def showSampleModelsPanel():
loadVerySimpleCellButton = G.addButton('Very simple cell',
loadModule,
extraData={
'module': 'verysimple_cell',
'model': 'VerySimpleCell',
'action': 'loadModel'
})
loadSimpleCellButton = G.addButton('Simple cell',
loadModule,
extraData={
'module': 'simple_cell',
'model': 'SimpleCell',
'action': 'loadModel'
})
loadSimpleNetworkButton = G.addButton('Simple network',
loadModule,
extraData={
'module': 'simple_network',
'model': 'SimpleNetwork',
'action': 'loadModel'
})
loadModelPanel = G.addPanel('Load Models',
items=[
loadVerySimpleCellButton,
loadSimpleCellButton,
loadSimpleNetworkButton
],
widget_id='loadModelPanel',
positionX=90,
positionY=10)
loadModelPanel.display()
def analysis(self):
#from matplotlib import pyplot
#pyplot.figure(figsize=(8,4)) # Default figsize is (8,6)
#pyplot.plot(self.t_vec, self.v_vec)
#pyplot.xlabel('time (ms)')
#pyplot.ylabel('mV')
#pyplot.show()
G.plotVariable('Plot', ['VerySimpleCell.v_vec'])
def showAnalysisPanel():
analysisButton = G.addButton('Plot',
loadModule,
extraData={'action': 'analysis'})
analysisPanel = G.addPanel('Analysis',
items=[analysisButton],
widget_id='analysisPanel',
positionX=90,
positionY=250)
analysisPanel.display()
def analysis(self):
#from matplotlib import pyplot
# pyplot.figure(figsize=(8,4)) # Default figsize is (8,6)
# pyplot.plot(self.t_vec, self.v_vec_soma, label='soma')
# pyplot.plot(self.t_vec, self.v_vec_dend, 'r', label='dend')
# pyplot.xlabel('time (ms)')
# pyplot.ylabel('mV')
# pyplot.legend()
# pyplot.show()
#plot voltage vs time
G.plotVariable('Plot', ['SimpleCell.v_vec_dend', 'SimpleCell.v_vec_soma'])
def plot_voltage(self):
"""Plot the recorded traces"""
#pyplot.figure(figsize=(8,4)) # Default figsize is (8,6)
#pyplot.plot(self.t_vec, self.soma_v_vec, color='black', label='soma(0.5')
#pyplot.plot(self.t_vec, self.dend_v_vec, color='red', label='dend(0.5)')
#pyplot.legend()
#pyplot.xlabel('time (ms)')
#pyplot.ylabel('mV')
#pyplot.ylim(-80,20)
#pyplot.title('Cell voltage')
#pyplot.show()
G.plotVariable('Plot', ['SimpleNetwork.soma_v_vec_' + str(self.cell_index), 'SimpleNetwork.dend_v_vec_' + str(self.cell_index)])
def loadModel(self):
G.createProject(name = 'Simple Cell')
print('Loading Model...')
self.soma = h.Section(name='soma')
self.dend = h.Section(name='dend')
self.dend.connect(self.soma(1))
# Surface area of cylinder is 2*pi*r*h (sealed ends are implicit).
self.soma.L = self.soma.diam = 12.6157 # Makes a soma of 500 microns squared.
self.dend.L = 200 # microns
self.dend.diam = 1 # microns
for sec in h.allsec():
sec.Ra = 100 # Axial resistance in Ohm * cm
sec.cm = 1 # Membrane capacitance in micro Farads / cm^2
# Insert active Hodgkin-Huxley current in the soma
self.soma.insert('hh')
self.soma.gnabar_hh = 0.12 # Sodium conductance in S/cm2
self.soma.gkbar_hh = 0.036 # Potassium conductance in S/cm2
self.soma.gl_hh = 0.0003 # Leak conductance in S/cm2
self.soma.el_hh = -54.3 # Reversal potential in mV
# Insert passive current in the dendrite
self.dend.insert('pas')
self.dend.g_pas = 0.001 # Passive conductance in S/cm2
self.dend.e_pas = -65 # Leak reversal potential mV
self.dend.nseg = 10
# add synapse (custom channel)
self.syn = h.AlphaSynapse(self.dend(1.0))
self.syn.e = 0 # equilibrium potential in mV
self.syn.onset = 20 # turn on after this time in ms
self.syn.gmax = 0.05 # set conductance in uS
self.syn.tau = 0.1 # set time constant
# record soma voltage and time
self.t_vec = h.Vector()
self.t_vec.record(h._ref_t)
G.createStateVariable(id = 'time', name = 'time', units = 'ms', neuron_variable = self.t_vec)
self.v_vec_soma = h.Vector()
self.v_vec_soma.record(self.soma(1.0)._ref_v) # change recoding pos
#TODO How do we extract the units?
G.createStateVariable(id = 'v_vec_soma', name = 'v_vec_soma', units = 'mV', neuron_variable = self.v_vec_soma)
self.v_vec_dend = h.Vector()
self.v_vec_dend.record(self.dend(1.0)._ref_v)
#TODO How do we extract the units?
G.createStateVariable(id = 'v_vec_dend', name = 'v_vec_dend', units = 'mV', neuron_variable = self.v_vec_dend)
# run simulation
h.tstop = 60 # ms
def set_recording(self):
"""Set soma, dendrite, and time recording vectors on the cell. """
self.soma_v_vec = h.Vector() # Membrane potential vector at soma
self.dend_v_vec = h.Vector() # Membrane potential vector at dendrite
self.t_vec = h.Vector() # Time stamp vector
self.soma_v_vec.record(self.soma(0.5)._ref_v)
G.createStateVariable(id = 'soma_v_vec_' + str(self.cell_index), name = 'soma_v_vec for cell ' + str(self.cell_index), units = 'mV', neuron_variable = self.soma_v_vec)
self.dend_v_vec.record(self.dend(0.5)._ref_v)
G.createStateVariable(id = 'dend_v_vec_' + str(self.cell_index), name = 'dend_v_vec for cell ' + str(self.cell_index), units = 'mV', neuron_variable = self.dend_v_vec)
self.t_vec.record(h._ref_t)
G.createStateVariable(id = 'time', name = 'time', units = 'ms', neuron_variable = self.t_vec)
def loadModel(self):
G.createProject(name='Very Simple Cell')
print('Loading Model...')
self.soma = h.Section(name='soma')
self.soma.insert('pas')
self.asyn = h.AlphaSynapse(self.soma(0.5))
self.asyn.onset = 20
self.asyn.gmax = 1
self.v_vec = h.Vector() # Membrane potential vector
self.t_vec = h.Vector() # Time stamp vector
self.v_vec.record(self.soma(0.5)._ref_v)
G.createStateVariable(id='v_vec',
name='v_vec',
units='mV',
neuron_variable=self.v_vec)
self.t_vec.record(h._ref_t)
G.createStateVariable(id='time',
name='time',
units='ms',
neuron_variable=self.t_vec)
h.tstop = 80.0
def showRunControlPanel():
# Init Panel
initPanel = G.addTextFieldAndButton("Init", 'v_init', True, ['h.stdinit()'])
# Init Run Button
initRunButton = G.addButton('Init & Run', ['current_experiment.state = "RUNNING"', 'h.run()', 'current_experiment.state = "COMPLETED"'])
# Stop Button
stopButton = G.addButton('Stop')
stopButton.on_click(['h.stoprun = 1'])
# Continue til
continueTilPanel = G.addTextFieldAndButton("Continue til", 'runStopAt', True, ['h.continuerun(runStopAt)', 'h.stoprun=1'])
# Continue for
continueForPanel = G.addTextFieldAndButton("Continue for", 'runStopIn', True, ['h.continuerun(t + runStopIn)', 'h.stoprun=1'])
# Single Step
singleStepButton = G.addButton('Single Step', ['h.steprun()'])
# t Panel
timePanel = G.addTextFieldAndButton("t", 't', False, [])
# TStop Panel
stopPanel = G.addTextFieldAndButton("Tstop", 'tstop', True, ['h.tstop_changed()'])
# dt Panel
dtPanel = G.addTextFieldAndButton("dt", 'dt', True, ['h.setdt()'])
# Points plotted Panel
pointsPlottedPanel = G.addTextFieldAndButton("Points plotted/ms", 'steps_per_ms', True, ['h.setdt()'])
# Scrn update invl Panel
scrnUpdateInvlPanel = G.addTextFieldAndButton("Scrn update invl", 'screen_update_invl', True, [])
# Real Time Texfield
realTimePanel = G.addTextFieldAndButton("Real Time", 'realtime', False, [])
# Init main panel
runControlPanel = G.addPanel('Run Control', items = [initPanel, initRunButton, stopButton, continueTilPanel, continueForPanel, singleStepButton, timePanel, stopPanel, dtPanel, pointsPlottedPanel, scrnUpdateInvlPanel, realTimePanel], widget_id = 'runControlPanel', positionX =600, positionY=10)
runControlPanel.display()
def __init__(self, numcells):
G.createProject(name = 'Simple Network')
self.spkt = h.Vector() # Spike time of all cells
self.spkid = h.Vector() # cell ids of spike times
self.create_cells(numcells) # call method to create cells