scip.segmentation package

scip.segmentation.export_labeled_mask(events: List[Mapping[str, Any]], out: Path, group_keys: List[str]) → List[Mapping[str, Any]]

scip.segmentation.segment(*, images: Bag, method: str, settings: Mapping[str, Any], export: bool, output: Path, gpu: bool, loader_module) → Bag

scip.segmentation.to_events(events: List[Mapping[str, Any]], *, group_keys: List[str] | None = None, parent_channel_index: int, **kwargs)

Converts the segmented objects into a list of dictionaries that can be converted to a dask.bag.Bag. The dictionaries contain the pixel information for one detected cell, or event, and the meta data of that event.

Submodules

scip.segmentation.cellpose module

scip.segmentation.watershed_dapi module

scip.segmentation.watershed_dapi.segment_block(events: List[Mapping[str, Any]], *, cell_diameter: int, dapi_channel_index: int, expansion_factor: float = 0.1) → List[dict]