Search found 38 matches

by Qroid_montreal
Tue Nov 04, 2014 4:05 pm
Forum: Modeling networks
Topic: Ephaptically coupling cells within a network
Replies: 7
Views: 8397

Re: Ephaptically coupling cells within a network

Hi Ted - I have a previously coded model that does "off-line" ephaptic coupling. I sent the NEURON membrane currents to an external file, calculated Ve in Matlab, and then used play to control the extracellular voltage in a second run of NEURON. I believe this worked, but it meant that my stimulatio...
by Qroid_montreal
Wed Oct 22, 2014 2:29 pm
Forum: Modeling networks
Topic: Ephaptically coupling cells within a network
Replies: 7
Views: 8397

Re: Ephaptically coupling cells within a network

Hi Ted - Sorry for the delay. I had a holiday for a week or so. I've started with your code. Everything works as you say and it's very instructive, so thank you immensely. There's one thing I'm confused about though, and that's how to adapt your code to model the spatial dependency of extracellular ...
by Qroid_montreal
Tue Oct 07, 2014 9:45 am
Forum: Modeling networks
Topic: Ephaptically coupling cells within a network
Replies: 7
Views: 8397

Re: Ephaptically coupling cells within a network

Hi Ted - thanks so much. I'll look this up on the forum and the NEURON book in the meantime.
by Qroid_montreal
Sun Oct 05, 2014 2:26 pm
Forum: Modeling networks
Topic: Ephaptically coupling cells within a network
Replies: 7
Views: 8397

Ephaptically coupling cells within a network

I have a question about how to couple cells ephaptically (i.e. membrane currents -> extracellular) in a network. I know how to play a precalculated stimulation to each segment using a vector list. So something like: segcount=0 forsec cells.o(i).all { // loop through each section of cells.o(i) if (is...
by Qroid_montreal
Sun Oct 05, 2014 1:41 pm
Forum: Modeling networks
Topic: How to set biophysical properties for a template
Replies: 8
Views: 8870

Re: How to set biophysical properties for a template

Hi Ted - thank you very much. I loaded the j4a.hoc file after modifying it to include the axon, then imported this into Cell Builder. To be honest any spontaneously spiking pyramidal cell model will do for my purposes, so I didn't spend much energy worrying about the treatment of spines. That's just...
by Qroid_montreal
Fri Oct 03, 2014 5:57 pm
Forum: Modeling networks
Topic: How to set biophysical properties for a template
Replies: 8
Views: 8870

Re: How to set biophysical properties for a template

Never mind! I just saw these instructions for creating subsets http://www.neuron.yale.edu/neuron/stati ... bsets.html, which I'm guessing is exactly what I'm describing.
by Qroid_montreal
Fri Oct 03, 2014 5:17 pm
Forum: Modeling networks
Topic: How to set biophysical properties for a template
Replies: 8
Views: 8870

Re: How to set biophysical properties for a template

Hi Ted - Thank you! That helps a lot. I'm now doing my best to set the biophysics in Cell Builder. However I've hit a problem. I Imported the Mainen and Sejnowski 1996 L5 pyramidal cell model into Cell Builder, and I see the morphometric data looks right in the shape plot. I started setting the biop...
by Qroid_montreal
Mon Sep 08, 2014 12:08 pm
Forum: Modeling networks
Topic: Changing cell locations also changes
Replies: 4
Views: 6526

Re: Changing cell locations also changes

Hi Ted - again, thanks so much. I included "tcell define_shape()" right after "tcell.position(0,offset*i,0)" and my pt3d values are now correct. This also explains why my Shape plots looked fine even when the output values weren't!
by Qroid_montreal
Mon Sep 08, 2014 11:43 am
Forum: Modeling networks
Topic: How to set biophysical properties for a template
Replies: 8
Views: 8870

Re: How to set biophysical properties for a template

p.s. Thanks for the warning. I checked and my hoc code does include "celsius = 37".
by Qroid_montreal
Mon Sep 08, 2014 11:40 am
Forum: Modeling networks
Topic: How to set biophysical properties for a template
Replies: 8
Views: 8870

Re: How to set biophysical properties for a template

Hi Ted - thanks so much. If I want to create a template with xopen -> Cell Builder -> Network Builder, what are my options for specifying the biophysics? Do I need to do it by hand in Cell Builder? Is it possible to modify the template hoc file with the appropriate lines of code? Like I said, I also...
by Qroid_montreal
Sun Sep 07, 2014 7:41 pm
Forum: Modeling networks
Topic: How to set biophysical properties for a template
Replies: 8
Views: 8870

How to set biophysical properties for a template

Hi - I'm trying to implement a network of pretty complicated neurons (Mainen and Sejnowski's layer V pyramidal cell, http://senselab.med.yale.edu/ModelDB/ShowModel.asp?model=2488 ). I thought I was doing it right, but I now realise I'm having problems specifying the biophysics. Following instruction...
by Qroid_montreal
Sun Sep 07, 2014 6:09 pm
Forum: Modeling networks
Topic: Changing cell locations also changes
Replies: 4
Views: 6526

Re: Changing cell locations also changes

Hi Ted - thanks very much. I replaced "tcell for(x) pt3dchange(x,x3d(x),y3d(x)+offset*i,z3d(x), diam3d(x))" with "tcell.position(0,offset*i,0)". area, diam, and L are now the same between cells, and shape plot shows the cells are in the right place. That's great. I'm having a small issue with output...
by Qroid_montreal
Sat Sep 06, 2014 6:33 pm
Forum: Modeling networks
Topic: Changing cell locations also changes
Replies: 4
Views: 6526

Changing cell locations also changes

Hi - I'm trying to simulate ephaptically-coupled neurons, and I'm having problems when changing cell locations with pt3dchange. I think I have the hang of creating multiple instances using a template. However, when I change their location using pt3dchange it seems to change other parameters like are...
by Qroid_montreal
Fri Aug 23, 2013 11:17 am
Forum: Getting started
Topic: Printing xyz positions of all straight line segments
Replies: 2
Views: 2004

Re: Printing xyz positions of all straight line segments

I think I see my mistake. "area" and "i_membrane" are range variables, so the input is normalised to between 0 and 1. "x3d" etc want an integer input, and don't return an error for non-integer input. So instead of forall for(x) {print secname(), x3d(x), y3d(x), z3d(x), area(x), i_membrane(x)} it sho...
by Qroid_montreal
Thu Aug 22, 2013 7:31 pm
Forum: Getting started
Topic: Printing xyz positions of all straight line segments
Replies: 2
Views: 2004

Printing xyz positions of all straight line segments

Hello, I have a feeling this is a pretty simple one, but I'm having trouble with it. I'm implementing the Mainen and Senowski model layer V cell http://senselab.med.yale.edu/modeldb/showmodel.asp?model=2488. What I'd like to do is calculate the electric potential V_e(x,t) around the cell. My plan is...