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Avoid tunnels from the mitochondria closing ("holding hands") - #191
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The closing in _postprocess_seg_3d (3D cross x 4, then 3x3 in-plane x 8) joins parts of a mitochondrion that only come close, e.g. the two ends of a curled one, and gives the object a tunnel. For mitochondria, use a weaker closing (x 2, x 3), fill the holes per slice along z, y and x (into background only), and remove the added components that touch the object in two or more places and give it a tunnel. The defaults of _postprocess_seg_3d are unchanged, so the compartment segmentation is not affected. Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
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where it works nicely (above)
and where it is worse (below) - but this is only happens at the z-dim ends of mitochondria where you see them crumble (also because the models prediction is low in these z-dim tiles)
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lufre1
marked this pull request as ready for review
November 2, 2026 14:28
Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
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any objections on merging this into main? |
constantinpape
approved these changes
Nov 5, 2026
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Looks good to me.
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The closing in _postprocess_seg_3d (3D cross x 4, then 3x3 in-plane x 8) joins parts of a mitochondrion that only come close, e.g. the two ends of a curled one, and gives the object a tunnel. For mitochondria, use a weaker closing (x 2, x 3), fill the holes per slice along z, y and x (into background only), and remove the added components that touch the object in two or more places and give it a tunnel.
The defaults of _postprocess_seg_3d are unchanged, so the compartment segmentation is not affected.