6:15 p.m.
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
6:56 p.m.
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_generators
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 to
users-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
------------------------------------------------------------------------------------------------
------------------------------------------------------------------------------------------------
1:20 p.m.
Dear Jochen,
Thank you, that was very helpful!
Does this mean this I only have to create one spike detector (multimeter)
and connect them to both the neuron populations?
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)
Best,
Daphne
On Fri, Feb 21, 2020 at 6:56 PM Jochen Martin Eppler <j.eppler(a)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_generators 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(a)nest-simulator.org
To unsubscribe send an email to users-leave(a)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(a)nest-simulator.org
To unsubscribe send an email to users-leave(a)nest-simulator.org
2:30 p.m.
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(a)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(a)nest-simulator.org
<mailto:users@nest-simulator.org>
> To unsubscribe send an email tousers-leave(a)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(a)nest-simulator.org
<mailto:users@nest-simulator.org>
To unsubscribe send an email to users-leave(a)nest-simulator.org
<mailto:users-leave@nest-simulator.org>
_______________________________________________
NEST Users mailing list -- users(a)nest-simulator.org
To unsubscribe send an email to users-leave(a)nest-simulator.org
--
Dr. Jochen Martin Eppler
Phone: +49(2461)61-96653
----------------------------------
Simulation Laboratory Neuroscience
Jülich Supercomputing Centre
Institute for Advanced Simulation
376
days inactive
377
days old
3 comments
2 participants
participants (2)
-
Daphne Cornelisse -
Jochen Martin Eppler