Mapping of hoc toploogy and 3D morphology

Managing anatomically complex model cells with the CellBuilder. Importing morphometric data with NEURON's Import3D tool or Robert Cannon's CVAPP. Where to find detailed morphometric data.
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Mapping of hoc toploogy and 3D morphology

Post by shyam_u2 » Tue Jun 06, 2017 3:10 pm

I recently exported a .asc file and created a hoc template. Everything works well, thanks to this forum and the well documented procedures on how to use import3D.
I am recording transmembrane currents from certain compartments/segments. I have the morphology plotted using the trees toolbox.
I need to create a map/figure which says that for example, currents recorded from 'nth' dendritic compartment corresponds to this dendrite (or point) in the 3D morphology plot. How do I map each compartment/segment in the hoc file to a particular point in the 3D morphology ?

Thanks in advance.

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Re: Mapping of hoc toploogy and 3D morphology

Post by ted » Fri Jun 09, 2017 8:12 am

Major advice (not suggestion) before addressing your question: don't think in terms of compartment indices. Think in terms of range.

If you want to indicate a particular segment of a cell, create a Shape, attach an instance of any* point process class to the segment of interest, and then use the Shape class's point_mark method to indicate the location of the point process. *Consider using one that doesn't do anything to simulations, e.g. an APCount.

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