Search found 6301 matches
- Sun Nov 05, 2023 1:00 am
- Forum: Modeling networks
- Topic: neuronal response to magnetically induced electric fields
- Replies: 4
- Views: 33408
Re: neuronal response to magnetically induced electric fields
if there is some function implemented in NEURON to simulate the characteristics of magnetically induced electric fields That is not included with NEURON. However, there are a lot of smart NEURON users who are interested in related problems, so maybe one or more of them has already implemented their...
- Fri Oct 27, 2023 9:48 am
- Forum: NEURON + Python
- Topic: Dealing with objects defined in functions
- Replies: 1
- Views: 12599
Re: Dealing with objects defined in functions
Here's an implementation that does almost everything via procedures, and contains some (not so) latent hints. Imports and definitions first from neuron import h, gui ### Model and simulation parameters # KISS when developing/debugging # this means small nets, short run times, few spikes # make symbo...
- Mon Oct 23, 2023 11:44 am
- Forum: NEURON + Python
- Topic: CoreNeuron verbose output
- Replies: 3
- Views: 12424
Re: CoreNeuron verbose output
Actually, h.verbose could be an interesting feature.
Just out of curiosity: what performance boost are you getting?
Just out of curiosity: what performance boost are you getting?
- Sat Oct 21, 2023 10:56 pm
- Forum: NEURON + Python
- Topic: CoreNeuron verbose output
- Replies: 3
- Views: 12424
Re: CoreNeuron verbose output
Try inserting
coreneuron.verbose = 0
after
coreneuron.enable = True
You might glean some other useful stuff from
https://github.com/neuronsimulator/nrn/ ... _direct.py
coreneuron.verbose = 0
after
coreneuron.enable = True
You might glean some other useful stuff from
https://github.com/neuronsimulator/nrn/ ... _direct.py
- Mon Oct 16, 2023 12:51 pm
- Forum: Other questions
- Topic: Implementing extracellular stimulation
- Replies: 14
- Views: 66662
Re: Extracellular stimulation and recording
Please do.I am assuming I should proceed with that first part of your reply?
- Mon Oct 16, 2023 12:36 pm
- Forum: Modeling networks
- Topic: Accessing tpre and tpost from STDP mod file
- Replies: 5
- Views: 13712
Re: Accessing tpre and tpost from STDP mod file
I forgot to mention that the NetCon that monitors the postsynaptic potential should have the same threshold as is specified in the NMODL's WATCH statement. For STDPE2, that would be the value of the RANGE variable thresh. For a synaptic mechanism S that can handle multiple input streams, the cleanes...
- Mon Oct 16, 2023 12:13 pm
- Forum: NEURON + Python
- Topic: h.parallelContext in a model being simulated on a cluster
- Replies: 3
- Views: 11913
Re: h.parallelContext in a model being simulated on a cluster
Interesting problem. Just in case you ran into a NEURON bug: what version of NEURON is running on your Mac, and what version is the cluster using?
- Fri Oct 13, 2023 1:17 pm
- Forum: Other questions
- Topic: Implementing extracellular stimulation
- Replies: 14
- Views: 66662
Re: Extracellular stimulation and recording
Yow, instead of quoting your message and replying to it, in a hurry I made the mistake of editing your message. At least I captured your questions so we can continue the discussion.
- Wed Oct 11, 2023 4:20 pm
- Forum: Modeling networks
- Topic: Accessing tpre and tpost from STDP mod file
- Replies: 5
- Views: 13712
Re: Accessing tpre and tpost from STDP mod file
The easy way to discover tpost is to attach a NetCon to the segment that has the instance of the STDPE2 class, and use that NetCon's record() method to capture local postsynaptic "spike times" to a Vector. What's not so clear to me is how you are capturing the tpre values. Are you recordin...
- Fri Oct 06, 2023 1:01 pm
- Forum: MSWin
- Topic: New installation of NEURON + Python
- Replies: 4
- Views: 37693
Re: New installation of NEURON + Python
I've noticed the installer from https://www.neuron.yale.edu/neuron/download is version 8.2.0, and it kept giving one of my students a "no module named hoc" error. They eventually used the installer found on nrn.readthedocs.io and it is version 8.2.3 and this works fine. Just thought I sho...
- Wed Oct 04, 2023 11:44 am
- Forum: Modeling networks
- Topic: Accessing tpre and tpost from STDP mod file
- Replies: 5
- Views: 13712
Re: Accessing tpre and tpost from STDP mod file
The first step is for you to disclose the code of the mod file that you are actually using (either include it in your next post, or better yet provide a URL to where you found it). Statements like
"the STDP mod file created by so and so"
mean almost nothing because text files are fungible.
"the STDP mod file created by so and so"
mean almost nothing because text files are fungible.
- Tue Oct 03, 2023 12:40 pm
- Forum: NEURON + Python
- Topic: Different total area from python and hoc cell class
- Replies: 5
- Views: 13364
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: 13364
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: 40149
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: 40149
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...