Search found 240 matches

by ramcdougal
Fri Jul 29, 2022 2:46 pm
Forum: Other questions
Topic: h.finitialize() fails with a hocobj call error
Replies: 5
Views: 182

Re: h.finitialize() fails with a hocobj call error

Here's a possible clue... it's looking for a .so file. Usually on Windows, the equivalent is a .dll Are you using the regular Windows version of NEURON or a version the windows subsystem for linux (WSL)? Either way, if you try running with python -i myprogram.py (that is, add the -i flag so it doesn...
by ramcdougal
Tue Jun 14, 2022 2:56 pm
Forum: Reaction-diffusion in NEURON
Topic: Detection of MOD files in rxd.Region 'o'
Replies: 3
Views: 376

Re: Detection of MOD files in rxd.Region 'o'

Try putting the Shell next to the dendrite... i.e. you want lo = 1

Code: Select all

fh = rxd.Region(h.allsec(), nrn_region='o', geometry=rxd.Shell(lo=1.0, hi=2.0))
The numbers here are in fractions of a radius not µm.
by ramcdougal
Mon Jun 13, 2022 4:03 pm
Forum: Reaction-diffusion in NEURON
Topic: Detection of MOD files in rxd.Region 'o'
Replies: 3
Views: 376

Re: Detection of MOD files in rxd.Region 'o'

We'll look into this. What you describe sounds like it should have worked.
by ramcdougal
Mon Jun 13, 2022 3:56 pm
Forum: NEURON + Python
Topic: Minor typo in tutorial
Replies: 1
Views: 128

Re: Minor typo in tutorial

Fixed. Thanks.

For what it's worth, the tutorials at https://nrn.readthedocs.io are generally more up-to-date than the ones on the NEURON yale site (but we haven't moved all of them over yet).
by ramcdougal
Thu Apr 14, 2022 1:09 pm
Forum: NetPyNE
Topic: Save rxd concentration
Replies: 3
Views: 331

Re: Save rxd concentration

If you're using NEURON 8.1+, the pure-NEURON solution is to either use h.SaveState (which saves ~everything) or rxd.save_state() and rxd.restore_state(), where the rxd-specific solutions represent state using byte-strings. See the (admittedly brief) discussion at https://nrn.readthedocs.io/en/latest...
by ramcdougal
Sat Apr 02, 2022 5:35 pm
Forum: Reaction-diffusion in NEURON
Topic: Assignments in time and time-dependent functions
Replies: 2
Views: 301

Re: Assignments in time and time-dependent functions

Unfortunately rxd doesn't directly support expressions that depend on time.

Algebraic expressions should just work. (There's an example of this in the documentation linked below.)

For math functions, you'll want to use rxdmath see the rxdmath discussion in the documentation
by ramcdougal
Sat Apr 02, 2022 5:23 pm
Forum: NEURON + Python
Topic: Uploading .swc file through .hoc
Replies: 3
Views: 320

Re: Uploading .swc file through .hoc

Roughly speaking the HOC code would look exactly like the Python, but drop the h. part. That said, HOC and Python are just two different interfaces to the same simulator. You can mix and match. e.g. from Python, you can run a HOC script called my_script.hoc via: h.load_file("my_script.hoc"...
by ramcdougal
Fri Mar 25, 2022 11:07 am
Forum: NetPyNE
Topic: After updating to MacOS 12.3 Monterey
Replies: 5
Views: 339

Re: After updating to MacOS 12.3 Monterey

This looks like an install from the PKG installer?

In particular, you'll find you have a NEURON folder in Applications. Remove that, and then enter the following into the terminal:

Code: Select all

pip3 install neuron
by ramcdougal
Mon Mar 07, 2022 11:40 am
Forum: Reaction-diffusion in NEURON
Topic: Using setpointer() and RXD concentrations
Replies: 3
Views: 1796

Re: Using setpointer() and RXD concentrations

Glu.nodes is a list of all Glu nodes. If there is only one, then it is unambiguously safe to use Glu.nodes[0] . Otherwise, you'll want to filter down to a specific node by specifying e.g. segment, possibly region if there are multiple by using () for the filtering... So something like Glu.nodes(som...
by ramcdougal
Tue Nov 16, 2021 6:42 pm
Forum: NetPyNE
Topic: elaborate visualization of neuron morphologies and synapses
Replies: 8
Views: 959

Re: elaborate visualization of neuron morphologies and synapses

I don't understand the distinction that you're making. Synapses are at some specific location, and using the mark method of a matplotlib/plotly h.PlotShape (or the point_mark method of a h.Shape), you can put points at specific locations in whatever style... e.g. with a matplotlib PlotShape, you can...
by ramcdougal
Tue Nov 16, 2021 2:18 pm
Forum: NetPyNE
Topic: elaborate visualization of neuron morphologies and synapses
Replies: 8
Views: 959

Re: elaborate visualization of neuron morphologies and synapses

Why not something like:

Code: Select all

ps = h.PlotShape(False)
ps.plot(pyplot).mark(h.soma[0](0.5)).mark(h.apical_dendrite[68](1))
plt.show()
You can pass regular matplotlib arguments to mark to specify color, marker type, etc.
by ramcdougal
Wed Jul 28, 2021 6:11 am
Forum: NEURON + Python
Topic: Preproducing updating PlotShape() figures in
Replies: 1
Views: 917

Re: Preproducing updating PlotShape() figures in

You don't have to use pyplot or plotly (I prefer the interactivity of plotly) for visualizing PlotShapes. If you have an existing process that worked with interviews windows, you can still use that. If you do use the pyplot version though, you can save to a png in the usual pyplot way, and use that ...
by ramcdougal
Mon Jul 19, 2021 5:10 am
Forum: Reaction-diffusion in NEURON
Topic: Pass ._ref_concentration to pc.source_var()?
Replies: 6
Views: 2393

Re: Pass ._ref_concentration to pc.source_var()?

If you got an error or unexpected result with source_var, can you please post it here?

That should just work.
by ramcdougal
Tue Jul 13, 2021 3:28 pm
Forum: NEURON Announcements
Topic: 2021 NEURON Online Course
Replies: 4
Views: 2622

Re: 2021 NEURON Online Course

You can always check out the YouTube playlist to see what's new and jump directly to videos of interest: https://www.youtube.com/playlist?list=P ... cdRSFwRLOU.
by ramcdougal
Tue Jun 29, 2021 10:49 am
Forum: Reaction-diffusion in NEURON
Topic: RxD with ParallelContext
Replies: 3
Views: 584

Re: RxD with ParallelContext

Yes. Intracellular reaction-diffusion (both 1D and 3D) parallelizes trivially as all cell-to-cell communication is through the regular spike exchange or gap junction mechanisms. (You still need ParallelContext for those, but you get the full speedup from splitting the cells onto different processors...