organoid_tracker.linking_analysis.links_postprocessor module

organoid_tracker.linking_analysis.links_postprocessor.bridge_gaps(experiment: Experiment, experiment_result: Experiment, miss_penalty=2.0)

connects tracks broken up by missed cell division (—-x—- -> ———)

organoid_tracker.linking_analysis.links_postprocessor.bridge_gaps2(experiment: Experiment, experiment_result: Experiment, miss_penalty=2.0)

connects tracks broken up by not having a proposed link between them (—-____ -> ———)

organoid_tracker.linking_analysis.links_postprocessor.connect_loose_ends(experiment: Experiment, experiment_result: Experiment, oversegmentation_penalty=2.0, window=4)

connects tracks broken up by overgsegmentation (—===—- -> ———)

organoid_tracker.linking_analysis.links_postprocessor.finetune_solution(experiment: Experiment, experiment_result: Experiment)

Adds, deletes or swaps single links to lower the energy of the solution

organoid_tracker.linking_analysis.links_postprocessor.pinpoint_divisions(experiment: Experiment, experiment_result: Experiment, min_penalty_diff=1.0)

if two cell detections are made before the division network expects a division we want to align these events

organoid_tracker.linking_analysis.links_postprocessor.postprocess(experiment: Experiment, margin_xy: int)

organoid_tracker.linking_analysis.links_postprocessor.remove_tracks_too_deep(experiment: Experiment, max_z: int)