Last modified by adavison on 2022/10/04 13:55
From version 11.3
edited by adavison
on 2021/09/30 14:01
Change comment: There is no comment for this version
To version 10.3
edited by adavison
on 2021/08/04 17:40
Change comment: There is no comment for this version

Summary

Details

Page properties
Content
... ... @@ -133,7 +133,7 @@
133 133   title="Response of neuron #0",
134 134   annotations="Simulated with NEST"
135 135  ).show()(%%)
136 -\\**Run script in terminal, show figure**
136 +\\**Run script in terminal**
137 137  )))
138 138  
139 139  As you'd expect, the bias current causes the membrane voltage to increase until it reaches threshold~-~--it doesn't increase in a straight line because it's a //leaky// integrate-and-fire neuron~-~--then once it hits the threshold the voltage is reset, and then stays at the same level for a short time~-~--this is the refractory period~-~--before it starts to increase again.
... ... @@ -140,101 +140,12 @@
140 140  
141 141  Now, all 100 neurons in our population are identical, so if we plotted the first neuron, the second neuron, ..., we'd get the same trace.
142 142  
143 -(% class="box infomessage" %)
144 -(((
145 -**Screencast** - current state of editor
146 -\\(% style="color:#000000" %)"""Simple network model using PyNN"""
147 -\\import pyNN.nest as sim(%%)
148 -(% style="color:#000000" %)from pyNN.utility.plotting import Figure, Panel(%%)
149 -(% style="color:#000000" %)sim.setup(timestep=0.1)(%%)
150 -(% style="color:#000000" %)cell_type  = sim.IF_curr_exp(v_rest=-65, v_thresh=-55, v_reset=-65, t_refrac=1, tau_m=10, cm=1, i_offset=0.1)(%%)
151 -(% style="color:#000000" %)population1 = sim.Population(100, cell_type, label="Population 1")
152 -population1.record("v")
153 -sim.run(100.0)(%%)
154 -(% style="color:#000000" %)data_v = population1.get_data().segments[0].filter(name='v')[0]
155 -Figure(
156 - Panel(
157 - data_v[:, (% style="color:#e74c3c" %)0:5(% style="color:#000000" %)],
158 - xticks=True, xlabel="Time (ms)",
159 - yticks=True, ylabel="Membrane potential (mV)"
160 - ),
161 - title="Response of (% style="color:#e74c3c" %)first five neurons(% style="color:#000000" %)",
162 - annotations="Simulated with NEST"
163 -).show()(%%)
164 -\\**Run script in terminal, show figure**
165 -)))
143 +Let's change that. In nature every neuron is a little bit different, so let's set the resting membrane potential and the spike threshold randomly from a Gaussian distribution, and let's plot membrane voltage from _all_ the  neurons.
166 166  
167 -Let's change that. In nature every neuron is a little bit different, so let's set the resting membrane potential and the spike threshold randomly from a Gaussian distribution.
168 -
169 -(% class="box infomessage" %)
170 -(((
171 -**Screencast** - current state of editor
172 -\\(% style="color:#000000" %)"""Simple network model using PyNN"""
173 -\\import pyNN.nest as sim(%%)
174 -(% style="color:#000000" %)from pyNN.utility.plotting import Figure, Panel(%%)
175 -(% style="color:#e74c3c" %)from pyNN.random import RandomDistribution(%%)
176 -(% style="color:#000000" %)sim.setup(timestep=0.1)(%%)
177 -(% style="color:#000000" %)cell_type  = sim.IF_curr_exp(
178 - (% style="color:#e74c3c" %) v_rest=RandomDistribution('normal', {'mu': -65.0, 'sigma': 1.0}),
179 - v_thresh=RandomDistribution('normal', {'mu': -55.0, 'sigma': 1.0}),
180 - v_reset=RandomDistribution('normal', {'mu': -65.0, 'sigma': 1.0}), (%%)
181 -(% style="color:#000000" %) t_refrac=1, tau_m=10, cm=1, i_offset=0.1)(%%)
182 -(% style="color:#000000" %)population1 = sim.Population(100, cell_type, label="Population 1")
183 -population1.record("v")
184 -sim.run(100.0)(%%)
185 -(% style="color:#000000" %)data_v = population1.get_data().segments[0].filter(name='v')[0]
186 -Figure(
187 - Panel(
188 - data_v[:, 0:5],
189 - xticks=True, xlabel="Time (ms)",
190 - yticks=True, ylabel="Membrane potential (mV)"
191 - ),
192 - title="Response of first five neurons (% style="color:#e74c3c" %)with heterogeneous parameters(% style="color:#000000" %)",
193 - annotations="Simulated with NEST"
194 -).show()(%%)
195 -\\**Run script in terminal, show figure**
196 -)))
197 -
198 198  Now if we run our simulation again, we can see the effect of this heterogeneity in the neuron population.
199 199  
200 -(% class="box successmessage" %)
201 -(((
202 -**Slide** showing addition of second population, and of connections between them
203 -)))
147 +TO BE COMPLETED
204 204  
205 -(% class="wikigeneratedid" %)
206 -So far we have a population of neurons, but there are no connections between them, we don't have a network. Let's add a second population of the same size as the first, but we'll set the offset current to zero, so they don't fire action potentials spontaneously.
207 -
208 -(% class="box infomessage" %)
209 -(((
210 -**Screencast** - current state of editor
211 -\\(% style="color:#000000" %)"""Simple network model using PyNN"""
212 -\\import pyNN.nest as sim(%%)
213 -(% style="color:#000000" %)from pyNN.utility.plotting import Figure, Panel(%%)
214 -(% style="color:#000000" %)from pyNN.random import RandomDistribution(%%)
215 -(% style="color:#000000" %)sim.setup(timestep=0.1)(%%)
216 -(% style="color:#000000" %)cell_type  = sim.IF_curr_exp(
217 - (% style="color:#e74c3c" %) (% style="color:#000000" %)v_rest=RandomDistribution('normal', {'mu': -65.0, 'sigma': 1.0}),
218 - v_thresh=RandomDistribution('normal', {'mu': -55.0, 'sigma': 1.0}),
219 - v_reset=RandomDistribution('normal', {'mu': -65.0, 'sigma': 1.0}), (%%)
220 -(% style="color:#000000" %) t_refrac=1, tau_m=10, cm=1, i_offset=0.1)(%%)
221 -(% style="color:#000000" %)population1 = sim.Population(100, cell_type, label="Population 1")(%%)
222 -(% style="color:#000000" %)population1.record("v")
223 -sim.run(100.0)(%%)
224 -(% style="color:#000000" %)data_v = population1.get_data().segments[0].filter(name='v')[0]
225 -Figure(
226 - Panel(
227 - data_v[:, 0:5],
228 - xticks=True, xlabel="Time (ms)",
229 - yticks=True, ylabel="Membrane potential (mV)"
230 - ),
231 - title="Response of first five neurons with heterogeneous parameters",
232 - annotations="Simulated with NEST"
233 -).show()(%%)
234 -\\**Run script in terminal, show figure**
235 -)))
236 -
237 -
238 238  (% class="wikigeneratedid" id="HSummary28Inthistutorial2CyouhavelearnedtodoX202629" %)
239 239  (% class="small" %)**Summary (In this tutorial, you have learned to do X…)**
240 240