path = path.replace('[', '')
path = path[:-1] # remove trailing zero from the name of the voltage table
primApicalPlotTableNames.append(path)
# Define variables to be used for the simulation
simTime = 1000e-3
simdt = 10e-6
plotdt = 0.1e-3
for i in range(10):
moose.setClock(i, simdt)
moose.setClock(8, plotdt)
# Use the hsolve method and run the simulation, and then plot the results for the soma and representative
# primary apical dendritic compartments
u.hsolve(CA1_cell[0], simdt)
moose.reinit()
moose.start(simTime)
plt.figure()
t = np.linspace(0, simTime, len(CA1_soma_Vm.vector))
plt.plot(t, CA1_soma_Vm.vector * 1e3, 'r', label='CA1_soma_Vm (mV)')
plt.plot(t,
primApicalPlotTables[0].vector * 1e3,
'k',
label=primApicalPlotTableNames[0] + ' (mV)')
plt.plot(t,
primApicalPlotTables[1].vector * 1e3,
'b',
label=primApicalPlotTableNames[1] + ' (mV)')
plt.plot(t,
primApicalPlotTables[2].vector * 1e3,
MS_soma_pulse = u.createPulse(MS_cell[0], 'rollingWave', pulse_dur, pulse_amp,
pulse_delay1, pulse_delay2)
# Create a neutral object to store the data in
MS_data = moose.Neutral('/MS_data')
MS_tables = []
for comp in MS_cell:
MS_tables.append(u.createDataTables(comp,MS_data,MS_soma_pulse))
# Create a variable for the table recording the voltage for the MS cell's soma
MS_soma_Vm = MS_tables[0][0]
# Define variables needed for running the simulation, and set the clocks for all the channels, compartments,
# and tables recording voltage and current during the simulation
simTime = 400e-3
simdt = 10e-6
plotdt = 0.2e-3
for i in range(10):
moose.setClock(i, simdt)
moose.setClock(8, plotdt)
# Run the experiment using the hsolve method and plot the voltage for the MS cell soma
u.hsolve(MS_cell[0], simdt)
moose.reinit()
moose.start(simTime)
t = np.linspace(0,simTime,len(MS_soma_Vm.vector))
plt.figure()
plt.plot(t,MS_soma_Vm.vector, 'r',label = 'soma_Vm')
plt.legend()
MS_soma_pulse = u.createPulse(MS_cell[0], 'rollingWave', pulse_dur, pulse_amp,
pulse_delay1, pulse_delay2)
# Create a neutral object to store the data in
MS_data = moose.Neutral('/MS_data')
MS_tables = []
for comp in MS_cell:
MS_tables.append(u.createDataTables(comp, MS_data, MS_soma_pulse))
# Create a variable for the table recording the voltage for the MS cell's soma
MS_soma_Vm = MS_tables[0][0]
# Define variables needed for running the simulation, and set the clocks for all the channels, compartments,
# and tables recording voltage and current during the simulation
simTime = 400e-3
simdt = 10e-6
plotdt = 0.2e-3
for i in range(10):
moose.setClock(i, simdt)
moose.setClock(8, plotdt)
# Run the experiment using the hsolve method and plot the voltage for the MS cell soma
u.hsolve(MS_cell[0], simdt)
moose.reinit()
moose.start(simTime)
t = np.linspace(0, simTime, len(MS_soma_Vm.vector))
plt.figure()
plt.plot(t, MS_soma_Vm.vector, 'r', label='soma_Vm')
plt.legend()
l23_soma_Vm = l23_tables[0][0]
l23_soma_Iex = l23_tables[0][1]
l23_seg2_dend4_121_Vm = l23_tables[100][0]
l23_seg2_dend4_121_Iex = l23_tables[100][1]
# Plot the simulation
simTime = 0.5
simdt = 2.5e-5
plotdt = 0.25e-3
for i in range(10):
moose.setClock(i, simdt)
moose.setClock(8, plotdt)
# Use the hsolve method for the experiment
u.hsolve(l23_cell[0].parent.path, l23_cell[0].path, simdt)
moose.reinit()
moose.start(simTime)
t = np.linspace(0, simTime, len(l23_soma_Vm.vector))
plt.plot(t, l23_soma_Vm.vector * 1e3, 'r', label='l23_soma_Vm (mV)')
plt.plot(t,
l23_seg2_dend4_121_Vm.vector * 1e3,
'b',
label='l23_seg2_dend4_121_Vm (mV)')
plt.plot(t, l23_soma_Iex.vector * 1e9, label='l23_soma_Iex (nA)')
plt.plot(t,
l23_seg2_dend4_121_Iex.vector * 1e9,
label='l23_seg2_dend4_121_Iex (nA)')
plt.xlabel('time (ms)')
plt.legend()
plt.show()