Use thresholded binarize and mask filtering in existing watershed code. #1671
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@@ Coverage Diff @@
## master #1671 +/- ##
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- Coverage 89.85% 89.84% -0.01%
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Files 239 239
Lines 8962 8964 +2
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+ Hits 8053 8054 +1
- Misses 909 910 +1
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shanaxel42
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Uses the labeling algorithms provided by #1680 and the area filter from #1673 to implement labeling. Depends on #1671, #1673, #1680 Test plan: ISS notebook yields 96 cells. The previous implementation did not support 3D and flattened everything along the Z axis. Processing in 3D exposed issues in `peak_local_max`. If we use the footprint + exclude borders approach, there is an off-by-one error in trimming the Z axis, resulting in completely blank images and no peaks. Therefore, we have to exclude the borders. Because of that, we detect more cells.
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Uses the labeling algorithms provided by #1680 and the area filter from #1673 to implement labeling. Depends on #1671, #1673, #1680 Test plan: ISS notebook yields 96 cells. The previous implementation did not support 3D and flattened everything along the Z axis. Processing in 3D exposed issues in `peak_local_max`. If we use the footprint + exclude borders approach, there is an off-by-one error in trimming the Z axis, resulting in completely blank images and no peaks. Therefore, we have to exclude the borders. Because of that, we detect more cells.
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Uses the labeling algorithms provided by #1680 and the area filter from #1673 to implement labeling. Depends on #1671, #1673, #1680 Test plan: ISS notebook yields 96 cells. The previous implementation did not support 3D and flattened everything along the Z axis. Processing in 3D exposed issues in `peak_local_max`. If we use the footprint + exclude borders approach, there is an off-by-one error in trimming the Z axis, resulting in completely blank images and no peaks. Therefore, we have to exclude the borders. Because of that, we detect more cells.
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Refactor the existing watershed code to use the new binarizer and mask filtering (for binary opening).
Depends on #1670, #1651
Test plan: still see 69 cells in the iss notebook.