http://imagej.273.s1.nabble.com/Find-connected-regions-3D-Flood-filling-3D-from-seed-region-tp5009839p5009861.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
>
> Hello Djoere,
>
> You might want to install the IJPB-plugins library. It comes with an
> efficient implementation of Connected Components in 3D that you can use to
> find the region you want after binarizing it with the proper threshold.
>
>
http://github.com/ijpb/ijpb-plugins>
> After installation, you should have the plugin under "Plugins > Fast
> Morphology > Binary Images > Connected Component Labeling".
>
> Let me know if you need more help,
>
> ignacio
> 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
>>
>> --
>> ImageJ mailing list:
http://imagej.nih.gov/ij/list.html>>
>
> --
> /***************************************************************/
> Thomas Boudier, Associate Professor, UPMC,
> Université Pierre et Marie Curie, Paris, France.
> BioInformatics Institute (BII)/IPAL, Singapore.
> /**************************************************************/
>
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