How to select object volume in 3d stack

[Citron, Bruce]

In a single slice, I can easily:  1. Threshold, then 2. Use the wand tool to
select an irregular region of interest, e.g., an irregularly shaped cell in
a micrograph.
I am having trouble doing this for a 3d confocal stack.  I can threshold so
that in all slices, the cell is all red.

€ How would I then perform the equivalent of the wand tool selections so
that all of the cell, in each z-slice, would be outlined and selected?
It would be like a seed fill, where all of the connected thresholded voxels
are connected into an irregular 3d ROI.
I would then want to determine volume and mean intensity.

I usually want to ignore other cells in the same image, but I would also be
interested in a 3d particle analysis with count, volumes and mean
intensities.

I tried Yawi3d, but I couldn¹t seem to get it to do what I wanted.
Thank you,
Bruce
--
Bruce A. Citron, Ph.D., Bay Pines VA


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[Thomas Boudier]

Hello,

The 3D tools you may have a look for 3D segmentation and analysis, also
manual segmentation :

http://imagejdocu.tudor.lu/doku.php?id=plugin:analysis:3d_object_counter:start

http://imagejdocu.tudor.lu/doku.php?id=plugin:stacks:3d_roi_manager:start

http://132.187.25.13/home/?category=Download&page=SegmentationEditor

hope this helps

Thomas




Le 13/06/2012 21:05, Bruce Citron a écrit :

> In a single slice, I can easily:  1. Threshold, then 2. Use the wand tool to
> select an irregular region of interest, e.g., an irregularly shaped cell in
> a micrograph.
> I am having trouble doing this for a 3d confocal stack.  I can threshold so
> that in all slices, the cell is all red.
>
> € How would I then perform the equivalent of the wand tool selections so
> that all of the cell, in each z-slice, would be outlined and selected?
> It would be like a seed fill, where all of the connected thresholded voxels
> are connected into an irregular 3d ROI.
> I would then want to determine volume and mean intensity.
>
> I usually want to ignore other cells in the same image, but I would also be
> interested in a 3d particle analysis with count, volumes and mean
> intensities.
>
> I tried Yawi3d, but I couldn¹t seem to get it to do what I wanted.
> Thank you,
> Bruce
> --
> Bruce A. Citron, Ph.D., Bay Pines VA
>
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>

... [show rest of quote]

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      Thomas Boudier, MCU Université Pierre et Marie Curie,
      Modélisation Cellulaire et Imagerie Biologique (EE1),
      IFR 83, Bat B 7ème étage, porte 723, Campus Jussieu.
      Tel : [phone]   Fax : [phone]
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