Search found 6290 matches
- Sun Jan 14, 2024 4:59 pm
- Forum: Getting started
- Topic: d_lambda setup
- Replies: 9
- Views: 21709
Re: d_lambda setup
Thank you. I'll review it and reply accordingly. In the meantime I decided to run a test of my own, using a simple model: cylindrical axon geometry: diam 1 um, length 1000 um, 0 end at 0,0,0, 1 end at 1000, 0, 0 (all units in um) biophysics: hh membrane at standard operating temperature (6.3 deg C),...
- Fri Jan 12, 2024 3:17 pm
- Forum: Getting started
- Topic: d_lambda setup
- Replies: 9
- Views: 21709
Re: d_lambda setup
You could just zip up all the source files that are needed to reproduce your results (hoc, mod, ses, swc, txt, dat--but also see viewtopic.php?t=1048) and email them to ted dot carnevale at yale dot edu
- Fri Jan 12, 2024 12:14 am
- Forum: Getting started
- Topic: d_lambda setup
- Replies: 9
- Views: 21709
Re: d_lambda setup
First, some important questions: What is your operational definition of "activating potential" (by what experimental procedure did you determine its numerical value)? Can you present a table of your results? An extracellular potential was applied to the axon. How? Specifically: What was yo...
- Thu Jan 11, 2024 3:10 pm
- Forum: Other questions
- Topic: Implementing extracellular stimulation
- Replies: 14
- Views: 54877
Re: Implementing extracellular stimulation
Your "3D mesh" defines a "stimulated volume" in space. Your first task is to decide the location and orientation of your model cell in that volume. That's something that you and your PI must do. Next, for each segment in your model, you have to do two things: (1) determine the co...
- Mon Jan 08, 2024 2:03 pm
- Forum: Other questions
- Topic: Implementing extracellular stimulation
- Replies: 14
- Views: 54877
Re: Extracellular stimulation and recording
Apologies for the double post, tried to edit and messed it up. OK, double post is now gone. BTW I'm an expert on messing up edits of posts. By "put in an electrode", I meant apply an extracellular stimulus. Got it. The reason for trying to get a different segment division of the model due...
- Fri Jan 05, 2024 12:37 am
- Forum: Other questions
- Topic: Implementing extracellular stimulation
- Replies: 14
- Views: 54877
Re: Extracellular stimulation and recording
I am working on a code where I extract small compartments of a model cell and put in an electrode (could be an IClamp? unsure about it) in each of the compartment. What do you mean by "put in an electrode"? Are you trying to inject current into the model cell, or are you trying to apply a...
- Sat Dec 16, 2023 1:29 am
- Forum: The GUI
- Topic: Programmatic GUI control (pressing buttons, etc.)
- Replies: 3
- Views: 16026
Re: Programmatic GUI control (pressing buttons, etc.)
NEURON's existing GUI is implemented with InterViews, which doesn't offer such functionality. There has been some work to develop a new GUI, but most development efforts have focussed on performance, taking advantage of new CPU architectures, code reorganization, and improving the development proces...
- Fri Dec 15, 2023 12:25 pm
- Forum: Modeling networks
- Topic: How to record variables of SEClamp adding to a soma?
- Replies: 1
- Views: 15255
Re: How to record variables of SEClamp adding to a soma?
First, let me thank you for your interest in using NEURON in your work. It looks like you already have significant experience with MATLAB. Now the good news. While your code isn't a "textbook example of best usage of hoc," it _is_ running properly--including recording the time course of va...
- Wed Dec 13, 2023 4:26 pm
- Forum: Other questions
- Topic: Re: Extracellular stimulation and recording
- Replies: 1
- Views: 10901
Re: Extracellular stimulation and recording
direct current model of transcutaneous electrical stimulation of the spinal cord. The volume conductor model was thought to be purely resistive, with multiple layers of tissues (skin, muscles, bones, etc.). COMSOL was used to simulate the electric field induced in the spinal cord. . . . how can I a...
- Wed Dec 13, 2023 3:10 pm
- Forum: NEURON hacks
- Topic: Conditional termination of simulation
- Replies: 10
- Views: 71698
Re: Conditional termination of simulation
how do I adapt the line nc.record(spikehappened)? I can specify the input arguments like using nc.record((spikehappened,(tsp, count, isi, previsi))), but how do I specify the outputs? Excellent question. I don't have an answer for it. If there is such an answer, maybe someone more knowledgable abou...
- Tue Nov 28, 2023 2:43 pm
- Forum: Other questions
- Topic: Applying Sinusoidal Voltage to Membrane
- Replies: 6
- Views: 39100
Re: Applying Sinusoidal Voltage to Membrane
I am trying to force the extracellular potential to follow a particular time course. . . . I want to apply a sine pulse with a amplitude of 1 V. So the electrode-tissue interface is not a part of your conceptual model. Instead, it is assumed that it is possible to force extracellular potential to a...
- Mon Nov 27, 2023 11:17 am
- Forum: NEURON + Python
- Topic: User defined function to set play vectors
- Replies: 2
- Views: 25659
Re: User defined function to set play vectors
Can anyone explain why these variables need to be available outside the scope of my function? "Can anyone"? Sure--and in particular, you. Create some variable x inside a function and assign it a value. Exit the function without passing the value of x to an external variable. Then try usin...
- Mon Nov 20, 2023 1:23 pm
- Forum: NEURON + Python
- Topic: Issue with SaveState
- Replies: 2
- Views: 12262
Re: Issue with SaveState
Quoting from the documentation of SaveState, which you will find at nrn.readthedocs.io: Between a save and a restore, it is important not to create or delete sections, NetCon objects, or point processes. Do not change the number of segments, insert or delete mechanisms, or change the location of poi...
- Mon Nov 20, 2023 1:07 pm
- Forum: NEURON hacks
- Topic: Conditional termination of simulation
- Replies: 10
- Views: 71698
Re: Conditional termination of simulation
Well, "crude but effective" is still effective. An alternative is to explicitly pass all variables whose values are to be changed as arguments, and return them as results, like so: a = somevalue b = someothervalue c = yetanothervalue def foo(a, b, c): . . . statements that change a, b, and...
- Wed Nov 15, 2023 11:43 pm
- Forum: Other questions
- Topic: Applying Sinusoidal Voltage to Membrane
- Replies: 6
- Views: 39100
Re: Applying Sinusoidal Voltage to Membrane
OK, three more questions, and then we can move on to specific suggestions for you. Are you assuming that the extracellular medium is purely resistive? Do you already have the time course of extracellular potential that you want to apply to the axon? Which programming language do you prefer to use in...