Importing 3D data: soma modelled as overlaid circles

codonn · Post by **codonn** » Mon Sep 17, 2007 1:26 pm

I'm trying to import Neurolucida structural data into NEURON.

When I import the .asc file using the Import3D tool, the cell image looks fine indicating that the 3-D structural information is OK.

However when I then try to Export to CellBuilder, several windows (labelled CellBuild[0], CellBuild[1], etc) open instead of one. This is because the soma is represented as several overlaid circles of different diameter corresponding to different image depths (this was done to get a more accurate shape for the soma compared to a simple sphere), and NEURON reads the different soma sections as different cells. Some neurites end up coming from different circular sections.

Is there a straightforward way to convert these circular 'slices' into a unified soma shape to export using CellBuilder? Or will I have to do it manually?

Post by **hines** » Tue Oct 02, 2007 9:12 am

At the moment you must do it manually.
But I'm curious. Is there any syntactic
indication in the file that the set of outlines
is meant to be a 3-d structure? If so
I'd be happy to extend the Import3d tool
to handle them properly. Feel free to send
the file to me via email.

codonn · Post by **codonn** » Wed Oct 03, 2007 9:10 am

I didn't trace the neurons myself, but the person who did tells me that no, there is no information in the neurolucida files that indicates that the circles are part of the same 3-D structure.

This is not too surprising (apparently it's quite an old version), but I thought there might be some way to tell NEURON to treat them as a single object.

I will email you one of the .asc files to see.