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kreshuklab / plant-seg

A tool for cell instance aware segmentation in densely packed 3D volumetric images
https://kreshuklab.github.io/plant-seg/
MIT License
99 stars 31 forks source link

Fix and document distance transform watershed for 2D pmaps/images #318

Closed qin-yu closed 2 months ago

qin-yu commented 2 months ago

From my understanding, stacked is just for per-slice processing of 3D pmaps, but for 2D and 3D whole-volume watershed we don't use anything stacked-related.

I documented this in the docstring and also improved the overall documentation as I receive many questions regarding this.

codecov[bot] commented 2 months ago

Codecov Report

Attention: Patch coverage is 62.93103% with 43 lines in your changes missing coverage. Please review.

Project coverage is 66.41%. Comparing base (8aa7747) to head (b9e5a70). Report is 10 commits behind head on plantsegv2.

Files with missing lines Patch % Lines
plantseg/viewer_napari/widgets/prediction.py 29.16% 34 Missing :warning:
plantseg/viewer_napari/widgets/segmentation.py 36.36% 7 Missing :warning:
plantseg/viewer_napari/widgets/dataprocessing.py 0.00% 2 Missing :warning:
Additional details and impacted files ```diff @@ Coverage Diff @@ ## plantsegv2 #318 +/- ## ============================================== + Coverage 66.35% 66.41% +0.06% ============================================== Files 66 67 +1 Lines 4541 4571 +30 ============================================== + Hits 3013 3036 +23 - Misses 1528 1535 +7 ```

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