Plugin type: 2dstack/filter
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## Plugin type: 2dstack/filter

These filters work on a stack of 2D images in a 3D manner by interpreting the images of the stack as slices of a 3D image. For spacial filters with a fixed filter width that is small compared to the number of slices the filter is applied in a true 3D manner. For other filters, that would normally require to work on the whole image domain at once, the image filter is only applied to a subset of the images at a time which results in a quasi-3D processing that may require additional post-processing.

#### Plugins:

byslice close dilate erode gauss label median mlv open regiongrow

##### byslice

Runs a filter on a per slice basis. In essence, this is a wrapper that makes it possible to add pure 2D filters to the stack filter pipeline without ducplicating the implementation.. Supported parameters are:

Name | Type | Default | Description
--- | --- | --- | ---
filter | factory | (required) | 2D filter to be applied. For supported plug-ins see Plugin type: 2dimage/filter

##### close

2D Stack morphological filter 'close'. Supported parameters are:

Name | Type | Default | Description
--- | --- | --- | ---
shape | factory | 6n | structuring element. For supported plug-ins see Plugin type: 3dimage/shape

##### dilate

2D Stack morphological filter 'dilate'. Supported parameters are:

Name | Type | Default | Description
--- | --- | --- | ---
shape | factory | 6n | structuring element. For supported plug-ins see Plugin type: 3dimage/shape

##### erode

2D Stack morphological filter 'erode'. Supported parameters are:

Name | Type | Default | Description
--- | --- | --- | ---
shape | factory | 6n | structuring element. For supported plug-ins see Plugin type: 3dimage/shape

##### gauss

Gauss 2D fifo filter. Supported parameters are:

Name | Type | Default | Description
--- | --- | --- | ---
w | int in [1, inf) | 1 | filter width parameter (2*w+1)

##### label

Stack Label filter. Supported parameters are:

Name | Type | Default | Description
--- | --- | --- | ---
map | string | (input,required) | Mapfile to save label numbers that are joined
n | factory | 4n | 2D neighbourhood shape to define connectedness. For supported plug-ins see Plugin type: 2dimage/shape

##### median

median 2D fifo filter. Supported parameters are:

Name | Type | Default | Description
--- | --- | --- | ---
w | int in [1, inf) | 1 | filter width parameter

##### mlv

Mean of Least Variance 2D stack image filter. Supported parameters are:

Name | Type | Default | Description
--- | --- | --- | ---
w | int in [1, inf) | 1 | filter width parameter

##### open

2D Stack morphological filter 'open'. Supported parameters are:

Name | Type | Default | Description
--- | --- | --- | ---
shape | factory | 6n | structuring element. For supported plug-ins see Plugin type: 3dimage/shape

##### regiongrow

Run a region-growing filter on a stack of images that comprise a 3D image. The region growing is based on class probabilities obtained from a c-means classification of the pixel intensities. One seed thresh is use to initiate a region, and another (lower) threshold is used to stop the region growing. By holding a number of 3D slices in the working memory to permit the region to grow "backwards " in the stack a Quasi-3D processing is achieved. However, with complex structures the region growing may not properly be segmented.. Supported parameters are:

Name | Type | Default | Description
--- | --- | --- | ---
class | int in [0, inf) | 2 | class to be segmented
depth | int in [1, inf) | 10 | number of slices to keep during processing
low | float in (0, 1] | 0.5 | low threshold for acceptance probability
map | string | (input,required) | seed class map
seed | float in (0, 1] | 0.98 | threshold for seed probability

#### Plugin consumers:

mia-2dstackfilter

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