Hi,

Right, in that case I would switch the order when assigning :

W_EE = np.zeros([len(E_neurons), len(E_neurons)])

W_IE = np.zeros([len(E_neurons), len(I_neurons)])

W_EI = np.zeros([len(I_neurons), len(E_neurons)])

W_II = np.zeros([len(I_neurons), len(I_neurons)])

So it would give a hint of the convention (at least for me), but as you said it is a convention, and indeed I was confused by it.

Thanks a lot.

From: Renato Duarte <rcfduarte@gmail.com>
Sent: Tuesday, 19 January 2021 13:04
To: NEST User Mailing List <users@nest-simulator.org>
Subject: [NEST Users] Re: Plot weight matrices example

Hello,

The use of "post-pre" notation when referring to synaptic connections is common practice in computational neuroscience.

It does often give rise to some confusion, but it is common, for example, to refer to a synaptic connection from neuron j to neuron i as ij (post<-pre).

This is the notation used in this example, where we refer to the connection from inhibitory to excitatory neurons (I->E) as EI (post-pre) and connections from excitatory to inhibitory neurons (E->I) as IE (post-pre).

It is just a matter of convention.

Best regards,

Renato Duarte

On Jan 19 2021, at 12:43 pm, Ing Jyh Tsang <ingjyh.tsang@uantwerpen.be> wrote:

HI,

I may be mistaken, but isn't the EI and IE index switched (https://nest-simulator.readthedocs.io/en/stable/auto_examples/plot_weight_matrices.html) ?

a_EI = nest.GetConnections(I_neurons, E_neurons)

c_EI = nest.GetStatus(a_EI, keys='weight')

a_IE = nest.GetConnections(E_neurons, I_neurons)

c_IE = nest.GetStatus(a_IE, keys='weight')

for idx, n in enumerate(a_EI):

W_EI[n[0] - min(I_neurons), n[1] - min(E_neurons)] += c_EI[idx]

for idx, n in enumerate(a_IE):

W_IE[n[0] - min(E_neurons), n[1] - min(I_neurons)] += c_IE[idx]

Thanks,

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