Search found 5376 matches

by ted
Fri Dec 14, 2018 5:40 pm
Forum: Getting started
Topic: sectioning neuron based on distance from soma
Replies: 9
Views: 75

Re: sectioning neuron based on distance from soma

I am working on a 3D Dentate Gyrus Granule Cell with 46 Dendrites. If the sections are connected into a single model cell, electrical signals generated in "active" dendrites will spread into "passive" dendrites. The effect of changing all channel densities in a single section to 0 may be big or it ...
by ted
Fri Dec 14, 2018 3:05 pm
Forum: Getting started
Topic: Parameters for the Ih current
Replies: 5
Views: 26

Re: Parameters for the Ih current

Excellent. Of the two URLs, the second one
http://lyle.neurophysics.eu/pdf/MIT-AITR-1161.pdf
returns the most legible document.

Chapter 4 should help resolve your questions. Similar discussions are presented in many standard textbooks on cellular neurophysiology.
by ted
Fri Dec 14, 2018 10:51 am
Forum: Getting started
Topic: Parameters for the Ih current
Replies: 5
Views: 26

Re: Parameters for the Ih current

that mod file has some mistakes in the units modlunit reports units inconsistencies in that particular file, but they are entirely benign and have no effect on numerical results. If you want more information about the Borg-Graham approach to describing channel gating, start by reading the reference...
by ted
Fri Dec 14, 2018 10:22 am
Forum: Getting started
Topic: sectioning neuron based on distance from soma
Replies: 9
Views: 75

Re: sectioning neuron based on distance from soma

If path distance to section center is supposed to govern channel density, then 1. nseg must be odd in all sections (otherwise, there will be no internal node at the 0.5 location, and distance(0.5) will return instead the distance to one of the nodes on either side of the section midpoint, depending ...
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: 28

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: 5
Views: 582

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: 5
Views: 582

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: 29

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: 41

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: 41

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: 31

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: 9
Views: 75

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: 109

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: 46

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: 45

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...