Hey Cedric, Have you thought of applying the background mask from the simple watershed to the final split mask? It seems that you should expect your foreground and background areas to be constant, so you should be able to create a boolean background mask (in code: > boolean_mask = watershed_mask == bg_label) from the first segmentation step and multiply the boolean mask by your split mask (> final_mask = boolean_mask * split_mask). This should preserve the foreground labels and set the background to zero uniformly. Best wishes, Brian On Tue, Apr 25, 2017 at 12:37 PM Cedric Espenel <cedric.espenel@gmail.com> wrote:

Hi everyone,

I work on a project where I try to track cell and cell division over-time. If cells are well separated, a simple watershed is fine, however, if cells start to overlap it doesn't work anymore.

If I had another step using random walker followed by a "join_segmentations" I can split touching cells as in follow:

​ ​So my foreground (the cells) were split in 3 which is what I want, but my background is also split. I might be missing something, but is there an easy way to "unify" my background, while keeping the foreground segmentation?

Best,

Cedric

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