plotLFP

A Python package that facilitates development and use of models of biological neural networks

Moderator: tom_morse

Post Reply
atknox
Posts: 5
Joined: Wed Aug 26, 2015 2:07 pm

plotLFP

Post by atknox » Fri Mar 02, 2018 6:44 pm

Hi,

I was excited to see that local field potentials were added! Unfortunately I was having trouble getting them to work, likely due to my own ignorance. I have the same code as in my previous post about plotRatePSD, where I create a network with the following populations:

netParams.popParams['PY'] = {'cellType': 'sPY','gridSpacing': netParams.sizeX / numcorticalcells, 'zRange':[0.95,1.0], 'yRange':[0.95,1.0], 'cellModel':'HH'}
netParams.popParams['IN'] = {'cellType': 'sIN','gridSpacing': netParams.sizeX / numcorticalcells, 'zRange':[0.95,1.0],'yRange':[49.95,50.0], 'cellModel':'HH'}
netParams.popParams['RE'] = {'cellType': 'sRE','gridSpacing': netParams.sizeX / numthalamiccells, 'zRange':[0.95,1.0],'yRange':[99.95,100.0], 'cellModel':'HH'}
netParams.popParams['TC'] = {'cellType': 'sTC','gridSpacing': netParams.sizeX / numthalamiccells, 'zRange':[0.95,1.0],'yRange':[149.95,150.0], 'cellModel':'HH'}

Then there's some code to finish setting up the network which I've omitted. The I tried two different things for creating the LFP plot:

#1) simConfig.analysis['plotLFP'] = True
#2) simConfig.analysis['plotLFP'] = {'electrodes':['avg'],'plots':['timeSeries']}

Both produce the following output:

Plotting LFP ...
There was an exception in plotLFP():
invalid __array_struct__
Done; plotting time = 0.94 s

Am I doing something wrong, or is there some sort of bug? I'm happy to provide more information if it would be helpful.

Thanks,
Andrew

salvadord
Posts: 70
Joined: Tue Aug 18, 2015 3:49 pm

Re: plotLFP

Post by salvadord » Wed Mar 21, 2018 6:20 pm

Hi Andrew,

Sorry for the delay responding -- unfortunately the email alerts for this forum are not working.

I have fixed a few minor bugs (including this one) since the release of this feature, so please try the github "development" version and let me know if it works; instructions to install here: http://neurosimlab.com/netpyne/install. ... nt-version

Thanks
Salva

Post Reply