Re: Tracing neurons in Sholl analysis

Posted by dpoburko on Jun 17, 2010; 3:32pm
URL: http://imagej.273.s1.nabble.com/Tracing-neurons-in-Sholl-analysis-tp3687379p3687382.html

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


On 6/17/2010 1:26 AM, Mark Longair wrote:

> Cris R<[hidden email]>  wrote:
>    
>> Dear List,
>>
>> I am trying to do Sholl analysis with the Sholl analysis plugin but I don't
>> know which would be the best way of tracing the neurons. If you have any
>> suggestion I would very much appreciate it.
>>
>> Thank you,
>>
>> Cris
>>      
> Cris,
>
> You could consider using Simple Neurite Tracer (bundled in Fiji)
> for the tracing.  As it happens, I'm working at the moment on
> adding Sholl analysis (a much requested feature!) [1] so
> hopefully soon you'll be able to do everything with just that
> plugin.
>
>    http://pacific.mpi-cbg.de/wiki/index.php/Simple_Neurite_Tracer
>
> regards,
> mark
>
>    [1] http://longair.net/mark/sholl-work-in-progress.png
>