[NEST Users] Re: How to stimulate neurons in a network with different amplitudes

Dear Daphne,

Thank you, that was very helpful!

Good!

Does this mean this I only have to create one spike detector (multimeter) and connect them to both the neuron populations?

Yes!

Like this:

# create spikedetector and multimeter spikedet = nest.Create('spike_detector') multimet = nest.Create('multimeter', params={'record_from': ['V_m']})

# connect devices to both populations nest.Connect(neurons_sub, spikedet) nest.Connect(neurons_supra, spikedet) nest.Connect(multimet, neurons_sub) nest.Connect(multimet, neurons_supra)

Or even like this:

|neurons_all = neurons_sub + neurons_supra nest.Connect(neurons_all, spikedet) nest.Connect(multimet, neurons_all) |

Cheers, Jochen!

On Fri, Feb 21, 2020 at 6:56 PM Jochen Martin Eppler <j.eppler@fz-juelich.de mailto:j.eppler@fz-juelich.de> wrote:

Dear Daphne,

there seems to be a misunderstanding about how the |dc_generator|
works. Each stimulation device in NEST only has one set of
parameters for /all/ neurons it creates input for. In your
situation, this means that you should rather create two
independent |dc_generator|s instead of just one. One would have
its amplitude set to Asub, the other would have it set to Asupra:

|dc_sub = nest.Create('dc_generator', params={'amplitude': Asub})
dc_supra = nest.Create('dc_generator', params={'amplitude': Asupra}) |

The way to have them stimulate only a subset of the neurons is by
only connecting the generator to the neurons you want stimulated,
i.e. the ones whose indices you draw. As indexing a neuron
population by a list of indices is still under development and not
quite ready yet, this becomes easier if you first draw the number
of neurons for each population, create the corresponding number of
neurons and connect the corresponding generator to all of them:

|N_sub = np.random.randint(1, N_total) neurons_sub =
nest.Create('iaf_cond_alpha', N_sub) neurons_supra =
nest.Create('iaf_cond_alpha', N_total - N_sub)
nest.Connect(dc_sub, neurons_sub) nest.Connect(dc_supra,
neurons_supra) |

I hope this helps.

Cheers,
Jochen!


On 21.02.20 18:15, Daphne Cornelisse wrote:

...

Dear nest community,

I have a network of 'iaf_cond_alpha' neurons and want to use the
'dc_generator' to apply two different current amplitudes to
the network. (see code below)

  * A subset of the neurons should receive a sub-threshold
    amplitude so that they won't spike.
  * A subset of the neurons should receive a
    suprathreshold amplitude, making them spike.

I created a random number of indices of neurons that should
receive a suprathreshold current, the rest of the neurons should
receive the subthreshold current.

However, there doesn't seem any way to set the current amplitude
to a subset of neurons. I have looked at all the examples using
the dc_generator but couldn't find anything about it.

How can this be done? Is it possible? If it's not possible could
you point me to the source code so I could potentially write a
something for it?

Thank you.

Kind regards,
Daphne


*=== code ===*

np.random.seed(0) # for reproducibility

# amplitudes
Asub = 300.6
Asupra = 367.4

# list of all neurons
neuron_idx_lst = np.arange(0,N_total)

# create random array, these are the neurons that should be
stimulated with supra Amplitude
supra_indices = np.random.randint(1, N_total,
size=int(N_total/neuron_groups-1))

# the rest should receive sub threshold current
sub_indices = np.setdiff1d(neuron_idx_lst,supra_indices)

# here is where it goes wrong
nest.SetStatus(dc_gen[supra_indices], params={'amplitude':Asupra,
'start':stim_start, 'stop':stim_end})

nest.SetStatus(dc_gen[sub_indices], params={'amplitude':Asub,
'start':stim_start, 'stop':stim_end})

>>> TypeError: tuple indices must be integers or slices, not tuple




_______________________________________________
NEST Users mailing list --users@nest-simulator.org  <mailto:users@nest-simulator.org>
To unsubscribe send an email tousers-leave@nest-simulator.org  <mailto:users-leave@nest-simulator.org>

​

-- 
Dr. Jochen Martin Eppler
Phone: +49(2461)61-96653
----------------------------------
Simulation Laboratory Neuroscience
Jülich Supercomputing Centre
Institute for Advanced Simulation



------------------------------------------------------------------------------------------------
------------------------------------------------------------------------------------------------
Forschungszentrum Juelich GmbH
52425 Juelich
Sitz der Gesellschaft: Juelich
Eingetragen im Handelsregister des Amtsgerichts Dueren Nr. HR B 3498
Vorsitzender des Aufsichtsrats: MinDir Volker Rieke
Geschaeftsfuehrung: Prof. Dr.-Ing. Wolfgang Marquardt (Vorsitzender),
Karsten Beneke (stellv. Vorsitzender), Prof. Dr.-Ing. Harald Bolt,
Prof. Dr. Sebastian M. Schmidt
------------------------------------------------------------------------------------------------
------------------------------------------------------------------------------------------------

_______________________________________________
NEST Users mailing list -- users@nest-simulator.org
<mailto:users@nest-simulator.org>
To unsubscribe send an email to users-leave@nest-simulator.org
<mailto:users-leave@nest-simulator.org>

---

NEST Users mailing list -- users@nest-simulator.org To unsubscribe send an email to users-leave@nest-simulator.org

​