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RENCI / Segmentor

3D segmention tool
MIT License
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Check holes for done regions #113

Closed davidborland closed 3 years ago

davidborland commented 3 years ago

Currently only checking that the region is contiguous.

davidborland commented 3 years ago

Implemented

JustKeepClimbing commented 3 years ago

hi @davidborland , when reviewing masks, I still notice missing pixels in some refined masks. As a quick test, I used the 'add new region' to create a mask and added a voxel-sized hole in it. I was able to mark the nucleus as 'done.'

davidborland commented 3 years ago

The way it is currently implemented, if you just create a region with just a single slice, holes would still be allowed. However if you have a region with 3 or more slices, any holes in the interior slices should not be allowed.

Basically, it is finding holes in the 3D shape where there is no path from the hole to the outside of the surface, which permits concavities in the surface, but not holes in the interior of the 3D volume.

If this behavior does not make sense, or if you think you are seeing examples that are violating this behavior, let me know.

davidborland commented 3 years ago

Allowed: image

davidborland commented 3 years ago

Not allowed: image

JustKeepClimbing commented 3 years ago

Oh, I see! Ok, that should be fine. What I tested only had two slices, so this is good to know. : )

davidborland commented 3 years ago

Sure thing. Let me know if you do see any problems.