organoid_tracker.position_analysis.position_markers module

Additional metadata of a position, like the cell type or the fluorescent intensity.

organoid_tracker.position_analysis.position_markers.get_normalized_intensity(experiment: Experiment, position: Position) → Optional[float]

@deprecated Old method, please use intensity_calculator.get_normalized_intensity instead.

organoid_tracker.position_analysis.position_markers.get_position_flags(experiment: Experiment) → Iterable[str]

Gets all used position flags of the experiment. These are simply all keys in experiment.position_data with the bool data type. In addition, the special flag UNCERTAIN_MARKER is always returned, as that flag is used in the error checker.

organoid_tracker.position_analysis.position_markers.get_position_type(position_data: PositionData, position: Position) → Optional[str]

Gets the type of the cell in UPPERCASE, interpreted as the intestinal organoid cell type.

organoid_tracker.position_analysis.position_markers.get_position_types(position_data: PositionData, positions: Set[Position]) → Dict[Position, Optional[str]]

Gets all known cell types of the given positions, with the names in UPPERCASE.

organoid_tracker.position_analysis.position_markers.get_positions_of_type(position_data: PositionData, requested_type: str) → Iterable[Position]

Gets all positions of the requested cell type.

organoid_tracker.position_analysis.position_markers.get_raw_intensity(position_data: PositionData, position: Position) → Optional[float]

Gets the raw intensity of the position.

organoid_tracker.position_analysis.position_markers.set_position_type(position_data: PositionData, position: Position, type: Optional[str])

Sets the type of the cell. Set to None to delete the cell type.

organoid_tracker.position_analysis.position_markers.set_raw_intensities(experiment: Experiment, raw_intensities: Dict[Position, int], volumes: Dict[Position, int])

@deprecated Old method, please use intensity_calculator.get_normalized_intensity instead.