Multi-compartment neuron example

Simple example of how to use the three-compartment iaf_cond_alpha_mc model neuron.
Three stimulation paradigms are illustrated: - externally applied current, one compartment at a time - spikes impinging on each compartment, one at a time - rheobase current injected to soma causing output spikes
Voltage and synaptic conductance traces are shown for all compartments.

First, we import all necessary modules for simulation, analysis and plotting.
import nest
import pylab

nest.ResetKernel()

Second, extract from the dictionary with receptor types and the list of recordable quantities from the neuron model. Receptor types and recordable quantities uniquely define the receptor type and the compartment while establishing synaptic connections or assigning multimeters.
syns = nest.GetDefaults('iaf_cond_alpha_mc')['receptor_types']
print("iaf_cond_alpha_mc receptor_types: {0}".format(syns))

rqs = nest.GetDefaults('iaf_cond_alpha_mc')['recordables']
print("iaf_cond_alpha_mc recordables   : {0}".format(rqs))

Third, the simulation parameters are assigned to variables.
nest.SetDefaults('iaf_cond_alpha_mc',
                 { 'V_th' : -60.0,     #threshold potential
                   'V_reset': -65.0,   #reset potential 
                   't_ref': 10.0,      #refractory period
                   'g_sp' : 5.0,       #somato-proximal coupling conductance
                   'soma'    : { 'g_L': 12.0 },       #somatic leak conductance
                   'proximal': { 'tau_syn_ex': 1.0,   #proximal excitatory synaptic time constants
                                 'tau_syn_in': 5.0 }, #proximal inhibitory synaptic time constants
                   'distal'  : { 'C_m': 90.0 }        #distal capacitance
                 })

Fourth, the nodes are created using Create. We store the returned handles in variables for later reference.
n = nest.Create('iaf_cond_alpha_mc')

Fifth, multimeters are created and connected to the neurons. The parameters specified for the multimeter include the list of quantities that should be recorded and the time interval at which quantities are measured.
mm = nest.Create('multimeter', 
                 params = {'record_from': rqs, 
                           'interval': 0.1})
nest.Connect(mm, n)

Sixth, create one current generator per compartment and configure stimulus regime that drives distal, proximal and soma, in that order. Configuration of the current generator includes the definition of the start,stop times and the amplitude of the injected current.
cgs = nest.Create('dc_generator', 3)
nest.SetStatus(cgs, 
               [{'start': 250.0, 'stop': 300.0, 'amplitude':  50.0},  # soma
                {'start': 150.0, 'stop': 200.0, 'amplitude': -50.0},  # proximal
                {'start':  50.0, 'stop': 100.0, 'amplitude': 100.0}]) # distal

Generators are connected to the correct compartments. Specification of the receptor_type uniquely defines the target compartment and receptor.
nest.Connect([cgs[0]], n, syn_spec = {'receptor_type': syns['soma_curr']})
nest.Connect([cgs[1]], n, syn_spec = {'receptor_type': syns['proximal_curr']})
nest.Connect([cgs[2]], n, syn_spec = {'receptor_type': syns['distal_curr']})

Create one excitatory and one inhibitory spike generator per compartment. Configure regime that drives distal, proximal and soma, in that order, excitation and inhibition alternating.
sgs = nest.Create('spike_generator', 6)
nest.SetStatus(sgs,
               [{'spike_times': [600.0, 620.0]}, # soma excitatory
                {'spike_times': [610.0, 630.0]}, # soma inhibitory
                {'spike_times': [500.0, 520.0]}, # proximal excitatory
                {'spike_times': [510.0, 530.0]}, # proximal inhibitory
                {'spike_times': [400.0, 420.0]}, # distal excitatory
                {'spike_times': [410.0, 430.0]}]) # distal inhibitory

Connect generators to correct compartments in the same way as in case of current generator
nest.Connect([sgs[0]], n, syn_spec = {'receptor_type': syns['soma_exc']})
nest.Connect([sgs[1]], n, syn_spec = {'receptor_type': syns['soma_inh']})
nest.Connect([sgs[2]], n, syn_spec = {'receptor_type': syns['proximal_exc']})
nest.Connect([sgs[3]], n, syn_spec = {'receptor_type': syns['proximal_inh']})
nest.Connect([sgs[4]], n, syn_spec = {'receptor_type': syns['distal_exc']})
nest.Connect([sgs[5]], n, syn_spec = {'receptor_type': syns['distal_inh']})

Run the simulation for 700ms.
nest.Simulate(700)

Now turn on intrinsic current in soma to make neuron to spike.
nest.SetStatus(n, {'soma': {'I_e': 150.0}})

Simulate the network for another 300ms.
nest.Simulate(300)

Retrieve recorded data from the multimeters
rec = nest.GetStatus(mm)[0]['events']

Create an array with the time points when the quantities were actually recorded
t = rec['times']

Plot time traces of the membrane potential measured in different compartments. V_m.s,V_m.p,V_m.d state for the membrane potential in soma, proximal and distal dendrites.
pylab.figure()
pylab.subplot(211)
pylab.plot(t, rec['V_m.s'], t, rec['V_m.p'], t, rec['V_m.d'])
pylab.legend(('Soma', 'Proximal dendrite', 'Distal dendrite'),loc='lower right')
pylab.axis([0, 1000, -76, -59])
pylab.ylabel('Membrane potential [mV]')
pylab.title('Responses of iaf_cond_alpha_mc neuron')

Plot time traces of the synaptic conductance measured in different compartments.
pylab.ylabel('Synaptic conductance [nS]')
mc_neuron
                                # -*- coding: utf-8 -*-
#
# mc_neuron.py
#
# This file is part of NEST.
#
# Copyright (C) 2004 The NEST Initiative
#
# NEST is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 2 of the License, or
# (at your option) any later version.
#
# NEST is distributed in the hope that it will be useful,
# but WITHOUT ANY WARRANTY; without even the implied warranty of
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
# GNU General Public License for more details.
#
# You should have received a copy of the GNU General Public License
# along with NEST.  If not, see <http://www.gnu.org/licenses/>.

'''
Multi-compartment neuron example
--------------------------------

Simple example of how to use the three-compartment `iaf_cond_alpha_mc model`
neuron.

Three stimulation paradigms are illustrated:
 - externally applied current, one compartment at a time
 - spikes impinging on each compartment, one at a time
 - rheobase current injected to soma causing output spikes

Voltage and synaptic conductance traces are shown for all compartments.
'''


'''
First, we import all necessary modules for simulation, analysis and
plotting.
'''

import nest
import pylab

nest.ResetKernel()

'''
Second, extract from the dictionary with receptor types and the list of
recordable quantities from the neuron model. Receptor types and
recordable quantities uniquely define the receptor type and the compartment 
while establishing synaptic connections or assigning multimeters.
'''

syns = nest.GetDefaults('iaf_cond_alpha_mc')['receptor_types']
print("iaf_cond_alpha_mc receptor_types: {0}".format(syns))

rqs = nest.GetDefaults('iaf_cond_alpha_mc')['recordables']
print("iaf_cond_alpha_mc recordables   : {0}".format(rqs))

'''
Third, the simulation parameters are assigned to variables.
'''

nest.SetDefaults('iaf_cond_alpha_mc',
                 { 'V_th' : -60.0,     #threshold potential
                   'V_reset': -65.0,   #reset potential 
                   't_ref': 10.0,      #refractory period
                   'g_sp' : 5.0,       #somato-proximal coupling conductance
                   'soma'    : { 'g_L': 12.0 },       #somatic leak conductance
                   'proximal': { 'tau_syn_ex': 1.0,   #proximal excitatory synaptic time constants
                                 'tau_syn_in': 5.0 }, #proximal inhibitory synaptic time constants
                   'distal'  : { 'C_m': 90.0 }        #distal capacitance
                 })

'''
Fourth, the nodes are created using `Create`. We store the returned
handles in variables for later reference.
'''

n = nest.Create('iaf_cond_alpha_mc')

'''
Fifth, `multimeter`s are created and connected to the neurons. 
The parameters specified for the multimeter include the list of quantities
that should be recorded and the time interval at which quantities are measured.
'''

mm = nest.Create('multimeter', 
                 params = {'record_from': rqs, 
                           'interval': 0.1})
nest.Connect(mm, n)

'''
Sixth, create one current generator per compartment and configure
stimulus regime that drives distal, proximal and soma, in that order.
Configuration of the current generator includes the definition of
the start,stop times and the amplitude of the injected current.
'''

cgs = nest.Create('dc_generator', 3)
nest.SetStatus(cgs, 
               [{'start': 250.0, 'stop': 300.0, 'amplitude':  50.0},  # soma
                {'start': 150.0, 'stop': 200.0, 'amplitude': -50.0},  # proximal
                {'start':  50.0, 'stop': 100.0, 'amplitude': 100.0}]) # distal

'''
Generators are connected to the correct compartments. 
Specification of the ``receptor_type`` uniquely defines the target
compartment and receptor.
'''

nest.Connect([cgs[0]], n, syn_spec = {'receptor_type': syns['soma_curr']})
nest.Connect([cgs[1]], n, syn_spec = {'receptor_type': syns['proximal_curr']})
nest.Connect([cgs[2]], n, syn_spec = {'receptor_type': syns['distal_curr']})

'''
Create one excitatory and one inhibitory spike generator per compartment.
Configure regime that drives distal, proximal and soma, in that order,
excitation and inhibition alternating.
'''

sgs = nest.Create('spike_generator', 6)
nest.SetStatus(sgs,
               [{'spike_times': [600.0, 620.0]}, # soma excitatory
                {'spike_times': [610.0, 630.0]}, # soma inhibitory
                {'spike_times': [500.0, 520.0]}, # proximal excitatory
                {'spike_times': [510.0, 530.0]}, # proximal inhibitory
                {'spike_times': [400.0, 420.0]}, # distal excitatory
                {'spike_times': [410.0, 430.0]}]) # distal inhibitory

'''
Connect generators to correct compartments in the same way as in case of
current generator
'''

nest.Connect([sgs[0]], n, syn_spec = {'receptor_type': syns['soma_exc']})
nest.Connect([sgs[1]], n, syn_spec = {'receptor_type': syns['soma_inh']})
nest.Connect([sgs[2]], n, syn_spec = {'receptor_type': syns['proximal_exc']})
nest.Connect([sgs[3]], n, syn_spec = {'receptor_type': syns['proximal_inh']})
nest.Connect([sgs[4]], n, syn_spec = {'receptor_type': syns['distal_exc']})
nest.Connect([sgs[5]], n, syn_spec = {'receptor_type': syns['distal_inh']})

'''
Run the simulation for 700ms.
''' 

nest.Simulate(700)

'''
Now turn on intrinsic current in soma to make neuron to spike.
'''

nest.SetStatus(n, {'soma': {'I_e': 150.0}})

'''
Simulate the network for another 300ms.
'''

nest.Simulate(300)

'''
Retrieve recorded data from the multimeters
'''

rec = nest.GetStatus(mm)[0]['events']

'''
Create an array with the time points when the quantities were actually
recorded
'''

t = rec['times']

'''
Plot time traces of the membrane potential measured in different compartments.
V_m.s,V_m.p,V_m.d state for the membrane potential in soma, proximal and distal dendrites.
'''

pylab.figure()
pylab.subplot(211)
pylab.plot(t, rec['V_m.s'], t, rec['V_m.p'], t, rec['V_m.d'])
pylab.legend(('Soma', 'Proximal dendrite', 'Distal dendrite'),loc='lower right')
pylab.axis([0, 1000, -76, -59])
pylab.ylabel('Membrane potential [mV]')
pylab.title('Responses of iaf_cond_alpha_mc neuron')

'''
Plot time traces of the synaptic conductance measured in different compartments. 
'''

pylab.subplot(212)
pylab.plot(t, rec['g_ex.s'], 'b-', t, rec['g_ex.p'], 'g-', t, rec['g_ex.d'], 'r-')
pylab.plot(t, rec['g_in.s'], 'b--', t, rec['g_in.p'], 'g--', t, rec['g_in.d'], 'r--')
pylab.legend(('g_ex.s', 'g_ex.p', 'g_in.d','g_in.s', 'g_in.p', 'g_in.d'))
pylab.axis([350, 700, 0, 1.15])
pylab.xlabel('Time [ms]')
pylab.ylabel('Synaptic conductance [nS]')