Search found 5820 matches

by ted
Fri Oct 02, 2020 11:25 am
Forum: NEURON + Python
Topic: External Stimuli not working
Replies: 1
Views: 581

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...
by ted
Thu Oct 01, 2020 12:34 am
Forum: UNIX/Linux
Topic: Configure fonts, etc in GUI
Replies: 2
Views: 240

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...
by ted
Wed Sep 30, 2020 11:33 am
Forum: NEURON + Python
Topic: implement Randles circuit in NEURON
Replies: 3
Views: 314

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 ...
by ted
Wed Sep 30, 2020 12:01 am
Forum: NEURON + Python
Topic: implement Randles circuit in NEURON
Replies: 3
Views: 314

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...
by ted
Tue Sep 29, 2020 11:05 am
Forum: Other questions
Topic: spatial discretization, and saving results
Replies: 1
Views: 221

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...
by ted
Mon Sep 14, 2020 3:17 pm
Forum: NEURON + Python
Topic: Frequency dependent activation of g protein models
Replies: 2
Views: 2922

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?
by ted
Mon Sep 14, 2020 3:10 pm
Forum: NEURON + Python
Topic: injecting continuous normally distributed noise in python
Replies: 2
Views: 1342

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 ...
by ted
Mon Sep 14, 2020 1:47 pm
Forum: NEURON + Python
Topic: Connect multiple cells using connection probabilities
Replies: 4
Views: 4091

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...
by ted
Mon Sep 14, 2020 1:46 pm
Forum: NEURON + Python
Topic: Connect multiple cells using connection probabilities
Replies: 4
Views: 4091

Re: Connect multiple cells using connection probabilities

gladonias wrote: Mon Sep 14, 2020 7:36 am Let's say you instantiated a model of a neuron into a variable named cell, you can get the total number of dendritic compartments with len(cell.dend).
Interesting. Can you provide a working example?
by ted
Mon Sep 14, 2020 12:03 pm
Forum: NEURON + Python
Topic: Netstim in automated repeating simulations
Replies: 2
Views: 302

Re: Netstim in automated repeating simulations

Great question. hoc and Python keep track of how many variables reference each object instance. An object instance persists as long as there is at least one variable that references it. If an object instance's "reference count" drops to 0, the object is destroyed and the memory that it use...
by ted
Thu Sep 10, 2020 12:29 am
Forum: Anatomically detailed models
Topic: Questions about geometry & area(x)
Replies: 3
Views: 6390

Re: Questions about geometry & area(x)

Trapezoidal integration has nothing to do with it. If a section's geometry is specified using the stylized method (specification of L and diam), each segment is treated as if it is cylindrical and its surface area is calculated from its diameter. If geometry is specified with the 3d (AKA pt3d) metho...
by ted
Tue Sep 08, 2020 5:07 pm
Forum: NEURON + Python
Topic: Multiple stimulation of POINT_PROCESS per run
Replies: 3
Views: 517

Re: Multiple stimulation of POINT_PROCESS per run

The original implementation of NMDA_Mg_T did not initialize Mg binding to ion channels correctly. Instead, initialization set channels to "unbound" (i.e. "completely free of Mg") state. Consequently, depending on parameter values, it was necessary to delay synaptic activation for...
by ted
Tue Sep 08, 2020 11:25 am
Forum: Other questions
Topic: Regarding diameter of geometry
Replies: 1
Views: 345

Re: Regarding diameter of geometry

Never apologize for using the GUI--the GUI has many tools that are powerful and easy to use. A quick way to learn a lot of useful information is to go straight to the Documentation page at NEURON's web site https://neuron.yale.edu/neuron/docs and check out the links under For NEURON beginners and es...
by ted
Wed Aug 26, 2020 9:14 am
Forum: Other questions
Topic: trouble with e_extracellular and play
Replies: 3
Views: 591

Re: trouble with e_extracellular and play

Actually the "step 4" code isn't doing what you think it is. Examine the time course of each segment's e_extracellular and you will see that only the last segment's e_extracellular is being driven by the sine wave. Why? The first pass through the loop for seg in axon1: y = h.Vector(np.sin(...
by ted
Tue Aug 25, 2020 8:13 am
Forum: Other questions
Topic: Change list of morphology file into hoc code
Replies: 2
Views: 393

Re: Change list of morphology file into hoc code

That code runs on neurons, but it doesn't run when I import it in the other simulation tool What "other simulation tool" do you mean? I want to fix the morpologies in the txt file so that hoc coding is possible. I guess you want to convert the Neurolucida text file to a hoc file. 1. Use t...