Search found 32 matches

by alexandrapierri
Tue Nov 16, 2021 10:28 pm
Forum: NetPyNE
Topic: elaborate visualization of neuron morphologies and synapses
Replies: 8
Views: 225

Re: elaborate visualization of neuron morphologies and synapses

in addition to my previous question, I would like to recreate the visualization methods used by netpynne GUI. In the tutorials, they only refer to matplotlib examples however, I would like to use the tool on the graphical interface ideally. Any directions on how to find and install that visualizatio...
by alexandrapierri
Tue Nov 16, 2021 6:51 pm
Forum: NetPyNE
Topic: elaborate visualization of neuron morphologies and synapses
Replies: 8
Views: 225

Re: elaborate visualization of neuron morphologies and synapses

thanks. What about 3D markers? The example you sent, very useful, appears to work on 2D dendrites. How do I adjust this for 3D?
by alexandrapierri
Tue Nov 16, 2021 5:04 pm
Forum: NetPyNE
Topic: elaborate visualization of neuron morphologies and synapses
Replies: 8
Views: 225

Re: elaborate visualization of neuron morphologies and synapses

thank you this is useful for layer color-coding. I would still like to be able to color-code the different synapses (inhibitory-excitatory) or even from different presynaptic populations. I see that netpynne graphics do that on different examples. I am looking into those examples to see what graphic...
by alexandrapierri
Mon Nov 15, 2021 4:41 pm
Forum: NetPyNE
Topic: elaborate visualization of neuron morphologies and synapses
Replies: 8
Views: 225

Re: elaborate visualization of neuron morphologies and synapses

thank you Ted I am looking for a way to annotate 3D points with layer information, or a method for displaying layers as well as indicating different synapse types by e.g. different colors. I haven't been able to find a method that does that using matplotlib according to the Shape plot documentation....
by alexandrapierri
Fri Nov 12, 2021 8:24 pm
Forum: NetPyNE
Topic: elaborate visualization of neuron morphologies and synapses
Replies: 8
Views: 225

elaborate visualization of neuron morphologies and synapses

hello I am looking for visualization tools of neural morphology to elaborately visualize the synapses on dendrites. I have noticed that NetPynne provides some pretty detailed visualizations of the cells and I was wondering what tools are used for that and/or whether NEURON provides any tools for ela...
by alexandrapierri
Sat Sep 18, 2021 3:43 pm
Forum: NEURON + Python
Topic: problem instantiating a hoc template from python
Replies: 3
Views: 269

Re: problem instantiating a hoc template from python

thank you! As a follow-up, I am using a script of yours Ted, to interpolate over the swc points in a hoc file. The "def interplocs" below expects two arguments, I realize the sec refers to the section and locs to the pt3 points. How do I call this definition from a separate python script t...
by alexandrapierri
Fri Sep 17, 2021 8:46 pm
Forum: NEURON + Python
Topic: problem instantiating a hoc template from python
Replies: 3
Views: 269

problem instantiating a hoc template from python

Hello I have a file called pyrcellfile.hoc, which contains a hoc template that defines a cell class called PYR. I want to use a Python script to load and instantiate my hoc file. My python script, myscript.py, looks like his: from neuron import h h.load_file("pyrcellfile.hoc") newpyr = h.P...
by alexandrapierri
Tue May 11, 2021 9:43 am
Forum: NEURON + Python
Topic: silencing netstim during simulation.
Replies: 2
Views: 473

Re: silencing netstim during simulation.

thanks for this most didactic response. My apologies for what may seem like excessive pedantry, but in writing these entries I realize that they will also be read by others who may not have the same background or local resources as the person who asked the question in the first place. I recently bo...
by alexandrapierri
Mon May 10, 2021 9:51 pm
Forum: NEURON + Python
Topic: silencing netstim during simulation.
Replies: 2
Views: 473

silencing netstim during simulation.

Hello Following other posts on the forum, I want to silence my netstim at a certain time (400ms) during my simulation. To do this I set netcon.active(0), or I've also tried to do netcon.weight=0 according to https://www.neuron.yale.edu/phpBB/viewtopic.php?p=17875#p17875 . I have a very novice syntax...
by alexandrapierri
Thu Feb 25, 2021 7:31 pm
Forum: NEURON + Python
Topic: hoc file is not a template
Replies: 6
Views: 745

Re: hoc file is not a template

thank you! I was originally under the impression that the hoc file relies on fewer mod files and not most of the box. I am getting a better sense of the model now. Regarding the same repository I downloaded the 39948 entry and tried to run the "izhi2004a.hoc" according to the README instru...
by alexandrapierri
Thu Feb 25, 2021 11:45 am
Forum: NEURON + Python
Topic: hoc file is not a template
Replies: 6
Views: 745

hoc file is not a template

Hello NEURON team I want to instantiate the izhekevic neuron Izhi2003a.hoc attached, but I get the error: "Izhi2003a is not a template" I did some basic troubleshooting and I added "load_file("import3d.hoc") and load_file("nrngui.hoc")" at the beginning of the...
by alexandrapierri
Tue Oct 22, 2019 11:07 am
Forum: NEURON + Python
Topic: accessing the same instantiation of a cell template from another python script
Replies: 4
Views: 1616

Re: accessing the same instantiation of a cell template from another python script

thank you Ted. I will work on your instructions.
If you could also point me to an example that would be really helpful.

thanks again,
Alexandra
by alexandrapierri
Wed Oct 16, 2019 5:38 pm
Forum: NEURON + Python
Topic: accessing the same instantiation of a cell template from another python script
Replies: 4
Views: 1616

accessing the same instantiation of a cell template from another python script

Hello developers I have the following novice problem. I want to call a given cell template from a hoc script and then access the exact same instantiation of that cell from a different python script. I fall upon a couple of syntax errors as I try to do that and was hoping for some guidance. my hoc ce...