Hey Bruno!
There is no straightforward way of doing what you want from Fiji. When you
call the Analyze Skeleton plugin from the Simple Neurite Tracer (SNT), a
new binary image is created from current traces and the analysis is run
using that image as input. So there is no connection between the list of
paths that you have in SNT and the output list of the analysis.
That been said, what you can do is to write a macro or script to find the
correspondences between both lists. You can export the paths as SWC files
(so you will have all the coordinates per path) and the detailed list of
branches as CSV (so you will have the coordinates of branches as well).
Now that I think about it, you can always use external software such as
L-measure to do the analysis of your SWC files:
http://www.ncbi.nlm.nih.gov/pubmed/18451794http://cng.gmu.edu:8080/Lm/Let me know what you think!
ignacio
PS: I'm forwarding the e-mail to the whole ImageJ list so everyone can
benefit from the conversation.
On Mon, Aug 25, 2014 at 10:55 PM, Bruno Berardino <
[hidden email]>
wrote:
> Hi Ignacio,
>
> I am Bruno Berardino, graduate student doing my PhD in the University of
> Buenos Aires, Argentina.
>
> I trying to use Analyze Skeleton to measure lengths of dendrites and axons
> in a 3D reconstruction with "Simple Neurite Tracer" in Fiji. I would need
> that the analyzing software recognizes the type of path I have chosen (i.e.
> "dendrite" of "axon") in order to measure their lengths as separated values.
>
> Would you know how to do that??
>
> Thank you for your time and the free software!
> Best regards,
> Bruno
>
>
--
Ignacio Arganda-Carreras, Ph.D.
Seung's lab, 46-5065
Department of Brain and Cognitive Sciences
Massachusetts Institute of Technology
43 Vassar St.
Cambridge, MA 02139
USA
Phone: (001) 617-324-3747
Website:
http://bioweb.cnb.csic.es/~iarganda/index_EN.html--
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