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viewing a network topologically

Posted: Wed Aug 06, 2008 12:27 pm
by refriend
I am working on a neuronal network simulation, including a method to generate a topologically correct 'network' shapeplot. This tool will be used as one method for visually validating a network's construction. My issue is specific to viewing a graphical version of a network (vs. a single model).

The only strategy I have at this moment is to iterate through a cell list and call upon each object's position(). I still haven't figured out how I would then plot this information. The more I read the online programming reference, the more I fear I am partially reinventing the wheel.

I'd like to retain the features of shapeplot and modelview but combine and extend them to visualize a complete network. Think in terms of a poor man's BlueBrain flythrough.

Is this feature, or components of it, already built into NEURON? Suggestions?

Thank you.

Re: viewing a network topologically

Posted: Wed Aug 06, 2008 12:48 pm
by wwlytton
you can use Hinton plots -- vec.hinton() -- to make x,y animations where each square is a single cell or a single compartment

you can also use shapeplot after distributing the cells appropriately

in the following image


I threw down some cells in Shape -- you can do the same thing with shapeplot so as to get the voltages (or other state var or parameter) showing

the key thing is to distribute the cells according to their location -- if you move all the segs of your soma, the dendrites will follow eg

cc.soma for(ii) pt3dchange(ii,x3d(ii)+x,y3d(ii)+y,z3d(ii), diam3d(ii))

where x,y is your x,y coordinates for that cell

Re: viewing a network topologically

Posted: Wed Aug 06, 2008 2:46 pm
by refriend
Thanks. I will give this idea a go.