Refactor watershed's label image generation using the new API #1681
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@@ Coverage Diff @@
## tonytung-refactor-label-base #1681 +/- ##
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+ Coverage 89.84% 90.13% +0.29%
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Files 239 239
Lines 8964 8945 -19
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+ Hits 8054 8063 +9
+ Misses 910 882 -28
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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.