organoid_tracker.linking_analysis.lineage_division_counter module

For counting how many times a cell (and its offspring) will divide.

organoid_tracker.linking_analysis.lineage_division_counter.get_division_count_in_lineage(starting_track: LinkingTrack, position_data: PositionData, last_time_point_number: int) → Optional[int]

Gets how many divisions there are in the lineage starting at the given cell. If the cell does not divide, then this method will return 0. If a lineage ended before the end of the experiment (as defined by last_time_point_number) and it was not because of an actual death, then it is assumed that the cell went out of view, and that no reliable clonal size can be calculated. In that case, this function returns None.

Any divisions occurring after last_time_point_number are ignored. This is useful if you want to look at only a limited time point window.

If a single cell goes out of the view, we don’t know if it would have divided. If this happens, and require_accurate is set to True, then this method returns None. Otherwise, it is assumed the cell doesn’t divide.

organoid_tracker.linking_analysis.lineage_division_counter.get_min_division_count_in_lineage(starting_track: LinkingTrack, last_time_point_number: int = 999999999)

Gets the number of divisions we could see up until last_time_point_number. This method returns a result even for lineages that are not fully tracked. In that case, the actual number of divisions may be higher, as we might be ignoring divisions that were happening outside the view.

organoid_tracker.linking_analysis.lineage_division_counter.get_number_of_cells_at_end(starting_track: LinkingTrack, last_time_point_number: int = 999999999)

Gets the number of divisions we could see up until last_time_point_number. This method returns a result even for lineages that are not fully tracked. In that case, the actual number of divisions may be higher, as we might be ignoring divisions that were happening outside the view.