organoid_tracker.linking_analysis.lineage_error_finder module

Used to find lineage trees with (potential) errors.

class organoid_tracker.linking_analysis.lineage_error_finder.LineageWithErrors(start: LinkingTrack)

Bases: object

Represents all (potential) errors in a complete lineage tree.

crumbs: Set[Position]

errored_positions: List[Position]

start: LinkingTrack

organoid_tracker.linking_analysis.lineage_error_finder.delete_problematic_lineages(experiment: Experiment): This deletes all positions in a lineage with errors. What remains should be a clean experiment with just the corrected data.

organoid_tracker.linking_analysis.lineage_error_finder.find_error_focus_min_divisions(experiment: Experiment) → int: Gets the minimum number of divisions a lineage must have to be in focus for error correction. If no value is defined, it returns 0.

organoid_tracker.linking_analysis.lineage_error_finder.find_error_focus_tracks(experiment: Experiment) → Optional[Set[LinkingTrack]]

Finds all tracks that are in focus for error correction. If no focus positions have been defined, returns None.

Note that this method may also return an empty set instead of None, which happens when all defined focus points do not have a track. This is useful to signal that the track focus system is in use, but no tracks are in focus.

organoid_tracker.linking_analysis.lineage_error_finder.find_lineage_index_with_crumb(lineages: List[LineageWithErrors], crumb: Optional[Position]) → Optional[int]: Attempts to find the given position in the lineages. Returns None if the position is None or if the position is in none of the lineages.

organoid_tracker.linking_analysis.lineage_error_finder.get_problematic_lineages(experiment: Experiment, crumbs: AbstractSet[Position], *, min_time_point: Optional[TimePoint] = None, max_time_point: Optional[TimePoint] = None) → List[LineageWithErrors]: Gets a list of all lineages with warnings in the experiment. The provided “crumbs” are placed in the right lineages, so that you can see to what lineages those cells belong.