organoid_tracker.imaging.io module

Classes for expressing the positions of positions

organoid_tracker.imaging.io.load_data_file(file_name: str, min_time_point: int = 0, max_time_point: int = 5000, *, experiment: Optional[Experiment] = None) → Experiment

Loads some kind of data file. This should support all data formats of our research group. Raises ValueError if the file fails to load. All data is dumped into the given experiment object.

organoid_tracker.imaging.io.load_positions_and_shapes_from_json(experiment: Experiment, json_file_name: str, min_time_point: int = 0, max_time_point: int = 5000)

Loads a JSON file that contains position positions, with or without shape information.

organoid_tracker.imaging.io.save_data_to_json(experiment: Experiment, json_file_name: str, *, write_new_format: bool = True)

Saves positions, shapes, scores and links to a JSON file. The file should end with the extension FILE_EXTENSION.

We can save in the old v1 or the newer v2 format, which stores the positions and tracks in a more efficient way. See TRACKING_FORMATS.md in the manual for more information.

organoid_tracker.imaging.io.save_positions_to_json(experiment: Experiment, json_file_name: str)

Saves a list of positions (pixel coordinate) to disk. Because the offset of the images is not saved, the offset is added to all positions. This method is mainly intended to export training data for neural networks, so it will ignore dead cells.