Search found 5372 matches

by ted
Wed Dec 12, 2018 10:20 am
Forum: Anatomically detailed models
Topic: Placing a point process at a known 3D location
Replies: 1
Views: 19

Re: Placing a point process at a known 3D location

Everything is not built into NEURON, but NEURON provides simple tools that enable building what you need with hoc and/or Python. For each section whose geometry has been specified using pt3d syntax, NEURON maintains an internal table of x,y,z coordinates and the corresponding diameter. Now would be ...
by ted
Wed Dec 12, 2018 10:05 am
Forum: Hot tips
Topic: Soma stacks and the Import3d tool
Replies: 4
Views: 563

Re: Soma stacks and the Import3d tool

For the benefit of others who may read this discussion thread-- Import3d can handle Neurolucida text files that contain a soma stack (a sequence of tracings of the perimeter of the soma performed at different levels along the z axis), but only if the tracings are arranged with monotonically increasi...
by ted
Mon Dec 10, 2018 5:39 pm
Forum: Hot tips
Topic: Soma stacks and the Import3d tool
Replies: 4
Views: 563

Re: Soma stacks and the Import3d tool

I'll have to be able to reproduce this in order to find out what is the cause and how it can be fixed. Please zip up the Neurolucida file and email it to me
ted dot carnevale at yale dot edu
by ted
Sun Dec 09, 2018 8:53 pm
Forum: General questions and discussions about computational neuroscience
Topic: Difference between weight vs. reversal potential for synaptic connections
Replies: 1
Views: 16

Re: Difference between weight vs. reversal potential for synaptic connections

In its most general usage, the term "synaptic weight" refers to the magnitude of the effect elicited in a postsynaptic cell by activity in a presynaptic cell. The larger the synaptic weight, the greater will be the effect on the postsynaptic cell. In the context of certain kinds of networks of artif...
by ted
Fri Dec 07, 2018 9:40 pm
Forum: Getting started
Topic: Attempting to generate Raster Plot for 2 cell network
Replies: 3
Views: 39

Re: Attempting to generate Raster Plot for 2 cell network

Let me try again. Might the attempted raster plot be empty because the spike time vectors are empty? The code in my previous post is one way to test that hypothesis.
by ted
Fri Dec 07, 2018 9:46 am
Forum: Getting started
Topic: Attempting to generate Raster Plot for 2 cell network
Replies: 3
Views: 39

Re: Attempting to generate Raster Plot for 2 cell network

Not so bad for a "total beginner."

The first question is: are there are any spike times to be plotted?

Code: Select all

for i=0,spikes.count()-1 (
  print i
  spikes.o(i).printf()
)
by ted
Thu Dec 06, 2018 1:51 pm
Forum: Other questions
Topic: replace object in list
Replies: 1
Views: 30

Re: replace object in list

For: objref alist alist=new List() alist.append(new Vector()) alist.o(0) = new Vector() // Does not work !!! Yep. According to the documentation of List in the Programmer's Reference, list .o(i) returns the object at index i. That is consistent with the documentation's statement that list .append( ...
by ted
Wed Dec 05, 2018 10:32 am
Forum: Getting started
Topic: sectioning neuron based on distance from soma
Replies: 4
Views: 56

Re: sectioning neuron based on distance from soma

That helps, but two important questions remain unanswered: Question 1: Groups of what? Sections? Questions 2 and 3: Based on distance of what from the soma? Section midpoint? proximal end? distal end? The goal is gradually have less channels the more we move away from the soma. If the goal is to hav...
by ted
Wed Dec 05, 2018 10:25 am
Forum: General questions and discussions about computational neuroscience
Topic: membrane potential dependency from ion concentrations?
Replies: 9
Views: 107

Re: membrane potential dependency from ion concentrations?

students do not pay fees for public university education. Then request a tax refund. Ask a friend from France for help. With regard to medical school, there's too much to learn, and too little time to learn it. Besides, after students graduate (at least in this country), they're going to be spendin...
by ted
Wed Dec 05, 2018 10:14 am
Forum: The GUI
Topic: Broken Voltage Grapher
Replies: 2
Views: 44

Re: Broken Voltage Grapher

Diagnosing the problem will require being able to reproduce it. Zip up the files necessary to reproduce it
(see viewtopic.php?f=28&t=1048)
and email the zip file to
ted dot carnevale at yale dot edu
and I'll let you know what I find out.
by ted
Tue Dec 04, 2018 10:59 am
Forum: NEURON + Python
Topic: Using VecStim() with CVode on
Replies: 3
Views: 42

Re: Using VecStim() with CVode on

In principle, adaptive integration should work well for a model that involves only one biophysical model cell--as long as all mechanisms are compatible with CVODE. But always remember that accuracy is the principal reason to use adaptive integration, not speed. While it is true that adaptive integra...
by ted
Sun Dec 02, 2018 2:55 pm
Forum: General questions and discussions about computational neuroscience
Topic: membrane potential dependency from ion concentrations?
Replies: 9
Views: 107

Re: membrane potential dependency from ion concentrations?

The proper setting for discussions like this would be a graduate seminar with a small number of students. I think so, too and it would have helped me. Is it too late to ask the instructors or institution for a tuition refund? Time to read about Donnan equilibrium. I did so, now. But Donnan equation...
by ted
Sun Dec 02, 2018 2:06 pm
Forum: Getting started
Topic: sectioning neuron based on distance from soma
Replies: 4
Views: 56

Re: sectioning neuron based on distance from soma

In order to provide a useful answer, I must ask you to refine your question. based on distance from the soma . . . I want to make a Proxima, Middle and Distal group Question 1: Groups of what? Sections? Questions 2 and 3: Based on distance of what from the soma? Section midpoint? proximal end? dista...
by ted
Thu Nov 29, 2018 12:28 pm
Forum: Modeling networks
Topic: Help using NetCon
Replies: 1
Views: 38

Re: Help using NetCon

First, thank you for your interest in NEURON. The rest of this post may sound like a music teacher asking an enthusiastic novice pianist to put aside Liszt's Transcendental Etudes for just long enough to practice some scales, but so be it. This is the quickest way to learn how to use NetCons: 1. Mak...
by ted
Wed Nov 28, 2018 10:55 am
Forum: General questions and discussions about computational neuroscience
Topic: membrane potential dependency from ion concentrations?
Replies: 9
Views: 107

Re: membrane potential dependency from ion concentrations?

The proper setting for discussions like this would be a graduate seminar with a small number of students. It doesn't seem likely to occur in a typical classroom. For simplification, i will additionally assume that i have blocked any other channels except the Kalium-channels The assumption is unneces...