automatic skeletonisation

[Jean Watermeyer]

Hi there,

I am looking for the best software to do automated segmentation of my
electron tomographic data.  The data are quite noisy 3D volumes
(cryo-EM) containing cellular material with filaments.  I want to
generate a map of the path of the filaments and the connections between
them in the most automated way possible.

Is there an ImageJ plugin that might be able to do this?

Thanks in advance,
Jean

--
Dr. Jean Watermeyer
Room 363 Malet Street Extension
Dept. of Biological Sciences
Birkbeck
Malet Street
London WC1E 7HX

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ImageJ mailing list: http://imagej.nih.gov/ij/list.html

[Ignacio Arganda-Carreras]

Dear Jean,

It's hard to say without looking at the images, but you can give a try to
some existing plugins:

http://fiji.sc/Skeletonize3D

http://fiji.sc/AnalyzeSkeleton

http://fiji.sc/Simple_Neurite_Tracer

Best,

ignacio



On Fri, Sep 5, 2014 at 12:57 PM, Jean Watermeyer <
[hidden email]> wrote:

> Hi there,
>
> I am looking for the best software to do automated segmentation of my
> electron tomographic data.  The data are quite noisy 3D volumes (cryo-EM)
> containing cellular material with filaments.  I want to generate a map of
> the path of the filaments and the connections between them in the most
> automated way possible.
>
> Is there an ImageJ plugin that might be able to do this?
>
> Thanks in advance,
> Jean
>
> --
> Dr. Jean Watermeyer
> Room 363 Malet Street Extension
> Dept. of Biological Sciences
> Birkbeck
> Malet Street
> London WC1E 7HX
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>

--
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: [phone]
Website: http://bioweb.cnb.csic.es/~iarganda/index_EN.html

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ImageJ mailing list: http://imagej.nih.gov/ij/list.html