elaborate visualization of neuron morphologies and synapses

A Python package that facilitates development and use of models of biological neural networks

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alexandrapierri
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Joined: Wed Jun 17, 2015 5:31 pm

elaborate visualization of neuron morphologies and synapses

Post by alexandrapierri »

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 elaborate morphology and synapse visualization.

thank you.
ted
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Re: elaborate visualization of neuron morphologies and synapses

Post by ted »

"Shape plots" (see the Programmer's Reference for documentation of the Shape and PlotShape classes) can be used to generate figures of parts of cells or any number of cells. These can be rendered by NEURON or by third-party Python libraries, e.g. matplotlib, plotly. To learn more, see Robert McDougal's presentations about using Python to build and work with NEURON models--starting with this one:
20210624 Python scripting day 1 https://youtu.be/ObSHSQCpkoo

You might also find this one to be useful:
20210706 Scripting and Morphologies https://youtu.be/yte708tOiVI
alexandrapierri
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Joined: Wed Jun 17, 2015 5:31 pm

Re: elaborate visualization of neuron morphologies and synapses

Post by alexandrapierri »

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. Is this possible?
ted
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Re: elaborate visualization of neuron morphologies and synapses

Post by ted »

What about the Shape plot class's color and color_list methods?
ramcdougal
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Re: elaborate visualization of neuron morphologies and synapses

Post by ramcdougal »

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.
alexandrapierri
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Re: elaborate visualization of neuron morphologies and synapses

Post by alexandrapierri »

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 graphics tools are used there, also any instructions on how to do this with NEURON would be great.
ramcdougal
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Location: Yale School of Public Health

Re: elaborate visualization of neuron morphologies and synapses

Post by ramcdougal »

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 put a black-x at soma(0.3) with:

Code: Select all

_ = ps.plot(plt, cmap=cm.RdBu).mark(soma(0.3), 'xk')
For a full example, see https://colab.research.google.com/drive ... sp=sharing
alexandrapierri
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Re: elaborate visualization of neuron morphologies and synapses

Post by alexandrapierri »

thanks. What about 3D markers? The example you sent, very useful, appears to work on 2D dendrites. How do I adjust this for 3D?
alexandrapierri
Posts: 32
Joined: Wed Jun 17, 2015 5:31 pm

Re: elaborate visualization of neuron morphologies and synapses

Post by alexandrapierri »

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 visualization tool would be very helpful. Thank you again. http://34.123.79.237/user/255e1f0b-5414 ... 5/geppetto
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