Search found 5842 matches
- Mon Oct 26, 2020 9:47 am
- Forum: Other questions
- Topic: Neurolucida text morphology changes when using import3D
- Replies: 3
- Views: 376
Re: Neurolucida text morphology changes when using import3D
Yes, there are many lessons to learn from this, like how to write code that is difficult for anyone else to use.
- Thu Oct 22, 2020 11:00 am
- Forum: Other questions
- Topic: Neurolucida text morphology changes when using import3D
- Replies: 3
- Views: 376
Re: Neurolucida text morphology changes when using import3D
I'll have to reproduce this for myself. Please send the necessary morphometric data file(s) to ted dot carnevale at yale dot edu
- Thu Oct 22, 2020 10:58 am
- Forum: Other questions
- Topic: Some questions on plot [Ca2+]i vs. distance
- Replies: 2
- Views: 345
Re: Some questions on plot [Ca2+]i vs. distance
Read the Programmer's Reference documentation of the RangeVarPlot class https://neuronsimulator.github.io/nrn/new_doc/visualization/rvarplt.html#rangevarplot . First, some definitions. Parent section and child section: The statement connect foo, bar connects section foo to section bar. bar is the pa...
- Mon Oct 12, 2020 4:55 pm
- Forum: UNIX/Linux
- Topic: Installing on Ubuntu 20.04 (GUI not working)
- Replies: 7
- Views: 954
Re: Installing on Ubuntu 20.04 (GUI not working)
Under Mint 19.3 (a Debian/Ubuntu variant) I did a fresh install of NEURON 8.x by executing pip3 install neuron as an ordinary user. However, when I tried checking a mod file for units inconsistencies, I found that the command modlunit failed. So did idraw but nrniv and nrnivmodl both worked. modluni...
- Tue Oct 06, 2020 2:37 pm
- Forum: UNIX/Linux
- Topic: Installing on Ubuntu 20.04 (GUI not working)
- Replies: 7
- Views: 954
Re: Installing on Ubuntu 20.04 (GUI not working)
If you want to load the GUI,
from neuron import h, gui
or
from neuron import h
h.load_file('nrngui.hoc')
Does that take care of the problem?
from neuron import h, gui
or
from neuron import h
h.load_file('nrngui.hoc')
Does that take care of the problem?
- Tue Oct 06, 2020 11:17 am
- Forum: UNIX/Linux
- Topic: Installing on Ubuntu 20.04 (GUI not working)
- Replies: 7
- Views: 954
Re: Installing on Ubuntu 20.04 (GUI not working)
So what's the current status? Does 7.6.7 work?I then installed using tar.gz file of 7.6.7 version
- Sun Oct 04, 2020 11:23 am
- Forum: UNIX/Linux
- Topic: Installing on Ubuntu 20.04 (GUI not working)
- Replies: 7
- Views: 954
Re: Installing on Ubuntu 20.04 (GUI not working)
Did you doAfter installing the package
sudo pip3 install neuron
or did you install from a .deb package?
If you used a .deb package, from where did you get it?
- Fri Oct 02, 2020 11:25 am
- Forum: NEURON + Python
- Topic: External Stimuli not working
- Replies: 1
- Views: 640
Re: External Stimuli not working
1. Is the model cell excitable? Attach an IClamp to the soma and apply a 1 ms current pulse that starts at t = 1 ms. Record and plot the current generated by the IClamp and v at the point of attachment. Adjust amplitude of the current pulse until a spike is elicited. Can't elicit a spike? Verify tha...
- Thu Oct 01, 2020 12:34 am
- Forum: UNIX/Linux
- Topic: Configure fonts, etc in GUI
- Replies: 2
- Views: 273
Re: Configure fonts, etc in GUI
Under Windows it's easy. Assuming that an instance of the PWManager class exists (it will exist if you started NEURON by executing nrngui, or if your code has executed a load_file("nrngui.hoc") statement), then an instance of the PWManager class will exist and you can use its scale() funct...
- Wed Sep 30, 2020 11:33 am
- Forum: NEURON + Python
- Topic: implement Randles circuit in NEURON
- Replies: 3
- Views: 359
Re: implement Randles circuit in NEURON
Further comments: 1. The linear circuit could be implemented with the Linear Circuit builder. 2. The simulation of neural activity and calculation of PHI_REC(t) do not have to be done in the same session. Instead, the simulation and calculation of PHI_LFP(t) could be done once, and PHI_LFP(t) saved ...
- Wed Sep 30, 2020 12:01 am
- Forum: NEURON + Python
- Topic: implement Randles circuit in NEURON
- Replies: 3
- Views: 359
Re: implement Randles circuit in NEURON
I'm not clear how to do this in the real-time simulation of NEURON. Let's use proper terminology. You mean "time domain simulation" not "real-time simulation." It's clear that you know the difference between time domain and frequency domain, but some who read this thread may not...
- Tue Sep 29, 2020 11:05 am
- Forum: Other questions
- Topic: spatial discretization, and saving results
- Replies: 1
- Views: 251
Re: spatial discretization, and saving results
1) I noticed in the gui a user can specify d_X in the geometry --> is there an equivalent way to do this when working in python? The d_X rule for spatial discretization is set nseg to the smallest odd number such that L/nseg <= d_X Code to do this is built into the CellBuilder. If you want to do it...
- Mon Sep 14, 2020 3:17 pm
- Forum: NEURON + Python
- Topic: Frequency dependent activation of g protein models
- Replies: 2
- Views: 3518
Re: Frequency dependent activation of g protein models
Yes, ModelDB would be a good place to start looking. Also, do you know of one or more published articles that provides a mathematical description of the exact phenomenon you want to represent in your model?
- Mon Sep 14, 2020 3:10 pm
- Forum: NEURON + Python
- Topic: injecting continuous normally distributed noise in python
- Replies: 2
- Views: 1383
Re: injecting continuous normally distributed noise in python
I've been trying to insert normally distributed noise onto my cells via IClamp . . . I have a vector of say 1x1000 (1 per ms) that I want to set as the amp value. Your code was heading in the right direction. Just a few changes and it will work. Here's a toy example (just a single cell) that might ...
- Mon Sep 14, 2020 1:47 pm
- Forum: NEURON + Python
- Topic: Connect multiple cells using connection probabilities
- Replies: 4
- Views: 4143
Re: Connect multiple cells using connection probabilities
I'm trying to connect multiple neuron cells . . . I need to take into account the connection probabilities between the cells. So I was thinking of multiplying the connection probability by the number of dendrites in the post synaptic cell. Why would that be useful? Is the number of dendrites presen...