Search found 10 matches

by gabrielggn
Fri Feb 17, 2023 1:30 pm
Forum: Other questions
Topic: Extracellular make difference in synaptic input
Replies: 1
Views: 5465

Extracellular make difference in synaptic input

Dear colleagues, I used extracellular mechanism with the xtra.mod mechanism to deal with the input. I just found that when I perform the same simulation (same synapses and events) but without extracellular, I don't get the same results (particullarly it seems that the high frequency voltage stimulat...
by gabrielggn
Thu Feb 09, 2023 7:12 am
Forum: NEURON + Python
Topic: Steady state init with voltage VS with SaveState
Replies: 4
Views: 13600

Re: Steady state init with voltage VS with SaveState

Finally, I did as explain in the last post using psection() function. The code to save the membrane/mechanisms+ions state was the following (using python) : def save_state(self, fn = None): l = [] for sec in self.cell.all: dic = sec.psection() v = np.array([ seg.v for seg in sec]) l.append( {"v...
by gabrielggn
Mon Feb 06, 2023 9:46 am
Forum: NEURON + Python
Topic: Steady state init with voltage VS with SaveState
Replies: 4
Views: 13600

Re: Steady state init with voltage VS with SaveState

Dear Ted, Thank you for your quick feedback. 1. Experimentalists typically wait until v near the spike trigger zone is flat for an amount of time on the order of at least several seconds if not minutes. And even then, they often want each recording to start with at least 1 ms during which that v rem...
by gabrielggn
Thu Feb 02, 2023 2:02 pm
Forum: NEURON + Python
Topic: Steady state init with voltage VS with SaveState
Replies: 4
Views: 13600

Steady state init with voltage VS with SaveState

Dear all, I am working with pyramidal cell models and my pipeline is pretty simple: Compute steady state of the cell given channel mechanismes ( voltage of all compartments do not vary more than 1e-6 mV from previous step) Preforming my modeling which involve synaptic inputs, calling h.finitialize()...
by gabrielggn
Fri Jan 27, 2023 12:35 am
Forum: NEURON + Python
Topic: Nstack - stack too deep in python
Replies: 2
Views: 12042

Re: Nstack - stack too deep in python

For those interested by an answer to this issue , I found my way out in changing the default NSTACK and NFRAME via the config NEURON's file. To do so you have to: 1. Going to "nrn/lib/nrn.default" 2. Search for NSTACK (ctrl +f ) 3. On the corresponding line change the value to the desired ...
by gabrielggn
Mon Sep 19, 2022 2:58 pm
Forum: NEURON + Python
Topic: Nstack - stack too deep in python
Replies: 2
Views: 12042

Nstack - stack too deep in python

Dear NEURON team, I am dealing with BBP cells from the 2015 study where they reconstructed a rodent cortical column. I got them from another study on modelDB where the original files are provided (see https://senselab.med.yale.edu/ModelDB/ShowModel?model=241165). I figured out how to use these model...
by gabrielggn
Mon Jun 27, 2022 6:12 am
Forum: Other questions
Topic: Extracellular Stim using python and/or xtra.mod
Replies: 6
Views: 8775

Re: Extracellular Stim using python and/or xtra.mod

Dear Ted, As you ask I made a simple ball and stick model to test my extracellular stimulation script. I did a soma (10um x 10um) connected to a dendrite (500 um x 2um) with passive mechanism (Ra =155 O.cm-1, Rm = 17.5 O.cm-2, e_pas=-60 mV) to reproduced the study. Here are my results : https://driv...
by gabrielggn
Fri Jun 24, 2022 3:22 am
Forum: Other questions
Topic: Extracellular Stim using python and/or xtra.mod
Replies: 6
Views: 8775

Re: Extracellular Stim using python and/or xtra.mod

Dear Ted, I used a complex model since this is what interest me here to compare with the results of the study I've mentionned. I did figured out how to replicate the results by the way and it involed another way to calculate x,y,z, with some center of mass of the cylinders as I explained in my previ...
by gabrielggn
Thu Jun 23, 2022 8:36 am
Forum: Other questions
Topic: Extracellular Stim using python and/or xtra.mod
Replies: 6
Views: 8775

Re: Extracellular Stim using python and/or xtra.mod

Dear Ted, Many thanks for your answer. I did plot RangeVarPlot and as I expected the "e_extracellular" potential is following the trend of the "v" over the soma to apical axis (in the direction of the electric field). It is not linear but It should be due to the fact that apical ...
by gabrielggn
Fri Jun 10, 2022 6:03 am
Forum: Other questions
Topic: Extracellular Stim using python and/or xtra.mod
Replies: 6
Views: 8775

Extracellular Stim using python and/or xtra.mod

Dear colleagues, I am quite new at NEURON programming and I'm a python programmer if I can say that. I am currently working in the field of transcranial stimulation and I am interested by the capabilities of NEURON to predict the effect of extracellular stimulation on complex geometrical neurons to ...