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Asked: 2026-06-16T17:16:37+00:00

I would like to use Fiji (ImageJ) for some simple pre-processing operation and to

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I would like to use Fiji (ImageJ) for some simple pre-processing operation and to create a binary mask. I am just using the GUI and I am not interested in an authomatic procedure.
I got the following mask: (this is just a slice, the actual mask is 3 D, 298 MB)

Original Mask

I need to extract a 3D connected object, so that the result would be:

Object Mask

Ideally I would like to click inside a point inside the object with a 3D equivalent of the Wand tool, select the object, invert the selection, multiply by 0. For a start, I tried to use the command Analyze – 3D objects Counter, but I guess the image is too big and complex (the operation freezes at step 2. Connecting Objects).
Is there any procedure I can follow?

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1 Answer

  1. Editorial Team

    In Fiji you could do the following:

    1. Invert the image with Edit > Invert.
    2. Select the point selection tool from the Fiji toolbar.
    3. Click in the region you want to extract the connected white pixels from, to place a point selection there.
    4. Run Plugins > Process > Find Connected Regions.
    5. Select Start from point selection? and change Stop after this number of regions are found to 1.
    6. Click OK.

    There’s some documentation for that plugin (which I wrote a long time ago). It uses a very naive algorithm for finding connected regions, but it’s good enough for many purposes.

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