Re: Find connected regions 3D / Flood filling 3D from seed region

Posted by Ignacio Arganda-Carreras on Oct 01, 2014; 1:14pm
URL: http://imagej.273.s1.nabble.com/Find-connected-regions-3D-Flood-filling-3D-from-seed-region-tp5009839p5009847.html

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 Wed, Oct 1, 2014 at 10:54 AM, Djoere Gaublomme <[hidden email]
> 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
>

--
Ignacio Arganda-Carreras, Ph.D.
Seung's lab, 46-5065
Department of Brain and Cognitive Sciences
Massachusetts Institute of Technology
43 Vassar St.
Cambridge, MA 02139
USA

Phone: [phone]
Website: http://bioweb.cnb.csic.es/~iarganda/index_EN.html

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