Search found 6290 matches

by ted
Tue Oct 03, 2023 12:40 pm
Forum: NEURON + Python
Topic: Different total area from python and hoc cell class
Replies: 5
Views: 9447

Re: Different total area from python and hoc cell class

Algorithmic details aside, there is one hard fact that should be kept in mind: most parameters of biological systems are known to only very limited precision. For a multitude of reasons, the precision of measurements of neuronal morphology obtained with light microscopy is at best about 0.2 um, but ...
by ted
Thu Sep 28, 2023 9:49 am
Forum: NEURON + Python
Topic: Different total area from python and hoc cell class
Replies: 5
Views: 9447

Re: Different total area from python and hoc cell class

First, a question. What version of NEURON are you using?

Next, a suggestion. Use as simple a workflow as possible, that is, import the morphometric data, but _don't_ discretize the model cell, and don't add or alter any biophysical properties. What results do you get?
by ted
Wed Sep 27, 2023 10:12 am
Forum: Anatomically detailed models
Topic: Interpreting the results of electrotonic analysis
Replies: 6
Views: 33353

Re: Interpreting the results of electrotonic analysis

Downloaded a zip file from NeuroMorpho that was supposed to contain a couple of "log files" and two morphology files: one that NeuroMorpho calls "Original" and another called "Standardized". Expanding the zip file revealed two morphology files, one called 2M3.asc (in Ne...
by ted
Tue Sep 26, 2023 11:49 pm
Forum: Anatomically detailed models
Topic: Interpreting the results of electrotonic analysis
Replies: 6
Views: 33353

Re: Interpreting the results of electrotonic analysis

From the printout generated by topology() that you provided, it looks like 1. there is only one root section 2. the root section is called soma 3. there is one axon and six dendritic trees and 4. the proximal ends of the axon and all dendritic trees are attached to the 1 end of the soma In the morni...
by ted
Tue Sep 26, 2023 12:41 pm
Forum: Anatomically detailed models
Topic: Interpreting the results of electrotonic analysis
Replies: 6
Views: 33353

Re: Interpreting the results of electrotonic analysis

Neuromorphic renderings of the electrotonic transformation might be pretty and seemingly intuitive, but many users find logA vs. X plots to be far more informative.
by ted
Tue Sep 26, 2023 12:36 pm
Forum: Anatomically detailed models
Topic: Interpreting the results of electrotonic analysis
Replies: 6
Views: 33353

Re: Interpreting the results of electrotonic analysis

Two suggestions. First, regarding how to interpret neuromorphic representations of electrotonus: work through this exercise https://nrn.readthedocs.io/en/latest/courses/electrotonic_analysis.html#electrotonic-analysis << note added after my initial post: at present, the "Shape" link in the...
by ted
Mon Sep 18, 2023 4:17 pm
Forum: NEURON hacks
Topic: Different Axial Resistance for different ions
Replies: 1
Views: 8671

Re: Different Axial Resistance for different ions

Hey! Relax, there's no need to be so formal. Is it possible to somehow define different axial resistances (Ra) for different ions? Everything is possible through programming, but the set of "everything" has many members that are ugly and awkward. You're asking for something that could eas...
by ted
Tue Sep 12, 2023 3:34 pm
Forum: OS X
Topic: Compiling Pulse Generator Error
Replies: 1
Views: 23491

Re: Compiling Pulse Generator Error

error: invalid active developer path (/Library/Developer/CommandLineTools) There's your clue. Have you installed the Command Line Tools? If not, see https://apple.stackexchange.com/questions/107307/how-can-i-install-the-command-line-tools-completely-from-the-command-line These pulse generators prod...
by ted
Tue Sep 12, 2023 3:26 pm
Forum: NEURON + Python
Topic: MulRunFitter & Python
Replies: 3
Views: 9967

Re: MulRunFitter & Python

One might well ask "How did ted make such an informed guess?" I now draw back the curtain of secrecy (faint of heart, pass not this line!) I executed nrngui then created an instance of the Multiple Run Fitter by clicking on NEURON Main Menu / Tools / Fitting / Multiple Run Fitter (of cours...
by ted
Mon Sep 11, 2023 10:46 am
Forum: NEURON + Python
Topic: MulRunFitter & Python
Replies: 3
Views: 9967

Re: MulRunFitter & Python

I found one post linking a model on modelDB that had a statement I suspect that one or more other statements must be executed before one tries to create an instance of the MulRunFitter class. Examine the source code for that entry in ModelDB (BTW, which entry is it?) and look for something similar ...
by ted
Thu Aug 24, 2023 12:17 pm
Forum: MSWin
Topic: " HHna is not a MECHANISM "
Replies: 5
Views: 12145

Re: " HHna is not a MECHANISM "

You're welcome. It works, but it should be much, much easier. It will take a while to figure out how to deal with Win 11.
by ted
Thu Aug 24, 2023 2:45 am
Forum: MSWin
Topic: " HHna is not a MECHANISM "
Replies: 5
Views: 12145

Re: " HHna is not a MECHANISM "

Installing NEURON should have created a folder on your desktop that has a name that starts with NEURON. Double click on that folder. Inside the folder is an icon with the label "bash". Double click on that. That should open a bash terminal. The prompt will look something like bash-5.2$ At ...
by ted
Wed Aug 23, 2023 12:43 pm
Forum: MSWin
Topic: MSWin11 + Anaconda, Neuron 8.2.2
Replies: 6
Views: 15723

Re: MSWin11 + Anaconda, Neuron 8.2.2

I'm very sorry you had all this difficulty. Looks like Win 11 has created some new work for us.
by ted
Wed Aug 23, 2023 12:38 pm
Forum: General questions and discussions about computational neuroscience
Topic: IMARIS vs. Neurolucida For NEURON Use
Replies: 10
Views: 61895

Re: IMARIS vs. Neurolucida For NEURON Use

You really need to have a detailed discussion with the person from whom you got these data. Here's what I found. I strongly suspect that the data are from an automated reconstruction, with minimal (if any) human supervision or intervention. That's an inference. What follows, however, is absolute fac...
by ted
Tue Aug 22, 2023 11:57 pm
Forum: MSWin
Topic: MSWin11 + Anaconda, Neuron 8.2.2
Replies: 6
Views: 15723

Re: MSWin11 + Anaconda, Neuron 8.2.2

For what it's worth
Might that also avoid the failure of neurondemo?