Improved large_nuclei splitting #244
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alex-l-kong
reviewed
Sep 28, 2020
| @@ -77,6 +78,8 @@ def compute_marker_counts(input_images, segmentation_masks, nuclear_counts=False | |||
| nuc_mask = segmentation_utils.split_large_nuclei(cell_segmentation_mask=cell_mask, | |||
| nuc_segmentation_mask=nuc_mask, | |||
| cell_ids=unique_cell_ids) | |||
| nuc_mask = remove_small_objects(ar=nuc_mask, min_size=5) | |||
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An alternative would be to put the call to remove_small_objects inside split_large_nuclei and add a parameter to split_large_nuclei to control the min_size parameter of remove_small_objects. If min_size is not None, then we make the additional call. This would be helpful if we plan on calling remove_small_objects every time after split_large_nuclei is called.
ackagel
reviewed
Sep 28, 2020
ark/utils/segmentation_utils.py
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| # only proceed if parts of the nucleus are outside of the cell | ||
| if nuc_count != np.sum(nuc_mask): | ||
| # only proceed if a non-negligible part of the nucleus is outside of the cell | ||
| if np.sum(nuc_mask) - nuc_count > 5: |
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this 5 should probably be a min_size parameter in the split_large_nuclei function.
alex-l-kong
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Jan 14, 2021
* tweak logic for large nuclei * no hardcoding Co-authored-by: alex-l-kong <31424707+alex-l-kong@users.noreply.github.com>
y2kbugger
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Jul 29, 2021
* tweak logic for large nuclei * no hardcoding Co-authored-by: alex-l-kong <31424707+alex-l-kong@users.noreply.github.com>
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What is the purpose of this PR?
Additional tweaks to the nuclei split logic. One issue that came up was if the nuclear mask was just a tiny bit bigger than the cell mask. For example, one pixel larger on one side. This resulted in potentially a single pixel being cut from the mask, relabeled, and given a new ID. This creates tons of new, tiny nuclear objects, which we don't want.
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