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Re: Tracing neurons in Sholl analysis

Posted by Mark Longair-2 on Aug 03, 2010; 9:26am
URL: http://imagej.273.s1.nabble.com/Tracing-neurons-in-Sholl-analysis-tp3687379p3687381.html

Cris,

There is now an interface for doing Sholl analysis in the
current version of Simple Neurite Tracer.  (You should do
"Help > Update Fiji" to make that you have the newest version.)

I would still regard this feature as experimental, since it's
new and the results haven't been validated against any other
data.  There is a tutorial here:

  http://pacific.mpi-cbg.de/wiki/index.php/Simple_Neurite_Tracer%3A_Sholl_analysis

I would be interested in any feedback, or suggestions for
pre-analyzed data that could be used for validation.

regards,
mark

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Mark Longair <[hidden email]> 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