organoid_tracker.linking_analysis.cell_error_finder module

organoid_tracker.linking_analysis.cell_error_finder.find_errors_in_all_dividing_cells(experiment: Experiment)

Rechecks all mother and daughter cells to verify that the mothers aren’t too young. Checking this accross the entire experiment is useful, as changes in links far away might affect the measured cell cycle length.

organoid_tracker.linking_analysis.cell_error_finder.find_errors_in_experiment(experiment: Experiment, marginalization=False) → Tuple[int, int]

Adds errors for all logical inconsistencies in the graph, like cells that spawn out of nowhere, cells that merge together and cells that have three or more daughters. Returns the amount of errors (excluding positions without links) and the number of positions without links.

organoid_tracker.linking_analysis.cell_error_finder.find_errors_in_just_these_positions(experiment: Experiment, *iterable: Position)

Checks all positions in the given iterable for logical errors, like cell merges, cell dividing into three daughters, cells moving too fast, ect.

Checks all of the given positions and all dividing cells in the experiment for logical errors, like cell merges, cell dividing into three daughters, cells moving too fast, ect. The reason dividing cells are also checked is that otherwise it’s not possible to detect when a young mother cell is no longer a young mother cell because far away in time some link changed.

organoid_tracker.linking_analysis.cell_error_finder.get_error(experiment: Experiment, position: Position, marginalization=False) → Optional[Error]