Search found 6301 matches
- Mon Jan 08, 2024 2:03 pm
- Forum: Other questions
- Topic: Implementing extracellular stimulation
- Replies: 14
- Views: 66657
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: 66657
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: 17999
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: 17157
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: 12311
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: 86633
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: 49542
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: 34944
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: 18970
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: 86633
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: 49542
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...
- Tue Nov 14, 2023 3:50 pm
- Forum: NEURON hacks
- Topic: Conditional termination of simulation
- Replies: 10
- Views: 86633
Re: Conditional termination of simulation
Good try. There is no need to write any NMODL code--everything can be done with hoc or Python or a combination of the two. Here's an example that assumes the existence of a section called soma with 100 um2 surface area and hh membrane properties. Omitted is the "from neuron import h, gui" ...
- Tue Nov 14, 2023 11:36 am
- Forum: Other questions
- Topic: Applying Sinusoidal Voltage to Membrane
- Replies: 6
- Views: 49542
Re: Applying Sinusoidal Voltage to Membrane
First you need to decide exactly what you are trying to do. This "apply a sinusoidal voltage to vary the membrane potential over time" means you want to force membrane potential to follow a specific time course. That is best done with a voltage clamp--specifically, an instance of NEURON's ...
- Fri Nov 10, 2023 12:48 pm
- Forum: Modeling networks
- Topic: neuronal response to magnetically induced electric fields
- Replies: 4
- Views: 33406
Re: neuronal response to magnetically induced electric fields
So changes to nrnivmodl since NEURON 7.8 have interfered with NEMO. Where did you find NEMO and what is the paper that presents this tool? I wonder if its developers would be interested in making it work under the latest version of NEURON, if that doesn't require too much of their effort.
- Sun Nov 05, 2023 1:18 am
- Forum: NEURON hacks
- Topic: Conditional termination of simulation
- Replies: 10
- Views: 86633
Re: Conditional termination of simulation
Use events. Specifically, 1. use an FInitializeHandler to set the spike count to 0 at the start of the simulation 2. usethe NetCon class's record() method to call a function every time the cell spikes. This function should do the following: increase the spike count by 1 if spike count == 1 tnow = t ...