Search found 5743 matches

by ted
Sat May 02, 2020 6:12 pm
Forum: Modeling networks
Topic: Switching synaptic connections in nested for loop
Replies: 7
Views: 613

Re: Switching synaptic connections in nested for loop

I get a weird response for my very first simulation. If I run the simulation quickly (even just 1ms) and then run it again, the response is normal. How do you know which result is "normal"? Both look abnormal to me, in that no cell appears to be initialized to steady state, nor does any cell settle...
by ted
Mon Apr 27, 2020 6:17 pm
Forum: Anatomically detailed models
Topic: morphology altered when Import3d exports to CellBuilder
Replies: 4
Views: 623

Re: morphology altered when Import3d exports to CellBuilder

Your bitmaps are looking down the Y axis onto the XZ plane (X axis horizontal, Z axis vertical, Y axis orthogonal to the plane of the image). I can't comment about the original morphometric data without seeing it for myself. However, I can tell you that in the imported model, what you are probably c...
by ted
Mon Apr 27, 2020 10:24 am
Forum: Anatomically detailed models
Topic: morphology altered when Import3d exports to CellBuilder
Replies: 4
Views: 623

Re: morphology altered when Import3d exports to CellBuilder

Rotation around the y axis. You're looking at the same thing, but from different angles.
by ted
Fri Apr 24, 2020 10:41 am
Forum: Anatomically detailed models
Topic: importing .asc (Neurolucida ASCII) files with Python
Replies: 4
Views: 3062

Re: importing .asc (Neurolucida ASCII) files with Python

no such file is present in the working directory If the file were in some other location, one could include the path to the file. For example, if the morphometric data file were in /home/data/project1, then changing the statement to morph_reader.input('/home/data/project1/C011098A-P4.asc') would fi...
by ted
Thu Apr 23, 2020 11:45 am
Forum: Anatomically detailed models
Topic: importing .asc (Neurolucida ASCII) files with Python
Replies: 4
Views: 3062

Re: importing .asc (Neurolucida ASCII) files with Python

The error message is could not open 0409_H50_01.asc NEURON: 0409_H50_01.asc :file is not open It means exactly what it says. The usual causes are either that no such file is present in the working directory, or that a "file permission" or "file ownership" issue prevents the file from being opened. B...
by ted
Wed Apr 15, 2020 4:20 pm
Forum: NEURON + Python
Topic: cell counting on an image with python
Replies: 3
Views: 635

Re: cell counting on an image with python

With regard to "neuron counting" (and might even be relevant to your question), MicroBrightField is presenting a 1 hour webinar on stereology on April 21 starting at 11 AM EDT. It's free but registration is required--see https://register.gotowebinar.com/regist ... 8440137741
by ted
Tue Apr 14, 2020 10:06 pm
Forum: NEURON + Python
Topic: cell counting on an image with python
Replies: 3
Views: 635

Re: cell counting on an image with python

That's an interesting problem, but far outside of the scope of the NEURON Forum. You might try doing a web search for "automated neuron counting". I just now did that with Duck Duck Go, and saw three or four possibly useful hits on the first page of results.
by ted
Thu Apr 09, 2020 12:05 pm
Forum: NEURON + Python
Topic: Record from multiple neurons
Replies: 2
Views: 428

Re: Record from multiple neurons

To emphasize what ramcdougal wrote For (4), you're trying to store values before the simulation has been run. There are no values to store at that point. (and remove any ambiguity that there might still be), the Vector record() method captures values "on the fly" in the course of a simulation. If yo...
by ted
Fri Apr 03, 2020 1:37 pm
Forum: NEURON + Python
Topic: inserting synaptic mechanisms from mod file
Replies: 1
Views: 452

Re: inserting synaptic mechanisms from mod file

First, a comment about the example code in your post: many of the statements in it are deprecated or useless or serve no useful purpose at the point at which they are executed. A strong suggestion: if you want a quick, up-to-date, and reasonably complete introduction to using Python to build NEURON ...
by ted
Fri Apr 03, 2020 10:49 am
Forum: Other questions
Topic: apply extracellular electric field and current
Replies: 3
Views: 660

Re: apply extracellular electric field and current

I used "record" as follows but still I can't calculate intracellular potential... //record membrane voltage objref dvm dvm = new Vector() dvm.record(&axon.v(.5)) //record extracellular voltage objref dvex dvex = new Vector() dvex.record(&axon.vext[1](.5))[/quote]You'll also want to record time, so ...
by ted
Sat Mar 28, 2020 11:05 am
Forum: Modeling networks
Topic: Minimal parallel ring network
Replies: 2
Views: 432

Re: Minimal parallel ring network

Thank you for posting your question, and for finding the problem and posting the solution so others who read this thread can learn. Bugs are common in non-trivial software projects. They can be minimized and often prevented by testing at every stage of development. In the context of implementing a c...
by ted
Fri Mar 27, 2020 10:49 am
Forum: Getting started
Topic: Question about tutorial
Replies: 9
Views: 4985

Re: Question about tutorial

You'll have to contact that tutorial's authors.

If you are starting a new modeling project with NEURON, it would be best for you to use Python to create the model specification etc.. Please see the link Scripting NEURON with Python on the Documentation page https://neuron.yale.edu/neuron/docs
by ted
Tue Mar 24, 2020 5:06 pm
Forum: Other questions
Topic: Importing stimulus waveforms
Replies: 3
Views: 554

Re: Importing stimulus waveforms

NEURON's defaut integrator is implicit Euler, which has first order accuracy. This means that a driven variable, be it a stimulus amplitude or a time-varying parameter, is effectively a staircase waveform--changes abruptly at each time step boundary, and remains constant until the next time step bou...
by ted
Tue Mar 24, 2020 12:35 pm
Forum: Other questions
Topic: Importing stimulus waveforms
Replies: 3
Views: 554

Re: Importing stimulus waveforms

if, for example, I use a TMS waveform recorded at 1 µs steps and a NEURON simulation time step dt of 5 µs for either of the two following cases, I get different results How different is "different"? Major qualitative difference, or just a noticeable quantitative difference while overall time course...
by ted
Mon Mar 16, 2020 11:36 am
Forum: Other questions
Topic: Action Potential propagation
Replies: 3
Views: 493

Re: Action Potential propagation

See the documentation of extracellular in the Programmer's Reference. The vext values are all referred to ground, which is assumed to have a potential of 0 mV. The hoc name for the potential at a point just outside the cell membrane of the currently accessed section is vext[0](x) where x is the norm...