examples-electrophysiology_AEC.txt

.. currentmodule:: brian

.. index::
   pair: example usage; plot
   pair: example usage; run
   pair: example usage; figure
   pair: example usage; show
   pair: example usage; sum
   pair: example usage; Clock
   pair: example usage; NeuronGroup
   pair: example usage; Equations
   pair: example usage; StateMonitor

.. _example-electrophysiology_AEC:

Example: AEC (electrophysiology)
================================

AEC experiment (current-clamp)

::

    from brian import *
    from brian.library.electrophysiology import *
    from time import time
    
    myclock = Clock(dt=.1 * ms)
    clock_rec = Clock(dt=.1 * ms)
    
    #log_level_debug()
    
    taum = 20 * ms
    gl = 20 * nS
    Cm = taum * gl
    Re = 50 * Mohm
    Ce = 0.1 * ms / Re
    
    eqs = Equations('''
    dvm/dt=(-gl*vm+i_inj)/Cm : volt
    I:amp
    ''')
    eqs += electrode(.6 * Re, Ce)
    eqs += current_clamp(vm='v_el', i_inj='i_cmd', i_cmd='I', Re=.4 * Re, Ce=Ce)
    setup = NeuronGroup(1, model=eqs, clock=myclock)
    board = AEC(setup, 'v_rec', 'I', clock_rec)
    recording = StateMonitor(board, 'record', record=True, clock=myclock)
    soma = StateMonitor(setup, 'vm', record=True, clock=myclock)
    
    run(50 * ms)
    board.command = .5 * nA
    run(200 * ms)
    board.command = 0 * nA
    run(150 * ms)
    board.start_injection()
    t1 = time()
    run(1 * second)
    t2 = time()
    print 'Duration:', t2 - t1, 's'
    board.stop_injection()
    run(100 * ms)
    board.estimate()
    print 'Re=', sum(board.Ke) * ohm
    board.switch_on()
    run(50 * ms)
    board.command = .5 * nA
    run(200 * ms)
    board.command = 0 * nA
    run(150 * ms)
    board.switch_off()
    figure()
    plot(recording.times / ms, recording[0] / mV, 'b')
    plot(soma.times / ms, soma[0] / mV, 'r')
    figure()
    plot(board.Ke)
    show()