Search found 6316 matches

by ted
Wed Jul 17, 2024 10:39 am
Forum: Getting started
Topic: Questions about "stylized" model and build a new n
Replies: 3
Views: 3108

Re: Questions about "stylized" model and build a new n

How did you decide the values for the membrane mechanisms and morphology? The same way that one would design a computational model of any other physical system. First determine the purpose of the model, which is usually to study some phenomenon of interest that occurs in a physical system. Then dec...
by ted
Mon Jul 15, 2024 12:19 pm
Forum: NEURON + Python
Topic: change the onset time of voltage clamp
Replies: 3
Views: 1313

Re: change the onset time of voltage clamp

Two recommendations. 1. For the reasons mentioned above, don't activate the synapse at 0 ms. Instead, let the model execute for at least 1 ms before activating the synapse. 2. Use an FInitializeHandler (default type is good for this) to do two things during model initialization: (1) set the SEClamp'...
by ted
Fri Jul 12, 2024 10:32 am
Forum: NEURON + Python
Topic: change the onset time of voltage clamp
Replies: 3
Views: 1313

Re: change the onset time of voltage clamp

I am simulating a neural dynamic when it receives a synaptic input at t=0. An important concern in any experiment, whether on a living cell or a computational model, is the initial state of the system (cell or model) before any stimulus or perturbation is applied. If it is not in a resting state at...
by ted
Fri Jul 05, 2024 12:42 pm
Forum: Other questions
Topic: extracellular stimulation
Replies: 12
Views: 9479

Re: extracellular stimulation

I already know the mechanism: with a short pulse, there isn’t enough time for the membrane to depolarize and reach the activation threshold. True, but that's easily overcome by increasing stimulus amplitude, and it's only half of the story. A longer duration extracellular pulse can (1) reduce excit...
by ted
Thu Jul 04, 2024 1:38 pm
Forum: Other questions
Topic: extracellular stimulation
Replies: 12
Views: 9479

Re: extracellular stimulation

in DBS, which the pulses are short, the high frequency is important to the AP generation. Stimulus pulse duration is important, but you'll never guess why unless you take the time to learn more about the mechanistic basis of cellular excitability. And that should be covered in a good introductory c...
by ted
Thu Jul 04, 2024 12:57 am
Forum: Other questions
Topic: extracellular stimulation
Replies: 12
Views: 9479

Re: extracellular stimulation

It is the rare EE major that has much reading, classroom, or hand-on exposure to neurophysiology, and in particular practical aspects of stimulating excitable tissue (nerve, muscle). That's something you'll have to correct sooner or later if you plan to work at the interface between engineering and ...
by ted
Wed Jul 03, 2024 1:57 pm
Forum: Other questions
Topic: extracellular stimulation
Replies: 12
Views: 9479

Re: extracellular stimulation

By setting a pulse duration of 100 ms, I see AP generation. However, if I reduce the pulse width to 0.1 ms, APs are not generated. Is this expected behavior
To help guide my answer, it would be useful to know if your background is primarily in physics/math/engineering, or in biology.
by ted
Mon Jul 01, 2024 2:10 pm
Forum: Other questions
Topic: extracellular stimulation
Replies: 12
Views: 9479

Re: extracellular stimulation

First thing to check: what are the anatomical and biophysical properties of your model cell? What does
somaL.psection()
tell you? and how about somaR.psection()?
by ted
Mon Jul 01, 2024 1:47 pm
Forum: The GUI
Topic: Problem with h.PlotShape
Replies: 7
Views: 6774

Re: Problem with h.PlotShape

Could it be Linux is not GUI based ?? I think you'd know by now if the OS and hardware on the machine on which you're running NEURON have GUI support. Are you executing NEURON on a laptop or desktop machine, or on some remote server? Assuming NOT the latter, what happens if you execute neurondemo i...
by ted
Wed Jun 26, 2024 1:41 pm
Forum: The GUI
Topic: Problem with h.PlotShape
Replies: 7
Views: 6774

Re: Problem with h.PlotShape

Instead of matplotlib and pyplot, try plotly.

Code: Select all

import plotly
 . . .
ps = h.PlotShape(False)
ps.plot(plotly).show()
by ted
Wed Jun 26, 2024 11:01 am
Forum: Other questions
Topic: extracellular stimulation
Replies: 12
Views: 9479

Re: extracellular stimulation

Oops, instead of replying to a copy of your original post, I edited it, inserting my replies. How careless of me; done when I was hurrying to get to the point but not cautious about how it was done. But at least I didn't destroy your questions, and perhaps my replies will be helpful to you and others.
by ted
Fri Jun 14, 2024 10:24 am
Forum: NEURON + Python
Topic: Loading a Linear Circuit Mechanism in Python
Replies: 1
Views: 7218

Re: Loading a Linear Circuit Mechanism in Python

This example of how to develop and use a Linear Circuit implementation of a gap junction via Python https://www.neuron.yale.edu/ftp/ted/neu ... cirgap.zip might provide some useful hints.
by ted
Thu Jun 13, 2024 10:51 am
Forum: OS X
Topic: NEURON-nightly and compiling mod files
Replies: 1
Views: 7929

Re: NEURON-nightly and compiling mod files

Interesting. Needs to be brought to the attention of the NEURON development team. Regarding what you should do, if your goal is to do science, decide what's most important to you--cosmetics, or results; spending time trying to work around problems in development code, or addressing scientific proble...
by ted
Fri May 24, 2024 12:02 pm
Forum: NEURON + Python
Topic: Can't we write tautable.hoc in Python?
Replies: 2
Views: 5746

Re: Can't we write tautable.hoc in Python?

Sure, if you want to rewrite those statements in Python, go ahead. Here's a seed to get you started. I have even corrected the comment in the second statement.

Code: Select all

vecv_KIR = h.Vector()
vecv_KIR.indgen(-100, 0, 10) # -100 to 0 with steps of 10
by ted
Tue May 21, 2024 12:41 pm
Forum: Getting started
Topic: square in soma in plotshape
Replies: 1
Views: 7999

Re: square in soma in plotshape

If a section's geometry is specified with the "stylized" method (assigning values to L and diam), the section will be a cylinder of length L and diameter diam, and it will look like a cylinder in graphical renderings that show diameter. If the geometry is specified with the pt3d method (a ...