.. currentmodule:: brian2

.. spike_initiation:

Example: spike_initiation
=========================


        .. only:: html

            .. |launchbinder| image:: file:///usr/share/doc/python-brian-doc/docs/badge.svg
            .. _launchbinder: https://mybinder.org/v2/gh/brian-team/brian2-binder/master?filepath=examples/compartmental/spike_initiation.ipynb

            .. note::
               You can launch an interactive, editable version of this
               example without installing any local files
               using the Binder service (although note that at some times this
               may be slow or fail to open): |launchbinder|_

        

Ball and stick with Na and K channels

::

    from brian2 import *
    
    defaultclock.dt = 0.025*ms
    
    # Morphology
    morpho = Soma(30*um)
    morpho.axon = Cylinder(diameter=1*um, length=300*um, n=100)
    
    # Channels
    gL = 1e-4*siemens/cm**2
    EL = -70*mV
    ENa = 50*mV
    ka = 6*mV
    ki = 6*mV
    va = -30*mV
    vi = -50*mV
    EK = -90*mV
    vk = -20*mV
    kk = 8*mV
    eqs = '''
    Im = gL*(EL-v)+gNa*m*h*(ENa-v)+gK*n*(EK-v) : amp/meter**2
    dm/dt = (minf-m)/(0.3*ms) : 1 # simplified Na channel
    dh/dt = (hinf-h)/(3*ms) : 1 # inactivation
    dn/dt = (ninf-n)/(5*ms) : 1 # K+
    minf = 1/(1+exp((va-v)/ka)) : 1
    hinf = 1/(1+exp((v-vi)/ki)) : 1
    ninf = 1/(1+exp((vk-v)/kk)) : 1
    I : amp (point current)
    gNa : siemens/meter**2
    gK : siemens/meter**2
    '''
    
    neuron = SpatialNeuron(morphology=morpho, model=eqs,
                           Cm=1*uF/cm**2, Ri=100*ohm*cm, method='exponential_euler')
    neuron.v = -65*mV
    neuron.I = 0*amp
    neuron.axon[30*um:60*um].gNa = 700*gL
    neuron.axon[30*um:60*um].gK = 700*gL
    
    # Monitors
    mon=StateMonitor(neuron, 'v', record=True)
    
    run(1*ms)
    neuron.main.I = 0.15*nA
    run(50*ms)
    neuron.I = 0*amp
    run(95*ms, report='text')
    
    plot(mon.t/ms, mon.v[0]/mV, 'r')
    plot(mon.t/ms, mon.v[20]/mV, 'g')
    plot(mon.t/ms, mon.v[40]/mV, 'b')
    plot(mon.t/ms, mon.v[60]/mV, 'k')
    plot(mon.t/ms, mon.v[80]/mV, 'y')
    xlabel('Time (ms)')
    ylabel('v (mV)')
    show()
    

