Re: How to select object volume in 3d stack

Posted by Thomas Boudier on
URL: http://imagej.273.s1.nabble.com/How-to-select-object-volume-in-3d-stack-tp4999044p4999059.html

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
>

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