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 interface for correcting over- and under-segmentation of cells based on nuclei segmentation.
This GUI interface allows the user to specify the input cell and nuclear segmentations, along with optional boundary
probability maps. The user can control the merging and splitting thresholds, and define quantiles to filter out
irregular nuclei. The widget schedules the correction task in the background and updates the displayed results accordingly.
Args:
cell_segmentation (Labels): Input label layer for cell segmentation.
nuclei_segmentation (Labels): Input label layer for nuclei segmentation.
boundary_pmaps (Image | None, optional): Optional boundary probability map or image to assist in segmentation refinement.
threshold (tuple[float, float], optional): Threshold range for merging (first value) and splitting (second value) cells.
The values should be between 0 and 100, corresponding to 0%-100% overlap. Default is (33, 66).
quantile (tuple[float, float], optional): Quantile range to filter nuclei size, ignoring outliers.
Values should be between 0 and 100. Default is (0.3, 99.9).
Returns:
Future[LayerDataTuple]: A future object that contains the corrected segmentation layer once the task completes.
Cell instances: None
Nuclear instances: None
Boundary image: Optional boundary probability map or image to assist in segmentation refinement.
Boundary threshold: Threshold range for merging (first value) and splitting (second value) cells.
Nuclei size filter: Quantile range to filter nuclei size, ignoring outliers.
