
  Implements the Image/Zoom/Original Scale command.
unzoom() - Method in class ij.gui.PlotCanvas
  Implements the Image/Zoom/Original Scale command.
unzoom(ImagePlus) - Static method in class ij.plugin.Zoom
update() - Method in class ij.gui.Plot
  Draws the plot again, ignored if the plot has not been drawn before or the plot is frozen.
update() - Method in class ij.plugin.frame.Channels
update() - Static method in class ij.plugin.frame.ColorPicker
update() - Static method in class ij.plugin.frame.ContrastAdjuster
  Updates the ContrastAdjuster.
update() - Static method in class ij.plugin.frame.LineWidthAdjuster
update() - Static method in class ij.plugin.frame.ThresholdAdjuster
  Notifies the ThresholdAdjuster that the image has changed.
update() - Static method in class ij.plugin.PointToolOptions
update(boolean, boolean) - Method in class ij.gui.Roi
  If 'add' is true, adds this selection to the previous one.
update(int, ImagePlus, Roi) - Method in class ij.measure.ResultsTable
update(ImageProcessor) - Method in class ij.ImageStack
  Updates this stack so its attributes, such as min, max, calibration table and color model, are the same as 'ip'.
update(Graphics) - Method in class ij.gui.ImageCanvas
update(Graphics) - Method in class ij.gui.ProgressBar
UPDATE_BLUE - Static variable in class ij.process.ImageProcessor
  Composite image projection modes.
UPDATE_DISPLAY - Static variable in interface ij.macro.MacroConstants
UPDATE_GREEN - Static variable in class ij.process.ImageProcessor
  Composite image projection modes.
UPDATE_RED - Static variable in class ij.process.ImageProcessor
  Composite image projection modes.
UPDATE_RESULTS - Static variable in interface ij.macro.MacroConstants
updateAllChannelsAndDraw() - Method in class ij.CompositeImage
updateAndDraw() - Method in class ij.CompositeImage
updateAndDraw() - Method in class ij.ImagePlus
  Updates this image from the pixel data in its associated ImageProcessor, then displays it.
updateAndDraw() - Method in class ij.plugin.frame.ContrastAdjuster
  Resets this ContrastAdjuster and brings it to the front.
updateAndRepaintWindow() - Method in class ij.ImagePlus
  Calls updateAndDraw to update from the pixel data and draw the image, and also repaints the image window to force the information displayed above the image (dimension, type, size) to be updated.
updateArrayInspector() - Method in class ij.macro.Interpreter
  Updates Array inspector if variable exists, otherwise closes ArrayInspector
updateChannelAndDraw() - Method in class ij.CompositeImage
updateChannelAndDraw() - Method in class ij.ImagePlus
  Updates this image from the pixel data in its associated ImageProcessor, then displays it.
updateChannels() - Static method in class ij.plugin.frame.Channels
updateClassName(String, String) - Method in class ij.plugin.frame.Editor
  Changes a plugins class name to reflect a new file name.
updateClipRect() - Method in class ij.gui.Roi
updateColumnHeadings(String) - Method in class ij.text.TextPanel
updateComposite(int[], int) - Method in class ij.process.ColorProcessor
updateComposite(int[], int) - Method in class ij.process.ImageProcessor
  This method is used by CompositeImage.updateImage() to create RGB images (for display) of a multi-channel composite images.
updateCounts() - Method in class ij.gui.PointRoi
  Updates the counts for each category in 'counters'
UPDATED - Static variable in class ij.ImagePlus
updateDebugWindow(String[], TextWindow) - Method in class ij.macro.Interpreter
updateDisplay() - Method in class ij.text.TextPanel
updateFont() - Static method in class ij.Menus
updateFullWindow - Variable in class ij.gui.Roi
updateHeadings() - Method in class ij.plugin.filter.Analyzer
  Redisplays the results table.
updateImage() - Method in class ij.CompositeImage
updateImage() - Method in class ij.gui.Plot
  Draws the plot again, ignored if the plot has not been drawn before or the plot is frozen.
updateImage() - Method in class ij.ImagePlus
  ImageCanvas.paint() calls this method when the ImageProcessor has generated a new image.
updateImage(ImagePlus) - Method in class ij.gui.ImageWindow
updateImageJMenus() - Static method in class ij.Menus
updateImagePlus(String, int) - Method in class ij.io.FileSaver
updateMenus() - Static method in class ij.Menus
  Updates the Image/Type and Window menus.
updatePlayPauseIcon() - Method in class ij.gui.ScrollbarWithLabel
updatePolygon() - Method in class ij.gui.PolygonRoi
updatePosition(int, int, int) - Method in class ij.ImagePlus
updateResults() - Method in class ij.measure.ResultsTable
  Updates the Results window.
updateSliceSelector() - Method in class ij.gui.StackWindow
  Updates the stack scrollbar.
updateStatusbarValue() - Method in class ij.ImagePlus
  Redisplays the (x,y) coordinates and pixel value (which may have changed) in the status bar.
updateTableOverlay(ImagePlus, int, int, int) - Static method in class ij.gui.Overlay
  Updates overlays created by the particle analyzer after rows are deleted from the Results table.
updateUrl(String) - Static method in class ij.io.Opener
  Can't open imagej.nih.gov URLs due to encryption so redirect to imagej.net mirror.
updateVirtualSlice() - Method in class ij.ImagePlus
  Use to update the image when the underlying virtual stack changes.
updateWideLine(float) - Method in class ij.gui.Roi
updateWindowList() - Method in class ij.plugin.frame.SyncWindows
updateWindowMenuItem(ImagePlus, String, String) - Static method in class ij.Menus
  Changes the name of an item in the Window menu.
updateWindowMenuItem(String, String) - Static method in class ij.Menus
  Changes the name of an item in the Window menu.
updateY(double, int) - Static method in class ij.plugin.filter.Analyzer
  Returns an updated Y coordinate based on the current "Invert Y Coordinates" flag.
updateY(int, int) - Static method in class ij.plugin.filter.Analyzer
  Returns an updated Y coordinate based on the current "Invert Y Coordinates" flag.
upperThreshold - Variable in class ij.process.ImageStatistics
  Maximum threshold when "Limit to threshold" enabled
url - Variable in class ij.io.FileInfo
URL - Static variable in class ij.IJ
  Deprecated.
URL2 - Static variable in class ij.IJ
  ImageJ website
URLOpener - Class in ij.plugin
  Opens TIFFs, ZIP compressed TIFFs, DICOMs, GIFs and JPEGs using a URL.
URLOpener() - Constructor for class ij.plugin.URLOpener
useFileChooser - Static variable in class ij.Prefs
  Use the file chooser to import and export image sequences on Windows and Linux
useInfo(String) - Static method in class ij.plugin.FolderOpener
useInvertingLut - Static variable in class ij.Prefs
  Open 8-bit images with inverting LUT so 0 is white and 255 is black.
useJFileChooser - Static variable in class ij.Prefs
  Use JFileChooser instead of FileDialog to open and save files.
useLineSubpixelConvention() - Method in class ij.gui.Roi
  Returns 'true' if this ROI uses for drawing the convention for line and point ROIs, where the coordinates are with respect to the pixel center.
useNamesAsLabels - Static variable in class ij.Prefs
  Use ROI names as "show all" labels in the ROI Manager
usePointer - Static variable in class ij.gui.ImageCanvas
usePointerCursor - Static variable in class ij.Prefs
  Use pointer cursor instead of cross
USER_FUNCTION - Static variable in interface ij.macro.MacroConstants
userFunction(double[], double) - Method in class ij.measure.CurveFitter
  This function is called by the Minimizer and calculates the sum of squared residuals for given parameters.
userFunction(double[], double) - Method in interface ij.measure.UserFunction
  A user-supplied function
UserFunction - Interface in ij.measure
  A plugin should implement this interface for minimizing a single-valued function or fitting a curve with a custom fit function.
useSystemProxies - Static variable in class ij.Prefs
  Set the "java.net.useSystemProxies" property
useTemplate(Plot) - Method in class ij.gui.Plot
  Adjusts the format with another plot as a template, using the current (usually default) templateFlags of this plot.
useTemplate(Plot, int) - Method in class ij.gui.Plot
  Adjusts the format (style) with another plot as a template.
UTILITIES_MENU - Static variable in class ij.Menus

## V

validDimensions() - Method in class ij.gui.StackWindow
validExtensions - Static variable in class ij.plugin.PluginInstaller
value - Variable in class ij.gui.HistogramWindow
value - Variable in class ij.macro.Symbol
valueChanged(ListSelectionEvent) - Method in class ij.plugin.frame.RoiManager
valueOf(String) - Static method in enum class ij.process.AutoThresholder.Method
  Returns the enum constant of this class with the specified name.
values() - Static method in enum class ij.process.AutoThresholder.Method
  Returns an array containing the constants of this enum class, in the order they are declared.
valueUnit - Variable in class ij.io.FileInfo
VAR - Static variable in interface ij.macro.MacroConstants
VAR - Static variable in class ij.plugin.Filters3D
Variable - Class in ij.macro
Variable() - Constructor for class ij.macro.Variable
Variable(double) - Constructor for class ij.macro.Variable
Variable(Variable[]) - Constructor for class ij.macro.Variable
Variable(String) - Constructor for class ij.macro.Variable
VARIABLE_FUNCTION - Static variable in interface ij.macro.MacroConstants
variableFunctionIDs - Static variable in interface ij.macro.MacroConstants
variableFunctions - Static variable in interface ij.macro.MacroConstants
VARIANCE - Static variable in class ij.plugin.filter.RankFilters
VERSION - Static variable in class ij.ImageJ
  Plugins should call IJ.getVersion() or IJ.getFullVersion() to get the version string.
VERSION_OFFSET - Static variable in class ij.io.RoiDecoder
versionLessThan(String) - Static method in class ij.IJ
  Displays an error message and returns true if the ImageJ version is less than the one specified.
verticalProfile - Static variable in class ij.Prefs
  Plot rectangular selectons vertically
VGAP - Static variable in class ij.gui.ImageWindow
virtualStack - Variable in class ij.io.FileInfo
VirtualStack - Class in ij
  This class represents an array of disk-resident images.
VirtualStack() - Constructor for class ij.VirtualStack
  Default constructor.
VirtualStack(int, int) - Constructor for class ij.VirtualStack
VirtualStack(int, int, int) - Constructor for class ij.VirtualStack
  Creates a virtual stack with no backing storage.
  See: Help>Examples>JavaScript>Terabyte VirtualStack
VirtualStack(int, int, int, String) - Constructor for class ij.VirtualStack
  Creates a virtual stack with no backing storage.
  See: Help>Examples>JavaScript>Terabyte VirtualStack
VirtualStack(int, int, ColorModel, String) - Constructor for class ij.VirtualStack
  Creates an empty virtual stack.
vistaHint - Static variable in class ij.Prefs
vListMap - Variable in class ij.plugin.frame.SyncWindows
  Hashtable to map list ids to image window ids.
vwins - Variable in class ij.plugin.frame.SyncWindows
  Indices of synchronized image windows are maintained in this Vector.

## W

wait(int) - Static method in class ij.IJ
  Delays 'msecs' milliseconds.
WAIT - Static variable in interface ij.macro.MacroConstants
WAIT_FOR_USER - Static variable in interface ij.macro.MacroConstants
WaitForUserDialog - Class in ij.gui
  This is a non-modal dialog box used to ask the user to perform some task while a macro or plugin is running.
WaitForUserDialog(String) - Constructor for class ij.gui.WaitForUserDialog
WaitForUserDialog(String, String) - Constructor for class ij.gui.WaitForUserDialog
waitTillActivated() - Method in class ij.ImagePlus
  Waits until the image window becomes activated.
Wand - Class in ij.gui
  This class implements ImageJ's wand (tracing) tool.
Wand(ImageProcessor) - Constructor for class ij.gui.Wand
  Constructs a Wand object from an ImageProcessor.
WAND - Static variable in class ij.gui.Toolbar
WandToolOptions - Class in ij.plugin
  This plugin implements the Edit/Options/Wand Tool command.
WandToolOptions() - Constructor for class ij.plugin.WandToolOptions
wasCanceled() - Method in class ij.gui.GenericDialog
  Returns true if the user clicked on "Cancel".
wasError() - Method in class ij.macro.Interpreter
wasOKed() - Method in class ij.gui.GenericDialog
  Returns true if the user has clicked on "OK" or a macro is running.
wavelengthToColor(double) - Static method in class ij.plugin.Colors
  Converts a wavelength (380-750 nm) to color.
weightedColor - Static variable in class ij.Prefs
  Color to grayscale conversion is weighted (0.299, 0.587, 0.114) if the variable is true.
weightedHistogram() - Method in class ij.process.ColorProcessor
weights - Variable in class ij.process.DownsizeTable
  For each source point, weights for adding it to the destination point given in the corresponding element of 'indices'
west(ImageProcessor) - Method in class ij.plugin.filter.Shadows
WHILE - Static variable in interface ij.macro.MacroConstants
whiteIsZero - Variable in class ij.io.FileInfo
whitePoint - Variable in class ij.process.ColorSpaceConverter
wideLine - Variable in class ij.gui.Roi
width - Variable in class ij.ImagePlus
width - Variable in class ij.io.FileInfo
width - Variable in class ij.process.ImageProcessor
width - Variable in class ij.process.ImageStatistics
WIDTH - Static variable in class ij.gui.ProgressBar
WIDTH_KEY - Static variable in class ij.gui.Arrow
WIDTH_KEY - Static variable in class ij.text.TextWindow
WIDTHD - Static variable in class ij.io.RoiDecoder
WildcardMatch - Class in ij.util
  This class allows for simple wildcard pattern matching.
WildcardMatch() - Constructor for class ij.util.WildcardMatch
WildcardMatch(char, char) - Constructor for class ij.util.WildcardMatch
win - Variable in class ij.ImagePlus
WINDOW_MENU_ITEMS - Static variable in class ij.Menus
windowActivated() - Method in class ij.ImagePlus
windowActivated(WindowEvent) - Method in class ij.gui.GenericDialog
windowActivated(WindowEvent) - Method in class ij.gui.HTMLDialog
windowActivated(WindowEvent) - Method in class ij.gui.ImageWindow
windowActivated(WindowEvent) - Method in class ij.gui.MessageDialog
windowActivated(WindowEvent) - Method in class ij.gui.NonBlockingGenericDialog
  Put the dialog into the foreground when the image we work on gets into the foreground
windowActivated(WindowEvent) - Method in class ij.gui.PlotWindow
  Called when the window is activated (WindowListener) Window layout is finished at latest a few millisec after windowActivated, then the 'wasActivated' boolean is set to tell the ImageCanvas that resize events should lead to resizing the canvas (before, creating the layout can lead to resize events)
windowActivated(WindowEvent) - Method in class ij.gui.RoiProperties
windowActivated(WindowEvent) - Method in class ij.gui.YesNoCancelDialog
windowActivated(WindowEvent) - Method in class ij.ImageJ
windowActivated(WindowEvent) - Method in class ij.macro.FunctionFinder
windowActivated(WindowEvent) - Method in class ij.plugin.CommandFinder
windowActivated(WindowEvent) - Method in class ij.plugin.frame.ColorThresholder
windowActivated(WindowEvent) - Method in class ij.plugin.frame.ContrastAdjuster
windowActivated(WindowEvent) - Method in class ij.plugin.frame.Editor
  Override windowActivated in PlugInFrame to prevent Mac menu bar from being installed.
windowActivated(WindowEvent) - Method in class ij.plugin.frame.LineWidthAdjuster
windowActivated(WindowEvent) - Method in class ij.plugin.frame.PlugInDialog
windowActivated(WindowEvent) - Method in class ij.plugin.frame.PlugInFrame
windowActivated(WindowEvent) - Method in class ij.plugin.frame.Recorder
  Override windowActivated in PlugInFrame.
windowActivated(WindowEvent) - Method in class ij.plugin.frame.RoiManager
windowActivated(WindowEvent) - Method in class ij.plugin.frame.ThresholdAdjuster
windowActivated(WindowEvent) - Method in class ij.plugin.Orthogonal_Views
windowClosed(WindowEvent) - Method in class ij.gui.GenericDialog
windowClosed(WindowEvent) - Method in class ij.gui.HTMLDialog
windowClosed(WindowEvent) - Method in class ij.gui.ImageWindow
windowClosed(WindowEvent) - Method in class ij.gui.MessageDialog
windowClosed(WindowEvent) - Method in class ij.gui.RoiProperties
windowClosed(WindowEvent) - Method in class ij.gui.YesNoCancelDialog
windowClosed(WindowEvent) - Method in class ij.ImageJ
windowClosed(WindowEvent) - Method in class ij.macro.FunctionFinder
windowClosed(WindowEvent) - Method in class ij.plugin.CommandFinder
windowClosed(WindowEvent) - Method in class ij.plugin.frame.PlugInDialog
windowClosed(WindowEvent) - Method in class ij.plugin.frame.PlugInFrame
windowClosed(WindowEvent) - Method in class ij.plugin.Orthogonal_Views
windowClosing(WindowEvent) - Method in class ij.gui.GenericDialog
windowClosing(WindowEvent) - Method in class ij.gui.HTMLDialog
windowClosing(WindowEvent) - Method in class ij.gui.ImageWindow
windowClosing(WindowEvent) - Method in class ij.gui.MessageDialog
windowClosing(WindowEvent) - Method in class ij.gui.NonBlockingGenericDialog
windowClosing(WindowEvent) - Method in class ij.gui.RoiProperties
windowClosing(WindowEvent) - Method in class ij.gui.YesNoCancelDialog
windowClosing(WindowEvent) - Method in class ij.ImageJ
windowClosing(WindowEvent) - Method in class ij.macro.FunctionFinder
windowClosing(WindowEvent) - Method in class ij.plugin.CommandFinder
windowClosing(WindowEvent) - Method in class ij.plugin.frame.PlugInDialog
windowClosing(WindowEvent) - Method in class ij.plugin.frame.PlugInFrame
windowClosing(WindowEvent) - Method in class ij.plugin.frame.SyncWindows
  Override parent windowClosing method to clean up synchronized resources on exit.
windowClosing(WindowEvent) - Method in class ij.plugin.Orthogonal_Views
windowDeactivated(WindowEvent) - Method in class ij.gui.GenericDialog
windowDeactivated(WindowEvent) - Method in class ij.gui.HTMLDialog
windowDeactivated(WindowEvent) - Method in class ij.gui.ImageWindow
windowDeactivated(WindowEvent) - Method in class ij.gui.MessageDialog
windowDeactivated(WindowEvent) - Method in class ij.gui.RoiProperties
windowDeactivated(WindowEvent) - Method in class ij.gui.YesNoCancelDialog
windowDeactivated(WindowEvent) - Method in class ij.ImageJ
windowDeactivated(WindowEvent) - Method in class ij.macro.FunctionFinder
windowDeactivated(WindowEvent) - Method in class ij.plugin.CommandFinder
windowDeactivated(WindowEvent) - Method in class ij.plugin.frame.PlugInDialog
windowDeactivated(WindowEvent) - Method in class ij.plugin.frame.PlugInFrame
windowDeactivated(WindowEvent) - Method in class ij.plugin.Orthogonal_Views
windowDeiconified(WindowEvent) - Method in class ij.gui.GenericDialog
windowDeiconified(WindowEvent) - Method in class ij.gui.HTMLDialog
windowDeiconified(WindowEvent) - Method in class ij.gui.ImageWindow
windowDeiconified(WindowEvent) - Method in class ij.gui.MessageDialog
windowDeiconified(WindowEvent) - Method in class ij.gui.RoiProperties
windowDeiconified(WindowEvent) - Method in class ij.gui.YesNoCancelDialog
windowDeiconified(WindowEvent) - Method in class ij.ImageJ
windowDeiconified(WindowEvent) - Method in class ij.macro.FunctionFinder
windowDeiconified(WindowEvent) - Method in class ij.plugin.CommandFinder
windowDeiconified(WindowEvent) - Method in class ij.plugin.frame.PlugInDialog
windowDeiconified(WindowEvent) - Method in class ij.plugin.frame.PlugInFrame
windowDeiconified(WindowEvent) - Method in class ij.plugin.Orthogonal_Views
windowIconified(WindowEvent) - Method in class ij.gui.GenericDialog
windowIconified(WindowEvent) - Method in class ij.gui.HTMLDialog
windowIconified(WindowEvent) - Method in class ij.gui.ImageWindow
windowIconified(WindowEvent) - Method in class ij.gui.MessageDialog
windowIconified(WindowEvent) - Method in class ij.gui.RoiProperties
windowIconified(WindowEvent) - Method in class ij.gui.YesNoCancelDialog
windowIconified(WindowEvent) - Method in class ij.ImageJ
windowIconified(WindowEvent) - Method in class ij.macro.FunctionFinder
windowIconified(WindowEvent) - Method in class ij.plugin.CommandFinder
windowIconified(WindowEvent) - Method in class ij.plugin.frame.PlugInDialog
windowIconified(WindowEvent) - Method in class ij.plugin.frame.PlugInFrame
windowIconified(WindowEvent) - Method in class ij.plugin.Orthogonal_Views
WindowManager - Class in ij
  This class consists of static methods used to manage ImageJ's windows.
windowOpened(WindowEvent) - Method in class ij.gui.GenericDialog
windowOpened(WindowEvent) - Method in class ij.gui.HTMLDialog
windowOpened(WindowEvent) - Method in class ij.gui.ImageWindow
windowOpened(WindowEvent) - Method in class ij.gui.MessageDialog
windowOpened(WindowEvent) - Method in class ij.gui.RoiProperties
windowOpened(WindowEvent) - Method in class ij.gui.YesNoCancelDialog
windowOpened(WindowEvent) - Method in class ij.ImageJ
windowOpened(WindowEvent) - Method in class ij.macro.FunctionFinder
windowOpened(WindowEvent) - Method in class ij.plugin.CommandFinder
windowOpened(WindowEvent) - Method in class ij.plugin.frame.PlugInDialog
windowOpened(WindowEvent) - Method in class ij.plugin.frame.PlugInFrame
windowOpened(WindowEvent) - Method in class ij.plugin.Orthogonal_Views
WindowOrganizer - Class in ij.plugin
  This class implements the Window menu's "Show All", "Main Window", "Cascade" and "Tile" commands.
WindowOrganizer() - Constructor for class ij.plugin.WindowOrganizer
windowStateChanged(WindowEvent) - Method in class ij.gui.ImageWindow
wipeBack() - Method in class ij.gui.PolygonRoi
wList - Variable in class ij.plugin.frame.SyncWindows
  List of currently displayed windows retrieved from ImageJ window manager.
WORD - Static variable in interface ij.macro.MacroConstants
write(byte[]) - Method in class ij.io.LogStream
write(byte[], int, int) - Method in class ij.io.LogStream
write(int) - Method in class ij.io.LogStream
write(Roi) - Method in class ij.io.RoiEncoder
  Save the Roi to the file of stream.
write(DataOutputStream) - Method in class ij.io.TextEncoder
  Saves the image as a tab-delimited text file.
write(DataOutputStream) - Method in class ij.io.TiffEncoder
write(OutputStream) - Method in class ij.io.ImageWriter
  Writes the image to the specified OutputStream.
write(OutputStream) - Method in class ij.io.TiffEncoder
  Saves the image as a TIFF file.
write(String) - Static method in class ij.IJ
  Deprecated.
  replaced by IJ.log(), ResultsTable.setResult() and TextWindow.append(). There are examples at http://imagej.nih.gov/ij/plugins/sine-cosine.html
WRITE - Static variable in interface ij.macro.MacroConstants
writeImage(ImagePlus, String, int) - Method in class ij.plugin.PNG_Writer
writeImage(ImagePlus, String, int, int) - Method in class ij.plugin.filter.AVI_Writer
  Writes an ImagePlus (stack) as AVI file.
Writer - Class in ij.plugin.filter
  Deprecated.
Writer() - Constructor for class ij.plugin.filter.Writer
  Deprecated.

## X

x - Variable in class ij.plugin.frame.SyncWindows
X - Static variable in class ij.gui.Plot
  Display points using an X-shaped mark.
X - Static variable in class ij.gui.PlotWindow
  Deprecated.
X_AXIS - Static variable in class ij.gui.PlotDialog
  Types of dialog.
X_CENTER_OF_MASS - Static variable in class ij.measure.ResultsTable
X_CENTROID - Static variable in class ij.measure.ResultsTable
X_FORCE2GRID - Static variable in class ij.gui.Plot
  flag for forcing frame to coincide with the grid/ticks in x direction (results in unused space)
X_GRID - Static variable in class ij.gui.Plot
  flag for drawing vertical grid lines for x axis
X_LEFT - Static variable in class ij.gui.PlotDialog
  Types of dialog.
X_LOG_NUMBERS - Static variable in class ij.gui.Plot
  flag for logarithmic x-axis
X_LOG_TICKS - Static variable in class ij.gui.Plot
  flag for ticks (major and minor, if space) on logarithmic x axis
X_MINOR_TICKS - Static variable in class ij.gui.Plot
  flag for drawing minor ticks on linear (non-logarithmic) x axis
X_NUMBERS - Static variable in class ij.gui.Plot
  flag for numeric labels of x-axis ticks
X_RANGE - Static variable in class ij.gui.Plot
  Flag for addressing the x axis, for copying from a template: copy/write x axis range.
X_RESOLUTION - Static variable in class ij.io.TiffDecoder
X_RIGHT - Static variable in class ij.gui.PlotDialog
  Types of dialog.
X_TICKS - Static variable in class ij.gui.Plot
  flag for drawing major ticks on linear (non-logarithmic) x axis
x1 - Variable in class ij.gui.Line
X1 - Static variable in class ij.io.RoiDecoder
x1d - Variable in class ij.gui.Line
x1R - Variable in class ij.gui.Line
x2 - Variable in class ij.gui.Line
X2 - Static variable in class ij.io.RoiDecoder
x2d - Variable in class ij.gui.Line
x2R - Variable in class ij.gui.Line
xCenter - Variable in class ij.process.EllipseFitter
  X centroid
xCenterOfMass - Variable in class ij.process.ImageStatistics
xCentroid - Variable in class ij.process.ImageStatistics
xCoordinates - Variable in class ij.process.EllipseFitter
  Initialized by makeRoi()
XD - Static variable in class ij.io.RoiDecoder
xInc - Variable in class ij.gui.ProfilePlot
XINC - Static variable in class ij.plugin.frame.Editor
XINC - Static variable in class ij.plugin.MacroInstaller
xloc - Static variable in class ij.gui.WaitForUserDialog
xMax - Variable in class ij.gui.Roi
xMax - Variable in class ij.process.ImageProcessor
xMin - Variable in class ij.process.ImageProcessor
xMouse - Variable in class ij.gui.ImageCanvas
xMouseStart - Variable in class ij.gui.ImageCanvas
xor(int) - Method in class ij.process.FloatProcessor
xor(int) - Method in class ij.process.ImageProcessor
  Binary exclusive OR of each pixel in the image or ROI with 'value'.
xor(int) - Method in class ij.process.ShortProcessor
xor(int[]) - Method in class ij.gui.Overlay
  Returns the bounds of this overlay.
xor(Roi[]) - Static method in class ij.gui.Roi
xor(ShapeRoi) - Method in class ij.gui.ShapeRoi
  Unary exclusive or operator.
XOR - Static variable in interface ij.process.Blitter
  dst=dst XOR src
xOrigin - Variable in class ij.measure.Calibration
  X origin in pixels.
xp - Variable in class ij.gui.PolygonRoi
xp2 - Variable in class ij.gui.PolygonRoi
xpf - Variable in class ij.gui.PolygonRoi
xpoints - Variable in class ij.gui.Wand
  The x-coordinates of the points in the outline.
xpoints - Variable in class ij.process.FloatPolygon
xSpline - Variable in class ij.gui.PolygonRoi
xSrcStart - Variable in class ij.gui.ImageCanvas
xstart - Variable in class ij.process.ImageStatistics
  Used internally by AnalyzeParticles
xValues - Variable in class ij.gui.ProfilePlot
XY_Reader - Class in ij.plugin
  This plugin implements the File/Import/XY Coordinates command.
XY_Reader() - Constructor for class ij.plugin.XY_Reader
XYCoordinates - Class in ij.plugin
  Writes the XY coordinates and pixel values of all non-background pixels to a tab-delimited text file.
XYCoordinates() - Constructor for class ij.plugin.XYCoordinates
XYWriter - Class in ij.plugin.filter
  Saves the XY coordinates of the current ROI boundary.
XYWriter() - Constructor for class ij.plugin.filter.XYWriter
xyYtoXYZ(double[]) - Method in class ij.process.ColorSpaceConverter
xyYtoXYZ(double, double, double) - Method in class ij.process.ColorSpaceConverter
XYZtoLAB(double[]) - Method in class ij.process.ColorSpaceConverter
  Convert XYZ to LAB.
XYZtoLAB(double, double, double) - Method in class ij.process.ColorSpaceConverter
  Convert XYZ to LAB.
XYZtoRGB(double[]) - Method in class ij.process.ColorSpaceConverter
  Convert XYZ to RGB
XYZtoRGB(double, double, double) - Method in class ij.process.ColorSpaceConverter
  Convert XYZ to RGB.
XYZtoxyY(double[]) - Method in class ij.process.ColorSpaceConverter
XYZtoxyY(double, double, double) - Method in class ij.process.ColorSpaceConverter

## Y

y - Variable in class ij.plugin.frame.SyncWindows
Y_AXIS - Static variable in class ij.gui.PlotDialog
  Types of dialog.
Y_BOTTOM - Static variable in class ij.gui.PlotDialog
  Types of dialog.
Y_CENTER_OF_MASS - Static variable in class ij.measure.ResultsTable
Y_CENTROID - Static variable in class ij.measure.ResultsTable
Y_FORCE2GRID - Static variable in class ij.gui.Plot
  flag for forcing frame to coincide with the grid/ticks in y direction (results in unused space)
Y_GRID - Static variable in class ij.gui.Plot
  flag for drawing horizontal grid lines for y axis
Y_LOG_NUMBERS - Static variable in class ij.gui.Plot
  flag for logarithmic y axis
Y_LOG_TICKS - Static variable in class ij.gui.Plot
  flag for ticks (major and minor, if space) on logarithmic y axis
Y_MINOR_TICKS - Static variable in class ij.gui.Plot
  flag for drawing minor ticks on linear (non-logarithmic) y axis
Y_NUMBERS - Static variable in class ij.gui.Plot
  flag for numeric labels of x-axis ticks
Y_RANGE - Static variable in class ij.gui.Plot
  Flag for addressing the y axis, for copying from a template: copy/write y axis range
Y_RESOLUTION - Static variable in class ij.io.TiffDecoder
Y_TICKS - Static variable in class ij.gui.Plot
  flag for drawing major ticks on linear (non-logarithmic) y axis
Y_TOP - Static variable in class ij.gui.PlotDialog
  Types of dialog.
y1 - Variable in class ij.gui.Line
Y1 - Static variable in class ij.io.RoiDecoder
y1d - Variable in class ij.gui.Line
y1R - Variable in class ij.gui.Line
y2 - Variable in class ij.gui.Line
Y2 - Static variable in class ij.io.RoiDecoder
y2d - Variable in class ij.gui.Line
y2R - Variable in class ij.gui.Line
ybase - Static variable in class ij.plugin.frame.ColorPicker
yCenter - Variable in class ij.process.EllipseFitter
  X centroid
yCenterOfMass - Variable in class ij.process.ImageStatistics
yCentroid - Variable in class ij.process.ImageStatistics
yCoordinates - Variable in class ij.process.EllipseFitter
  Initialized by makeRoi()
YD - Static variable in class ij.io.RoiDecoder
Yen - Enum constant in enum class ij.process.AutoThresholder.Method
Yen(int[]) - Static method in class ij.process.AutoThresholder
YesNoCancelDialog - Class in ij.gui
  A modal dialog box with a one line message and "Yes", "No" and "Cancel" buttons.
YesNoCancelDialog(Frame, String, String) - Constructor for class ij.gui.YesNoCancelDialog
YesNoCancelDialog(Frame, String, String, String, String) - Constructor for class ij.gui.YesNoCancelDialog
yesPressed() - Method in class ij.gui.YesNoCancelDialog
  Returns true if the user dismissed dialog by pressing "Yes".
YINC - Static variable in class ij.plugin.frame.Editor
YINC - Static variable in class ij.plugin.MacroInstaller
yLabel - Variable in class ij.gui.ProfilePlot
yloc - Static variable in class ij.gui.WaitForUserDialog
yMax - Variable in class ij.gui.HistogramWindow
yMax - Variable in class ij.gui.Roi
yMax - Variable in class ij.process.ImageProcessor
yMin - Variable in class ij.process.ImageProcessor
yMouse - Variable in class ij.gui.ImageCanvas
yMouseStart - Variable in class ij.gui.ImageCanvas
yOrigin - Variable in class ij.measure.Calibration
  Y origin in pixels.
yp - Variable in class ij.gui.PolygonRoi
yp2 - Variable in class ij.gui.PolygonRoi
ypf - Variable in class ij.gui.PolygonRoi
ypoints - Variable in class ij.gui.Wand
  The y-coordinates of the points in the outline.
ypoints - Variable in class ij.process.FloatPolygon
ySpline - Variable in class ij.gui.PolygonRoi
ySrcStart - Variable in class ij.gui.ImageCanvas
ystart - Variable in class ij.process.ImageStatistics
  Used internally by AnalyzeParticles

## Z

Z_POSITION - Static variable in class ij.io.RoiDecoder
ZAxisProfiler - Class in ij.plugin
  Implements the Image/Stacks/Plot Z-axis Profile command, which plots the selection mean gray value versus slice number.
ZAxisProfiler() - Constructor for class ij.plugin.ZAxisProfiler
ZCT - Static variable in class ij.plugin.HyperStackConverter
ZERO_TRANSPARENT - Static variable in class ij.io.RoiDecoder
zeroClip() - Method in class ij.measure.Calibration
  Returns true if zero clipping is enabled.
ZIP - Static variable in class ij.io.FileInfo
ZIP - Static variable in class ij.io.Opener
ZIP_ARCHIVE - Static variable in class ij.io.FileInfo
ZIP_WITH_DIFFERENCING - Static variable in class ij.io.FileInfo
zipUncompress(byte[]) - Method in class ij.io.ImageReader
  TIFF Adobe ZIP support contributed by Jason Newton.
zoom(String) - Method in class ij.gui.PlotCanvas
  Zoom operations that are handled by ij.plugin.Zoom
Zoom - Class in ij.plugin
  This plugin implements the commands in the Image/Zoom submenu.
Zoom() - Constructor for class ij.plugin.Zoom
zoom100Percent() - Method in class ij.gui.ImageCanvas
  Implements the Image/Zoom/View 100% command.
zoom100Percent() - Method in class ij.gui.PlotCanvas
  Implements the Image/Zoom/View 100% command: Sets the original frame size as specified in Edit/Options/Plots (unless the plot is frozen)
zoomIn(int, int) - Method in class ij.gui.ImageCanvas
  Zooms in by making the window bigger.
zoomIn(int, int) - Method in class ij.gui.PlotCanvas
  Zooms in by modifying the plot range; sx and sy are screen coordinates
zoomOut(int, int) - Method in class ij.gui.ImageCanvas
  Zooms out by making the source rectangle (srcRect) larger and centering it on (x,y).
zoomOut(int, int) - Method in class ij.gui.PlotCanvas
  Zooms out by modifying the plot range; sx and sy are screen coordinates
zoomTargetOX - Variable in class ij.gui.ImageCanvas
  Image (=offscreen) coordinates where the cursor was moved to for zooming
zoomTargetOY - Variable in class ij.gui.ImageCanvas
zOrigin - Variable in class ij.measure.Calibration
  Z origin in pixels.
ZProjector - Class in ij.plugin
  This plugin performs a z-projection of the input stack.
ZProjector() - Constructor for class ij.plugin.ZProjector
ZProjector(ImagePlus) - Constructor for class ij.plugin.ZProjector
  Construction of ZProjector with image to be projected.
zScale(ImagePlus, int, int) - Method in class ij.plugin.Resizer
zSelector - Variable in class ij.gui.StackWindow
ZTC - Static variable in class ij.plugin.HyperStackConverter

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