Use import3D_swc_read to read the morphology from swc file

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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zyc
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Joined: Sun Feb 19, 2017 9:15 pm

Use import3D_swc_read to read the morphology from swc file

Post by zyc » Thu Jul 19, 2018 2:55 am

Dear all
I have some problems while using import3D_swc_read() to read swc file. I notice that there are more than 9000 3D points in swc file, but when I load this swc file into NEURON, it shows that this model contains only 1974 segments. I guess some 3D points in swc are merged when I use import3D_swc_read(). Is there anyway to keep all the 3D points in swc file in NEURON? Thank you so much.

ramcdougal
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Location: Yale School of Medicine

Re: Use import3D_swc_read to read the morphology from swc file

Post by ramcdougal » Thu Jul 19, 2018 3:48 am

Every segment corresponds to a location where membrane potential is computed. In particular, this is a distinct concept from the 3D shape of the cell. Segments can contain arbitrarily many 3D points and the surface area, etc for that segment will be computed correctly.

In Python with NEURON 7.5+, you can display the total number of 3D points instantiated via:

Code: Select all

print(sum(sec.n3d() for sec in h.allsec()))

ted
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Re: Use import3D_swc_read to read the morphology from swc file

Post by ted » Thu Jul 19, 2018 7:44 am

Sections, segments, and how the shapes and sizes of parts of a model are essential concepts. Time to read the documentation:
Conceptual Overview of Sections
https://www.neuron.yale.edu/neuron/stat ... metry.html

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