Re: Tracing neurons in Sholl analysis

Posted by Mark Longair-2 on Jun 19, 2010; 11:28am
URL: http://imagej.273.s1.nabble.com/Tracing-neurons-in-Sholl-analysis-tp3687379p3687383.html

Damon Poburko <[hidden email]> wrote:

>
> Dear Mark,
>
>     I've just started using Simple Neurite Tracer, and it's
> awesome. Strong Work! The tracing is great. But for some of my
> analysis, I need to be able to calculate the minimum distance of some
> other marker to a neuron. I previously used NeuonJ, which let me
> export all of the vertices for each trace. I could then do the
> addition calculations in Excel. So my question (/ feature request) is
> whether it's possible to export the stored vertices that make up the
> traces/paths?
>
> Many Thanks,
> Damon

Damon,

Thanks for your kind remarks.  The .traces file that you save
from the plugin has information about all the vertices - it's
just gzipped XML, and the format is described here:

  http://homepages.inf.ed.ac.uk/s9808248/imagej/tracer/file-format.html

As you've probably seen, you can also export higher level
information about the files via the "Export as CSV" option, but
that doesn't have vertex level information - only the .traces
file does at the moment.

As ever, I'm very open to patches to provide other features that
people might need.

regards,
mark