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Add BCSS Dataset #156

Merged
merged 9 commits into from
Oct 19, 2023
Merged

Add BCSS Dataset #156

merged 9 commits into from
Oct 19, 2023

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anwai98
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@anwai98 anwai98 commented Oct 17, 2023

(WIP) Implementation for the Breast Cancer Semantic Segmentation dataset.
(TODOs):

  • need to fix data download using gdown (download limit for folders is upto 50 files, need to take care of that) warning raised
  • need to take care of the semantic instances (there are more than one tissue region segmentations available, need to add an optional argument to request for all instances / some instances, as desired)

@anwai98 anwai98 marked this pull request as ready for review October 18, 2023 13:31
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anwai98 commented Oct 18, 2023

@constantinpape This one's ready to go. Let me know how it looks.

torch_em/data/datasets/bcss.py Outdated Show resolved Hide resolved
torch_em/data/datasets/bcss.py Outdated Show resolved Hide resolved
torch_em/data/datasets/bcss.py Outdated Show resolved Hide resolved
self,
labels: np.ndarray
) -> np.ndarray:
"""Returns the transformed labels (use-case for SAM)
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For the same use-case we should use connected components (skimage.measure.label) instead of just relabeling.
This way we can separate disconnected pieces, and have an instance segmentation, which will be better for SAM.
(Since this is just the sample script it's not important to update this here, but please keep it in mind for SAM.)

@constantinpape constantinpape merged commit b8d9cd9 into constantinpape:main Oct 19, 2023
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@anwai98 anwai98 deleted the bcss branch October 19, 2023 16:36
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2 participants