Soma - Simple Neurite Tracer

reconstruction
simpleneuritetracer
Tags: #<Tag:0x00007fa30f4eae08> #<Tag:0x00007fa30f4eac78>

#1

Hello All,

I reconstruct neurons using the Simple Neurite Tracer plugin. I save the .traces file as an swc file to export these traces to another software. I noticed the soma is not visible. How do I export swc files with the correct soma size and dendrite thickness? Thank you!


#2

Hi @IR23, Currently, SNT only allows for the one-point representation of soma. Under search circumstances - and because the one point-soma representation is mostly used for visualization - what ends-up happening is that the program rendering the traces renders the soma as a ball or cylinder of some pleasant thickness. By default, SNT assigns a radius of zero to the soma (unless you fit a diameter to it, as explained below), so my guess is your rendering program (Which program is it?) is displaying a zero-wide soma. You would have to check with its manual/ code to find out exactly what it is doing.

The second part of your question: Thickness attributes in SNT are calculated automatically by the 'Fit/Fill>Fit diameters" command in the Path Manager. Note that it is also possible to use to fit a diameter to the soma, so it will no longer be saved as a zero-radius compartment.

As soon as I fix some pending issues, I will add a command to manually assign a radius to Paths, and make it available, as usual, through the Neuroanatomy update site.


#3

Hi Tiago,

Thank you for the reply. I’ve attempted to add a soma using the “fill out” command. However, only 2 out of 6 neurons contained a fill similar to the soma size. Do you have any tips? Thank you for working on the SNT!