Search found 6290 matches
- Tue Oct 03, 2023 12:40 pm
- Forum: NEURON + Python
- Topic: Different total area from python and hoc cell class
- Replies: 5
- Views: 9448
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 ...
- Thu Sep 28, 2023 9:49 am
- Forum: NEURON + Python
- Topic: Different total area from python and hoc cell class
- Replies: 5
- Views: 9448
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?
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?
- 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...
- 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...
- 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.
- 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...
- Mon Sep 18, 2023 4:17 pm
- Forum: NEURON hacks
- Topic: Different Axial Resistance for different ions
- Replies: 1
- Views: 8673
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...
- 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...
- 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...
- 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 ...
- 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.
- 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 ...
- 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.
- 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: 61896
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...
- 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
Might that also avoid the failure of neurondemo?For what it's worth