Posted by
Thomas Boudier on
Oct 02, 2014; 1:33am
URL: http://imagej.273.s1.nabble.com/Find-connected-regions-3D-Flood-filling-3D-from-seed-region-tp5009839p5009860.html
Hi Djoere,
Not sure to fully understand, but it seems that you have some seeds, and
want to aggregate voxels to these seeds based on some criteria. May be
have a look to some spots detection plugins like
http://imagejdocu.tudor.lu/doku.php?id=plugin:segmentation:3d_spots_segmentation:start&s[]=spots&s[]=detection
you need two images, one with seeds (may be you need to "draw" your
rois) and a signal image, it uses local threshold to aggregate voxels to
the seeds, in your case, local threshold is a constant.
Hope this helps
Thomas
On 01/10/14 16:54, Djoere Gaublomme wrote:
> Hi,
>
> I want to perform an action on a large 3D image stack (8-bit grayscale,
> approximately 800x800x800 and 500 MB).
> The action I want to do is to start from a selected ROI (preferably
> based on a separate Mask image) and find all neighbouring voxels with
> the same gray values (for clarification: I only want to select voxels
> that have the same gray value as a selected neighbouring voxel). It
> does not matter whether gray value information is retained in the
> resulting image or not.
>
> For now, the only solution I found was to add an object to the 3D
> Manager from the Mask image, then put this selection on the grayscale
> stack and run "Find Connected Regions"
> [
http://www.longair.net/edinburgh/imagej/find-connected-regions/ , with
> the following parameters : run("Find Connected Regions", "
> display_one_image display_results regions_must regions_for_values_over=1
> minimum_number_of_points=1 stop_after=-1"); ]
>
> However, this takes forever to process, so I am wondering if there is a
> faster alternative (and preferably one that is macro-friendly).
> I have tried Flood Fill (3D), but this does not appear to work with a
> seed region.
>
> Thanks in advance!
>
> Djoere
>
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Thomas Boudier, Associate Professor, UPMC,
Université Pierre et Marie Curie, Paris, France.
BioInformatics Institute (BII)/IPAL, Singapore.
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