Search found 163 matches

by ramcdougal
Mon Aug 27, 2018 9:24 pm
Forum: Anatomically detailed models
Topic: area() function -- stylized method -- 3d-method
Replies: 4
Views: 1702

Re: area() function -- stylized method -- 3d-method

There is some discussion about how segment areas and volumes are calculated at: https://www.neuron.yale.edu/neuron/static/py_doc/modelspec/programmatic/topology/geometry.html#d-specification-of-geometry To say what hines said another way: in your first case, you're defining a tapered shape while the...
by ramcdougal
Mon Aug 27, 2018 8:07 pm
Forum: Reaction-diffusion in NEURON
Topic: Reaction-Diffusion in HOC
Replies: 5
Views: 17799

Re: Reaction-Diffusion in HOC

Most likely that means that either Python is not installed, or it is installed but NEURON can't connect to it (likely a path issue). You're free to program NEURON models in HOC or Python, but to use the rxd module, Python must be installed and loadable by NEURON To check for this, check the return v...
by ramcdougal
Fri Aug 24, 2018 12:38 pm
Forum: Adding new mechanisms and functions to NEURON
Topic: Ineffective simulation with small duration current injection
Replies: 2
Views: 1256

Re: Ineffective simulation with small duration current injection

Are you using a fixed time step or variable? I assume variable step will choose time points at the beginning and end of each current change... And thus you would see the current injection having an effect. If fixed, what is dt? Note that for fixed step, the default timestep (0.025 ms) is longer than...
by ramcdougal
Wed Aug 22, 2018 6:13 am
Forum: NEURON + Python
Topic: Not able to run simulation more than once from a NEURON+Python script
Replies: 4
Views: 2335

Re: Not able to run simulation more than once from a NEURON+Python script

Doesn't solve the mystery, but...

Assuming the morphology is not changing with successive runs, you could load it once before entering the loop, and see this particular issue entirely
by ramcdougal
Mon Aug 13, 2018 1:31 pm
Forum: Adding new mechanisms and functions to NEURON
Topic: Computational Optogenetics: modelling ChR2 in NMODL
Replies: 2
Views: 1348

Re: Computational Optogenetics: modelling ChR2 in NMODL

You can probably do what you want by using Vector.play . In brief, Vector.play allows you to use two Vectors (one listing time points and one with the values) to control an arbitrary memory location (e.g. a current, or in your case a variable in a MOD file). Example that plays a stimulus into the in...
by ramcdougal
Mon Aug 13, 2018 1:06 pm
Forum: Adding new mechanisms and functions to NEURON
Topic: A question about USEION statement
Replies: 1
Views: 1132

Re: A question about USEION statement

Currents of the same type from different mechanisms add.

You can test this yourself by creating two trivial mod files that generate a constant current, and measuring the current when one vs both are inserted.
by ramcdougal
Thu Aug 09, 2018 12:36 pm
Forum: Adding new mechanisms and functions to NEURON
Topic: HOC kernel for Jupyter
Replies: 3
Views: 1763

Re: HOC kernel for Jupyter

If you're working on a HOC kernel, I also encourage this... But: (1) Consider teaching in Python instead of HOC. That's what we do for the official NEURON courses. The Python programmer's reference is not only the default version, but it's also more up-to-date and has more examples. (2) As long as y...
by ramcdougal
Tue Aug 07, 2018 7:48 am
Forum: NEURON + Python
Topic: Neuron 7.5 + Python 3.7
Replies: 2
Views: 3175

Re: Neuron 7.5 + Python 3.7

Upgrade to NEURON 7.6.1 (the current release version) to use Python 3.7.

Older versions of NEURON are not compatible with Python 3.7.
by ramcdougal
Tue Jul 31, 2018 4:57 am
Forum: Anatomically detailed models
Topic: Changing diameters of reconstructed neurons
Replies: 5
Views: 1859

Re: Changing diameters of reconstructed neurons

My mistake, sorry. I made that post on my phone without checking it.

You're right. diam3d is ready only. Use pt3dchange to set the diameter: the

Code: Select all

forall { 
  for (j = 0; j < n3d(); j+=1) { 
    pt3dchange(j, diam3d(j)*1.0)
  } 
} 
by ramcdougal
Mon Jul 30, 2018 6:20 am
Forum: Anatomically detailed models
Topic: Changing diameters of reconstructed neurons
Replies: 5
Views: 1859

Re: Changing diameters of reconstructed neurons

Use diam3d instead of diam, and forall sections adjust indices from 0 to n3d -1, inclusive. EDIT: The idea is right but this code is wrong. diam3d is read only and diameters most he changed with pt3dchange. See my next post. forall { for (j = 0; j < n3d(); j+=1) { diam3d(j) = diam3d(j)*1.0 } } There...
by ramcdougal
Sun Jul 29, 2018 8:28 pm
Forum: General questions and discussions about computational neuroscience
Topic: AMR for increasing computation speed
Replies: 2
Views: 2865

Re: AMR for increasing computation speed

Not exactly what you're looking for, but check out Rempe and Chopp 2006, A Predictor‐Corrector Algorithm for Reaction‐Diffusion Equations Associated with Neural Activity on Branched Structures. In particular, section 8 is entitled "spatial adaptivity." They demonstrate this on a morphologically deta...
by ramcdougal
Thu Jul 19, 2018 3:48 am
Forum: Anatomically detailed models
Topic: Use import3D_swc_read to read the morphology from swc file
Replies: 2
Views: 1413

Re: Use import3D_swc_read to read the morphology from swc file

Every segment corresponds to a location where membrane potential is computed. In particular, this is a distinct concept from the 3D shape of the cell. Segments can contain arbitrarily many 3D points and the surface area, etc for that segment will be computed correctly. In Python with NEURON 7.5+, yo...
by ramcdougal
Mon Jun 11, 2018 5:25 pm
Forum: Anatomically detailed models
Topic: Making whole cells out of Mcintyre myelinated axon model (2002) and testing short and long-term plasticity between them
Replies: 15
Views: 4082

Re: Making whole cells out of Mcintyre myelinated axon model (2002) and testing short and long-term plasticity between t

In addition to the text editors that ted mentioned, consider Visual Studio Code. It's free and runs on all platforms. More importantly for NEURON: the first time you open a HOC or MOD file, it will prompt you to install an extension that provides NEURON syntax highlighting.
by ramcdougal
Mon Jun 11, 2018 1:24 pm
Forum: NEURON + Python
Topic: Neuron code
Replies: 20
Views: 6612

Re: Neuron code

Ion channel genealogy lists 524 NEURON calcium channel models, not all distinct. If you click that link, you'll see them grouped by similarity. Clicking on an individual model (dot) in the figure will load it in the channel details pane on the bottom right. The info tab (opened by default) contains ...
by ramcdougal
Mon Jun 11, 2018 12:34 pm
Forum: NEURON + Python
Topic: Neuron code
Replies: 20
Views: 6612

Re: Neuron code

Note that Hodgkin and Huxley considered only the role of sodium, potassium, and leak currents. In particular, it follows that the hh mechanism does not generate a calcium current.