import3D question

When Python is the interpreter, what is a good
design for the interface to the basic NEURON
concepts.

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maxwellphenderson
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import3D question

Post by maxwellphenderson » Tue Nov 01, 2011 1:32 pm

Hi, I am trying to use NEURON/Python to create a neural network with detailed morphology, and I have several swc files that I wanted to import. I was originally reading over import3D assuming it was also available for use inside a script; is that the case? Or is import3D only a GUI thing at this point in time? Otherwise, what would be the best plan for creating a 3D neural network starting off with a bunch of different swc files? Thanks!

ted
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Re: import3D question

Post by ted » Tue Nov 01, 2011 1:56 pm

Morphometric reconstructions are subject to many kinds of artifact, and it is not a good idea to use any reconstruction in a serious modeling project without first examining it for errors and, if possible, repairing such errors as one discovers. It is easiest to start with interactive examination of the shape encoded by the morphometric data, and wrap up with tests on the resulting hoc code by, among other things, checking pt3d diameters and verifying connectivity of all sections. These tests are most conveniently done with the Import3D tool and a few hoc idioms (easily expressed in Python if one insists). Under no conditions would I ever think of blind automatic conversion of morphometric data to multicompartmental models--that would be the surest way to end up running simulations with anatomically flawed models, only to discover later (when a reviewer or reader examines your models) that it was all a waste of time.

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