Remove false positives from a segmentation layer using a foreground probability layer.
Segmentation: Segmentation layer to remove false positives.
Foreground: Foreground probability layer.
Threshold: Threshold value to remove false positives.
Widget: Use Nuclei to Fix Under- and Over-segmentation
Widget for correcting over- and under-segmentation of cells based on nuclei segmentation.
This widget allows users to adjust cell segmentation by leveraging nuclei segmentation. It supports
merging over-segmented cells and splitting under-segmented cells, with optional boundary refinement.
Args:
segmentation_cells (Labels): Input layer representing segmented cell instances.
segmentation_nuclei (Labels): Input layer representing segmented nuclei instances.
boundary_pmaps (Image | None, optional): Optional boundary probability map (same shape as input layers).
Higher values indicate probable cell boundaries, used to refine segmentation.
threshold (tuple[float, float], optional): Merge and split thresholds as percentages (0-100).
- The first value is the merge threshold: cells with nuclei overlap below this value are merged.
- The second value is the split threshold: cells with nuclei overlap above this value are split.
Default is (33, 66).
quantile (tuple[float, float], optional): Minimum and maximum quantile values for filtering nuclei sizes (0-100).
- The first value excludes the smallest nuclei (e.g., "0.3" excludes the smallest 0.3%).
- The second value excludes the largest nuclei (e.g., "99.9" excludes the largest 0.1%).
Default is (0.3, 99.9).
Returns:
None
Boundary image: Optional boundary probability map (same shape as input layers).
Higher values indicate probable cell boundaries, used to refine segmentation.
Boundary Threshold (%): Set the percentage range for merging (first value) and splitting (second value) cells. For example, "33" means cells with less than 33% overlap with nuclei are merged, and "66" means cells with more than 66% overlap are split.
Nuclei Size Filter (%): Set the size range to filter nuclei, represented as percentages. For example, "0.3" excludes the smallest 30%, and "99.9" excludes the largest 0.1% of nuclei.
