Simple Neurite tracer/ from coordinates in .swc file to a macro

[Aurélien Dauphin]

Dear ImageJ list,

I work with Simple Neurite tracer and make traces of neurons. I save
these traces in .swc format and would love to use the coordinates (x, y,
z) of each voxels along the traces in a macro.

Have you any idea of how I can do that ?

My aim would be to get the voxel intensity at that coordinate in my
color channel images and then make a Plot profile in 3D for each channel.

Thanks in advance
Aurélien

--
Dr. Aurélien Dauphin

Plateforme d'Imagerie Cellulaire de la Pitié-Salpêtrière
Bât. ICM
Hôpital de la Pitié Salpêtrière
47 Bd de l'Hôpital,
75013 Paris
Tel : ++33 (1) 57 27 45 10
http://picps.upmc.fr/
http://icm-institute.org/menu/fondation/se-rendre-a-licm

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

[lechristophe]

Hi Aurelien,

Mark Longhair (Neurite Tracer author) gave me a script here to analyze
traces files in term of intensity, maybe this can help:

https://groups.google.com/forum/#!topic/fiji-users/8Bnqn9kJg5E


I didn't test it because in the end I used NeuronJ to trace neurites
(actually using two successive tracings on XY and XZ projections to trace
in 3D)

Christophe




2014-02-18 16:17 GMT+01:00 Aurélien Dauphin <[hidden email]>:

> Dear ImageJ list,
>
> I work with Simple Neurite tracer and make traces of neurons. I save these
> traces in .swc format and would love to use the coordinates (x, y, z) of
> each voxels along the traces in a macro.
>
> Have you any idea of how I can do that ?
>
> My aim would be to get the voxel intensity at that coordinate in my color
> channel images and then make a Plot profile in 3D for each channel.
>
> Thanks in advance
> Aurélien
>
> --
> Dr. Aurélien Dauphin
>
> Plateforme d'Imagerie Cellulaire de la Pitié-Salpêtrière
> Bât. ICM
> Hôpital de la Pitié Salpêtrière
> 47 Bd de l'Hôpital,
> 75013 Paris
> Tel : ++33 (1) 57 27 45 10
> http://picps.upmc.fr/
> http://icm-institute.org/menu/fondation/se-rendre-a-licm
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>

... [show rest of quote]

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