organoid_tracker.linking_analysis.linking_markers module

Extra markers used to describe the linking data. For example, you can mark the end of a lineage as a cell death.

class organoid_tracker.linking_analysis.linking_markers.EndMarker(value, names=<not given>, *values, module=None, qualname=None, type=None, start=1, boundary=None)

Bases: Enum

DEAD = 1

OUT_OF_VIEW = 2

SHED = 3

SHED_OUTSIDE = 4

STIMULATED_SHED = 5

get_display_name(): Gets a user-friendly display name.

static is_shed(marker: Optional[EndMarker]) → bool

class organoid_tracker.linking_analysis.linking_markers.StartMarker(value, names=<not given>, *values, module=None, qualname=None, type=None, start=1, boundary=None)

Bases: Enum

GOES_INTO_VIEW = 1

UNSURE = 2

get_display_name(): Gets a user-friendly display name.

organoid_tracker.linking_analysis.linking_markers.find_death_and_shed_positions(links: Links, position_data: PositionData) → Iterable[Position]: Gets all positions that were marked as a cell death or a cell shedding event.

organoid_tracker.linking_analysis.linking_markers.find_death_positions(links: Links, position_data: PositionData) → Iterable[Position]: Gets all positions that were marked as a cell death event.

organoid_tracker.linking_analysis.linking_markers.find_errored_positions(position_data: PositionData, *, min_time_point: Optional[TimePoint] = None, max_time_point: Optional[TimePoint] = None) → Iterable[Position]: Gets all positions that have a (non suppressed) error in the given time point range.

organoid_tracker.linking_analysis.linking_markers.find_shed_positions(links: Links, position_data: PositionData) → Iterable[Position]: Gets all positions that were marked as a cell shedding event.

organoid_tracker.linking_analysis.linking_markers.find_stimulated_shed_positions(links: Links, position_data: PositionData) → Iterable[Position]: Gets all positions that were marked as a cell death event.

organoid_tracker.linking_analysis.linking_markers.get_error_marker(position_data: PositionData, position: Position) → Optional[Error]: Gets the error marker for the given link, if any. Returns None if the error has been suppressed using suppress_error_marker.

organoid_tracker.linking_analysis.linking_markers.get_mother_score(position_data: PositionData, position: Position) → float: Gets the mother score of the given position, or 0 if absent.

organoid_tracker.linking_analysis.linking_markers.get_position_type(position_data: PositionData, position: Position) → Optional[str]: Deprecated - use position_markers.get_position_type

organoid_tracker.linking_analysis.linking_markers.get_track_end_marker(position_data: PositionData, position: Position) → Optional[EndMarker]: Gets a death marker, which provides a reason why the cell lineage ended.

organoid_tracker.linking_analysis.linking_markers.get_track_start_marker(position_data: PositionData, position: Position) → Optional[StartMarker]: Gets the appearance marker. This is used to explain why a cell appeared out of thin air.

organoid_tracker.linking_analysis.linking_markers.has_mother_scores(position_data: PositionData) → bool: Gets if there is at least a single mother score recorded.

organoid_tracker.linking_analysis.linking_markers.has_shapes(position_data: PositionData) → bool: Gets whether there is shape information stored for at least one position in the experiment.

organoid_tracker.linking_analysis.linking_markers.is_error_suppressed(position_data: PositionData, position: Position, error: Error) → bool: Returns True if the given error is suppressed. If another type of error is suppressed, this method returns False.

organoid_tracker.linking_analysis.linking_markers.is_live(position_data: PositionData, position: Position) → bool: Returns true if the position is a live cell, i.e. it does not have a shed or death marker.

organoid_tracker.linking_analysis.linking_markers.is_uncertain(position_data: PositionData, position: Position) → bool: Returns True if the given position is marked as uncertain. A person can mark a position as uncertain if it is not clear whether there is actually a position marker there. The error checker will warm for such cases.

organoid_tracker.linking_analysis.linking_markers.set_error_marker(position_data: PositionData, position: Position, error: Optional[Error]): Sets an error marker for the given position.

organoid_tracker.linking_analysis.linking_markers.set_mother_score(position_data: PositionData, position: Position, value: float): Sets the mother score to the given value.

organoid_tracker.linking_analysis.linking_markers.set_track_end_marker(position_data: PositionData, position: Position, end_marker: Optional[EndMarker]): Sets a reason why the track ended at the given point.

organoid_tracker.linking_analysis.linking_markers.set_track_start_marker(position_data: PositionData, position: Position, start_marker: Optional[StartMarker]): Sets a reason why the track ended at the given point.

organoid_tracker.linking_analysis.linking_markers.set_uncertain(position_data: PositionData, position: Position, uncertain: bool): Marks the given position as certain/uncertain. See is_uncertain for more info.

organoid_tracker.linking_analysis.linking_markers.suppress_error_marker(position_data: PositionData, position: Position, error: Error): Suppresses an error. Even if set_error_marker is called afterwards, the error will not show up in get_error_marker.

organoid_tracker.linking_analysis.linking_markers.unsuppress_error_marker(position_data: PositionData, position: Position): Unsuppresses an error. If the error was not suppressed, or there was no error, this method does nothing.