Search found 34 matches

by ziemek
Tue Dec 10, 2019 3:11 pm
Forum: Reaction-diffusion in NEURON
Topic: rxd, crxd and dx
Replies: 2
Views: 450

rxd, crxd and dx

Hi! I have 2 related question: What is the difference between rxd and crxd? What exactly define dx param for Region when I use: rxd.set_solve_type(dimension=3) I understand that this is the maximum size of 3D mesh element. But how exactly the mesh is defined? Does rxd create the mesh automaticaly on...
by ziemek
Tue Dec 10, 2019 2:41 pm
Forum: Anatomically detailed models
Topic: Precise 3D morphology
Replies: 6
Views: 699

Precise 3D morphology

Is there any way to define precise 3D morphology based on vertex/triangles in x,y,z space? SWC format as well as hoc's pt3dadd() function define cylindrical compartments, which in case of small morphological elements (like precise spine geometry) may differ too much from the needs. There is SWC Plus...
by ziemek
Tue Dec 10, 2019 2:10 pm
Forum: NEURON + Python
Topic: How to access HOC arrays from Python?
Replies: 2
Views: 525

Re: How to access HOC arrays from Python?

Thanks for the help, the way you described hoc's references from Python's code work well for me.
by ziemek
Wed Dec 04, 2019 8:00 am
Forum: NEURON + Python
Topic: How to access HOC arrays from Python?
Replies: 2
Views: 525

How to access HOC arrays from Python?

I have a Migliore cell morphology which is created based on the following compartments (written in HOC): public soma, axon, dendrite, apical_dend, user5 {create axon[1]} {create soma[1]} {create dendrite[52]} {create apical_dend[70]} {create user5[49]} which are then used to build a morphology based...
by ziemek
Tue Dec 03, 2019 5:34 am
Forum: The GUI
Topic: GUI RunControl panel and Window size
Replies: 1
Views: 479

GUI RunControl panel and Window size

I have 2 questions: How can I start RunControl panel from Python to avoid clicking each time on Tools->RunControl. Is it possible? How can I change size of the PlotShape window? I tried this: ps = h.PlotShape(True) ps.view(0,0,0,0,0,0,800,800) ps.show(0) But I'm not quite sure what view() params mea...
by ziemek
Tue Dec 03, 2019 3:35 am
Forum: The GUI
Topic: GUI 2 with Python
Replies: 1
Views: 325

GUI 2 with Python

When I look closely to the NEURON Python I found package called gui2 which seems to work with JavaScript and HTML: https://github.com/neuronsimulator/nrn/tree/e5b6aa8bb504ec9c71c86b9abd49c3de3f98729e/share/lib/python/neuron/gui2 I also noticed that you have some Notebook tutorial which utilise the n...
by ziemek
Tue Dec 03, 2019 3:06 am
Forum: NEURON + Python
Topic: Shape plot update from Python
Replies: 2
Views: 502

Re: Shape plot update from Python

It works straight forward. Thanks!
by ziemek
Mon Dec 02, 2019 1:22 pm
Forum: NEURON + Python
Topic: Shape plot update from Python
Replies: 2
Views: 502

Shape plot update from Python

I would like to monitor "cai" variable across shape plot. After I execute this code it shows correctly what I want to monitor, except that it wont update with each steps: ps = h.PlotShape(True) ps.variable('cai') ps.scale(0, 0.01) ps.show(0) ps.exec_menu('Shape Plot') When I specify the same paramet...
by ziemek
Sat Nov 30, 2019 4:31 am
Forum: Adding new mechanisms and functions to NEURON
Topic: using diam and L params inside MODL file
Replies: 5
Views: 788

Re: using diam and L params inside MODL file

Thanks for your help and comments, they are very valuable to me. I started with RxD and it works nice but I have 4 follow-up questions and one comment. Questions: if you don't specify geometry for the Region - it assumes the whole compartment's segment as a "single shell"? If I do specify geometry -...
by ziemek
Tue Nov 26, 2019 5:26 am
Forum: Adding new mechanisms and functions to NEURON
Topic: using diam and L params inside MODL file
Replies: 5
Views: 788

Re: using diam and L params inside MODL file

OK, so I would like to model Ca2+ radial diffusion from the top of the head of the dendritic spine -> through the neck -> to the dendrite (and in the dendrite radially and axially - as well, so Ca2+ may diffuse to the next spine). Basically I would like to model a whole-cell Ca2+ diffusion. EDIT: I ...
by ziemek
Mon Nov 25, 2019 11:16 am
Forum: Adding new mechanisms and functions to NEURON
Topic: using diam and L params inside MODL file
Replies: 5
Views: 788

using diam and L params inside MODL file

Hi, I want to use compartment's params (diam, L) inside my MODL mechanism "mymodl": NEURON { SUFFIX mymodl } UNITS { (um) = (micron) } ASSIGNED { diam (um) L (um) } STATE { my_diam (um) my_L (um) } BREAKPOINT { my_diam = diam my_L = L } hoc file looks like that: load_file("nrngui.hoc") create soma a...
by ziemek
Mon Nov 25, 2019 6:16 am
Forum: Adding new mechanisms and functions to NEURON
Topic: NMODL: COMPARTMENT statement in the KINETIC section
Replies: 2
Views: 414

Re: NMODL: COMPARTMENT statement in the KINETIC section

You're right. After I carefully studied chapters 3 and 9 I got it. For those who may have similar questions - please read first: Compartment size in the section on Chemical reactions in Chapter 3 and then get back to the Chapter 9 . As to answer my questions (if anyone has similar problems): 1/4. CO...
by ziemek
Thu Nov 21, 2019 7:47 am
Forum: Adding new mechanisms and functions to NEURON
Topic: NMODL: COMPARTMENT statement in the KINETIC section
Replies: 2
Views: 414

NMODL: COMPARTMENT statement in the KINETIC section

From the Neuron Book, chapter 9. Ca2+ shells diffusion is defined as follows: KINETIC state { COMPARTMENT i, diam*diam*vol[ i ] {ca CaBuffer Buffer} } How does the COMPARTMENT statement work? Why there is diam^2? What is its relation to the volume? if shell_volume=diam*diam*vol[ i ] -> does the rate...
by ziemek
Wed Nov 20, 2019 9:51 am
Forum: Adding new mechanisms and functions to NEURON
Topic: Calcium diffusion and shells
Replies: 5
Views: 596

Re: Calcium diffusion and shells

Thanks, indeed readline did the trick.

If anyone has the same problem in the future - this answer may help: https://askubuntu.com/questions/194523/ ... u-readline
by ziemek
Tue Nov 19, 2019 7:27 am
Forum: Adding new mechanisms and functions to NEURON
Topic: Calcium diffusion and shells
Replies: 5
Views: 596

Re: Calcium diffusion and shells

Thanks for help. Unfortunatelly there is an error while I make nrnivmodl "/usr/local/nrn/share/nrn/libtool" --tag=CC --mode=link gcc -module -g -O2 -o libnrnmech.la -rpath "/usr/local/nrn/x86_64/lib" cadif.lo mod_func.lo -L"/usr/local/nrn/x86_64/lib" -lnrnoc -loc -lmemacs -lscopmath -lsparse13 -lrea...