Index

A

add() (organoid_tracker.core.beacon_collection.BeaconCollection method) (organoid_tracker.core.concurrent.ConcurrentSet method) (organoid_tracker.core.position_collection.PositionCollection method) add_all_splines() (in module organoid_tracker.coordinate_system.orientation_spline_adder) add_and_return_8bit() (in module organoid_tracker.util.bits) add_axis_to_axes_list() (in module organoid_tracker.guizela_tracker_compatibility.axis_lib) (in module organoid_tracker.guizela_tracker_compatibility.axis_lib_v2) add_beacons() (organoid_tracker.core.beacon_collection.BeaconCollection method) add_connection() (organoid_tracker.core.connections.Connections method) add_connections() (organoid_tracker.core.connections.Connections method) add_data() (organoid_tracker.comparison.report.ComparisonReport method) add_data_from_time_point_dict() (organoid_tracker.core.connections.Connections method) (organoid_tracker.core.position_collection.PositionCollection method) (organoid_tracker.core.position_data.PositionData method) add_data_to_experiment() (in module organoid_tracker.guizela_tracker_compatibility.guizela_data_importer) add_experiment() (organoid_tracker.gui.gui_experiment.GuiExperiment method) add_filter() (organoid_tracker.core.image_filters.ImageFilters method) add_from_function() (organoid_tracker.core.mask.Mask method) add_from_labeled() (organoid_tracker.core.mask.Mask method) add_images() (in module organoid_tracker.imaging.image_adder) add_link() (organoid_tracker.core.links.Links method) add_links() (organoid_tracker.core.links.Links method) add_orientation_track() (organoid_tracker.coordinate_system.sphere_representer.SphereRepresentation method) add_point() (organoid_tracker.coordinate_system.sphere_representer.SphereRepresentation method) (organoid_tracker.core.spline.Spline method) (organoid_tracker.guizela_tracker_compatibility.axis_lib.Axis method) (organoid_tracker.guizela_tracker_compatibility.axis_lib_v2.Axis method) (organoid_tracker.guizela_tracker_compatibility.track_lib.Track method) (organoid_tracker.guizela_tracker_compatibility.track_lib_v2.Track method) (organoid_tracker.guizela_tracker_compatibility.track_lib_v3.Track method) (organoid_tracker.guizela_tracker_compatibility.track_lib_v4.Track method)

add_positions() (organoid_tracker.core.position_collection.PositionCollection method) add_positions_data() (organoid_tracker.core.position_collection.PositionCollection method) (organoid_tracker.core.position_data.PositionData method) add_spline() (organoid_tracker.core.spline.SplineCollection method) add_track() (organoid_tracker.coordinate_system.sphere_representer.SphereRepresentation method) (organoid_tracker.core.links.Links method) add_track_colored_by_spline_position() (organoid_tracker.coordinate_system.orientation_spline_adder.ColoredTrackAdder method) add_track_to_tracklist() (in module organoid_tracker.guizela_tracker_compatibility.track_lib) all_splines() (organoid_tracker.core.spline.SplineCollection method) allow_extra_tabs (organoid_tracker.imaging.file_loader.LoadInto attribute) angle_between_vectors() (in module organoid_tracker.imaging.angles) angular_difference() (organoid_tracker.coordinate_system.spherical_coordinates.SphericalCoordinate method) applies_to() (organoid_tracker.core.marker.Marker method) array (organoid_tracker.core.images.Image property) attr_float() (organoid_tracker.util.xml_wrapper.XmlWrapper method) attr_str() (organoid_tracker.util.xml_wrapper.XmlWrapper method) Axis (class in organoid_tracker.guizela_tracker_compatibility.axis_lib) (class in organoid_tracker.guizela_tracker_compatibility.axis_lib_v2)

B

Beacon (class in organoid_tracker.core.beacon_collection) beacon (organoid_tracker.core.beacon_collection.ClosestBeacon property) beacon_index (organoid_tracker.core.beacon_collection.ClosestBeacon attribute) beacon_position (organoid_tracker.core.beacon_collection.ClosestBeacon attribute) beacon_type (organoid_tracker.core.beacon_collection.Beacon attribute) (organoid_tracker.core.beacon_collection.ClosestBeacon attribute) BeaconCollection (class in organoid_tracker.core.beacon_collection) beacons (organoid_tracker.core.experiment.Experiment property)

black() (organoid_tracker.core.Color static method) blue (organoid_tracker.core.Color property) blur_radius (organoid_tracker.image_loading.builtin_image_filters.GaussianBlurFilter attribute) body (organoid_tracker.core.UserError attribute) bounding_box() (organoid_tracker.core.images.Image method) BoundingBox (class in organoid_tracker.core.bounding_box) bridge_gaps() (in module organoid_tracker.linking_analysis.links_postprocessor) bridge_gaps2() (in module organoid_tracker.linking_analysis.links_postprocessor) build_constraint_matrix() (in module organoid_tracker.local_marginalization.local_marginalization_functions)

C

calculate_angle() (organoid_tracker.core.spline.SplinePosition method) calculate_distances() (organoid_tracker.core.connections.Connections method) calculate_distances_over_time() (organoid_tracker.core.connections.Connections method) calculate_rotation_of_track() (in module organoid_tracker.linking_analysis.particle_rotation_calculator) calculate_time_correctness_statistics() (organoid_tracker.comparison.links_comparison.LinksReport method) calculate_time_detection_statistics() (organoid_tracker.comparison.positions_comparison.DetectionReport method) calculate_time_statistics() (organoid_tracker.comparison.report.ComparisonReport method) calculate_z_correctness_statistics() (organoid_tracker.comparison.links_comparison.LinksReport method) calculate_z_detection_statistics() (organoid_tracker.comparison.positions_comparison.DetectionReport method) calculate_z_statistics() (organoid_tracker.comparison.report.ComparisonReport method) can_save_images() (organoid_tracker.core.image_loader.ImageLoader method) (organoid_tracker.image_loading.builtin_merging_image_loaders.ChannelAppendingImageLoader method) (organoid_tracker.image_loading.builtin_merging_image_loaders.ChannelSummingImageLoader method) (organoid_tracker.image_loading.folder_image_loader.FolderImageLoader method) Category (class in organoid_tracker.comparison.report) CELL_MERGE (organoid_tracker.linking_analysis.errors.Error attribute) CellCompartment (class in organoid_tracker.linking_analysis.cell_compartment_finder) CellFate (class in organoid_tracker.linking_analysis.cell_fate_finder) CellFateType (class in organoid_tracker.linking_analysis.cell_fate_finder) center_around() (organoid_tracker.core.mask.Mask method) channel_name (organoid_tracker.core.images.ChannelDescription attribute) ChannelAppendingImageLoader (class in organoid_tracker.image_loading.builtin_merging_image_loaders) ChannelDescription (class in organoid_tracker.core.images) ChannelSummingImageLoader (class in organoid_tracker.image_loading.builtin_merging_image_loaders) check_completeness() (in module organoid_tracker.local_marginalization.local_marginalization_functions) check_time_point() (organoid_tracker.core.position.Position method) clamp() (in module organoid_tracker.core) clear() (organoid_tracker.gui.undo_redo.UndoRedo method) clear_all() (organoid_tracker.plugin.registry.Registry method) clear_channel() (organoid_tracker.core.image_filters.ImageFilters method) clear_tracking_data() (organoid_tracker.core.experiment.Experiment method) close() (organoid_tracker.core.experiment.Experiment method) (organoid_tracker.core.image_loader.ImageLoader method) (organoid_tracker.image_loading.builtin_merging_image_loaders.ChannelAppendingImageLoader method) (organoid_tracker.image_loading.builtin_merging_image_loaders.ChannelSummingImageLoader method) (organoid_tracker.image_loading.builtin_merging_image_loaders.TimeAppendingImageLoader method) close_image_loader() (organoid_tracker.core.images.Images method) ClosestBeacon (class in organoid_tracker.core.beacon_collection) Cluster (class in organoid_tracker.connection_analysis.cluster_finder) Color (class in organoid_tracker.core) color (organoid_tracker.core.experiment.Experiment property) (organoid_tracker.core.marker.Marker property) color_error_rates() (in module organoid_tracker.local_marginalization.tree_drawing) color_map (organoid_tracker.coordinate_system.orientation_spline_adder.ColoredTrackAdder attribute) ColoredTrackAdder (class in organoid_tracker.coordinate_system.orientation_spline_adder) colormap (organoid_tracker.core.images.ChannelDescription attribute) combine_events() (in module organoid_tracker.local_marginalization.local_marginalization_functions) CombinedAction (class in organoid_tracker.gui.undo_redo) compare_links() (in module organoid_tracker.comparison.lineage_comparison) (in module organoid_tracker.comparison.links_comparison) compare_positions() (in module organoid_tracker.comparison.positions_comparison) ComparisonReport (class in organoid_tracker.comparison.report) compute_lineage_error_probability() (in module organoid_tracker.local_marginalization.tree_drawing) compute_track_error_probability() (in module organoid_tracker.local_marginalization.tree_drawing) ConcurrentSet (class in organoid_tracker.core.concurrent) config_type_bool() (in module organoid_tracker.config) config_type_csv_file() (in module organoid_tracker.config) config_type_float() (in module organoid_tracker.config) config_type_image_shape_xyz_to_zyx() (in module organoid_tracker.config) config_type_int() (in module organoid_tracker.config) config_type_json_file() (in module organoid_tracker.config) config_type_str() (in module organoid_tracker.config) ConfigFile (class in organoid_tracker.config) connect_loose_ends() (in module organoid_tracker.linking_analysis.links_postprocessor) connect_tracks() (organoid_tracker.core.links.Links method) Connections (class in organoid_tracker.core.connections) connections (organoid_tracker.core.experiment.Experiment property) (organoid_tracker.core.full_position_snapshot.FullPositionSnapshot attribute)

ConnectorByDistance (class in organoid_tracker.connecting.connector_by_distance) construct_microstates() (in module organoid_tracker.local_marginalization.local_marginalization_functions) contains_connection() (organoid_tracker.core.connections.Connections method) contains_link() (organoid_tracker.core.links.Links method) contains_position() (organoid_tracker.core.beacon_collection.BeaconCollection method) (organoid_tracker.core.links.Links method) (organoid_tracker.core.position_collection.PositionCollection method) contains_time_point() (organoid_tracker.core.connections.Connections method) contant_timing() (organoid_tracker.core.resolution.ImageTimings static method) copy() (organoid_tracker.core.connections.Connections method) (organoid_tracker.core.global_data.GlobalData method) (organoid_tracker.core.image_filters.ImageFilter method) (organoid_tracker.core.image_filters.ImageFilters method) (organoid_tracker.core.image_loader.ImageLoader method) (organoid_tracker.core.image_loader.NullImageLoader method) (organoid_tracker.core.images.ImageOffsets method) (organoid_tracker.core.images.Images method) (organoid_tracker.core.link_data.LinkData method) (organoid_tracker.core.links.Links method) (organoid_tracker.core.Name method) (organoid_tracker.core.position_collection.PositionCollection method) (organoid_tracker.core.position_data.PositionData method) (organoid_tracker.core.resolution.ImageTimings method) (organoid_tracker.core.spline.Spline method) (organoid_tracker.core.warning_limits.WarningLimits method) (organoid_tracker.image_loading.array_image_loader.SingleImageLoader method) (organoid_tracker.image_loading.builtin_image_filters.GaussianBlurFilter method) (organoid_tracker.image_loading.builtin_image_filters.InterpolatedMinMaxFilter method) (organoid_tracker.image_loading.builtin_image_filters.MultiplyPixelsFilter method) (organoid_tracker.image_loading.builtin_image_filters.ThresholdFilter method) (organoid_tracker.image_loading.builtin_merging_image_loaders.ChannelAppendingImageLoader method) (organoid_tracker.image_loading.builtin_merging_image_loaders.ChannelSummingImageLoader method) (organoid_tracker.image_loading.builtin_merging_image_loaders.TimeAppendingImageLoader method) (organoid_tracker.image_loading.folder_image_loader.FolderImageLoader method) copy_selected() (organoid_tracker.core.experiment.Experiment method) corners_split() (in module organoid_tracker.neural_network.position_detection_cnn.split_images) count_beacons_at_time_point() (organoid_tracker.core.beacon_collection.BeaconCollection method) count_experiments_in_list_file() (in module organoid_tracker.imaging.list_io) count_lines() (organoid_tracker.util.moving_average.LinesAverage method) count_nearby_deaths_in_past() (organoid_tracker.linking_analysis.cell_nearby_death_counter.NearbyDeaths method) count_pixels() (organoid_tracker.core.mask.Mask method) count_positions() (organoid_tracker.comparison.report.ComparisonReport method) (organoid_tracker.core.position_collection.PositionCollection method) count_values_at_min_max_x() (organoid_tracker.util.moving_average.LinesAverage method) counts_in_standard_deviation_values (organoid_tracker.util.moving_average.MovingAverage attribute) create_connections() (in module organoid_tracker.connecting.connector_using_angles) (organoid_tracker.connecting.connector_by_distance.ConnectorByDistance method) create_image() (in module organoid_tracker.imaging.depth_colored_image_creator) create_image_list_without_positions() (in module organoid_tracker.neural_network.position_detection_cnn.training_data_creator) create_image_with_divisions_list() (in module organoid_tracker.neural_network.division_detection_cnn.training_data_creator) create_image_with_positions_list() (in module organoid_tracker.neural_network.division_detection_cnn.training_data_creator) (in module organoid_tracker.neural_network.position_detection_cnn.training_data_creator) create_labels() (organoid_tracker.neural_network.position_detection_cnn.training_data_creator.ImageWithPositions method) create_mask_for() (in module organoid_tracker.core.mask) create_masked_and_normalized_image() (organoid_tracker.core.mask.Mask method) create_masked_image() (organoid_tracker.core.mask.Mask method) create_masked_image_nan() (organoid_tracker.core.mask.Mask method) create_min_max_filter() (in module organoid_tracker.image_loading.builtin_image_filters) create_movie() (in module organoid_tracker.imaging.depth_colored_image_creator) create_prediction_mask() (in module organoid_tracker.neural_network.position_detection_cnn.peak_calling) create_run_script() (in module organoid_tracker.util.run_script_creator) create_time_point_dict() (organoid_tracker.core.position_collection.PositionCollection method) (organoid_tracker.core.position_data.PositionData method) crop_2d() (in module organoid_tracker.imaging.cropper) crop_3d() (in module organoid_tracker.imaging.cropper) crop_3d_to_2d() (in module organoid_tracker.imaging.cropper) cross() (organoid_tracker.core.vector.Vector3 method) crumbs (organoid_tracker.linking_analysis.lineage_error_finder.LineageWithErrors attribute)

D

daughters (organoid_tracker.linking.cell_division_finder.Family attribute) DEAD (organoid_tracker.linking_analysis.linking_markers.EndMarker attribute) deaths (organoid_tracker.linking_analysis.lineage_fate_finder.LineageFate attribute) debug_plot() (organoid_tracker.comparison.report.Statistics method) debug_sanity_check() (organoid_tracker.core.links.Links method) default() (organoid_tracker.imaging.io.NumpyToJsonEncoder method) delete_data() (organoid_tracker.comparison.report.ComparisonReport method) delete_data_with_name() (organoid_tracker.core.position_collection.PositionCollection method) (organoid_tracker.core.position_data.PositionData method) delete_lineages_not_in_first_time_point() (in module organoid_tracker.linking_analysis.links_filter) delete_point() (organoid_tracker.guizela_tracker_compatibility.axis_lib.Axis method) (organoid_tracker.guizela_tracker_compatibility.axis_lib_v2.Axis method) (organoid_tracker.guizela_tracker_compatibility.track_lib.Track method) (organoid_tracker.guizela_tracker_compatibility.track_lib_v2.Track method) (organoid_tracker.guizela_tracker_compatibility.track_lib_v3.Track method) (organoid_tracker.guizela_tracker_compatibility.track_lib_v4.Track method) delete_positions_without_links() (in module organoid_tracker.linking_analysis.links_filter) delete_problematic_lineages() (in module organoid_tracker.linking_analysis.lineage_error_finder) detach_all_for_time_point() (organoid_tracker.core.position_collection.PositionCollection method) detach_position() (organoid_tracker.core.position_collection.PositionCollection method) Details (class in organoid_tracker.comparison.report) details (organoid_tracker.comparison.report.Details property) DetectionReport (class in organoid_tracker.comparison.positions_comparison) difference() (in module organoid_tracker.imaging.angles) difference_um() (organoid_tracker.core.beacon_collection.ClosestBeacon method) dilate_xy() (organoid_tracker.core.mask.Mask method) direction (organoid_tracker.imaging.lines.Line3 attribute)

direction_2d() (in module organoid_tracker.imaging.angles) direction_change() (in module organoid_tracker.imaging.angles) direction_change_of_line() (in module organoid_tracker.imaging.angles) direction_to_point() (in module organoid_tracker.imaging.lines) display_name (organoid_tracker.core.marker.Marker property) distance (organoid_tracker.core.spline.SplinePosition attribute) distance() (organoid_tracker.core.vector.Vector2 method) (organoid_tracker.core.vector.Vector3 method) distance_squared() (organoid_tracker.core.position.Position method) (organoid_tracker.image_loading.builtin_image_filters.IntensityPoint method) distance_to_point() (in module organoid_tracker.imaging.lines) distance_um (organoid_tracker.core.beacon_collection.ClosestBeacon attribute) distance_um() (organoid_tracker.core.position.Position method) divide() (organoid_tracker.core.vector.Vector3 method) DIVIDING (organoid_tracker.linking_analysis.cell_compartment_finder.CellCompartment attribute) division_lookahead_time_points (organoid_tracker.core.experiment.Experiment property) divisions (organoid_tracker.linking_analysis.lineage_fate_finder.LineageFate attribute) do() (organoid_tracker.gui.undo_redo.CombinedAction method) (organoid_tracker.gui.undo_redo.ReversedAction method) (organoid_tracker.gui.undo_redo.UndoableAction method) (organoid_tracker.gui.undo_redo.UndoRedo method) dot() (organoid_tracker.core.vector.Vector2 method) (organoid_tracker.core.vector.Vector3 method) draw_2d() (organoid_tracker.coordinate_system.sphere_representer.SphereRepresentation method) draw_3d() (organoid_tracker.coordinate_system.sphere_representer.SphereRepresentation method) draw_lineages_colored() (organoid_tracker.linking_analysis.lineage_drawing.LineageDrawing method) draw_marker_2d() (in module organoid_tracker.core.marker) draw_sphere() (in module organoid_tracker.util.mpl_helper_3d)

E

EndMarker (class in organoid_tracker.linking_analysis.linking_markers) ends (organoid_tracker.linking_analysis.lineage_fate_finder.LineageFate attribute) energy_to_prob() (in module organoid_tracker.local_marginalization.local_marginalization_functions) ensure_8bit() (in module organoid_tracker.util.bits) Error (class in organoid_tracker.linking_analysis.errors) ERROR (organoid_tracker.linking_analysis.errors.Severity attribute) errored_positions (organoid_tracker.linking_analysis.lineage_error_finder.LineageWithErrors attribute) excluded_errors (organoid_tracker.core.warning_limits.WarningLimits attribute) execute_command() (organoid_tracker.gui.gui_experiment.GuiExperiment method)

exists() (organoid_tracker.core.spline.SplineCollection method) expanded() (organoid_tracker.core.bounding_box.BoundingBox method) Experiment (class in organoid_tracker.core.experiment) experiment (organoid_tracker.gui.gui_experiment.SingleGuiTab property) (organoid_tracker.imaging.file_loader.LoadInto attribute) experiment_name (organoid_tracker.neural_network.position_detection_cnn.training_data_creator.ImageWithPositions attribute) export_links() (in module organoid_tracker.guizela_tracker_compatibility.guizela_data_exporter) extra() (organoid_tracker.core.marker.Marker method) extra_experiments (organoid_tracker.imaging.file_loader.LoadInto attribute)

F

f1_score (organoid_tracker.comparison.report.Statistics attribute) f1_score_overall (organoid_tracker.comparison.report.Statistics attribute) factor (organoid_tracker.image_loading.builtin_image_filters.MultiplyPixelsFilter attribute) FAILED_SHAPE (organoid_tracker.linking_analysis.errors.Error attribute) false_negatives (organoid_tracker.comparison.report.Statistics attribute) false_positives (organoid_tracker.comparison.report.Statistics attribute) Family (class in organoid_tracker.linking.cell_division_finder) FILE_NAME (organoid_tracker.config.ConfigFile attribute) FileLoader (class in organoid_tracker.imaging.file_loader) FileLoaderType (class in organoid_tracker.imaging.file_loader) filter() (organoid_tracker.core.image_filters.ImageFilter method) (organoid_tracker.core.image_filters.ImageFilters method) (organoid_tracker.image_loading.builtin_image_filters.GaussianBlurFilter method) (organoid_tracker.image_loading.builtin_image_filters.InterpolatedMinMaxFilter method) (organoid_tracker.image_loading.builtin_image_filters.MultiplyPixelsFilter method) (organoid_tracker.image_loading.builtin_image_filters.ThresholdFilter method) filters (organoid_tracker.core.images.Images attribute) find_all_connections() (organoid_tracker.core.connections.Connections method) find_all_data_names() (organoid_tracker.core.connections.Connections method) (organoid_tracker.core.link_data.LinkData method) (organoid_tracker.core.links.Links method) (organoid_tracker.core.position_collection.PositionCollection method) (organoid_tracker.core.position_data.PositionData method) find_all_data_of_lineage() (organoid_tracker.core.links.Links method) find_all_data_of_link() (organoid_tracker.core.link_data.LinkData method) (organoid_tracker.core.links.Links method) find_all_data_of_position() (organoid_tracker.core.position_collection.PositionCollection method) (organoid_tracker.core.position_data.PositionData method) find_all_descending_tracks() (organoid_tracker.core.links.LinkingTrack method) find_all_links() (organoid_tracker.core.links.Links method) find_all_links_with_data() (organoid_tracker.core.link_data.LinkData method) (organoid_tracker.core.links.Links method) find_all_positions() (organoid_tracker.core.links.Links method) find_all_positions_in_track_of() (in module organoid_tracker.linking_analysis.track_positions_finder) find_all_positions_with_data() (organoid_tracker.core.position_collection.PositionCollection method) (organoid_tracker.core.position_data.PositionData method) find_all_previous_and_descending_tracks() (organoid_tracker.core.links.LinkingTrack method) find_all_previous_tracks() (organoid_tracker.core.links.LinkingTrack method) find_all_tracks() (organoid_tracker.core.links.Links method) find_all_tracks_and_ids() (organoid_tracker.core.links.Links method) find_all_tracks_in_same_lineage() (organoid_tracker.core.links.LinkingTrack method) find_all_tracks_in_time_point() (organoid_tracker.core.links.Links method) find_appeared_positions() (organoid_tracker.core.links.Links method) find_close_positions() (in module organoid_tracker.linking.nearby_position_finder) find_closest_beacon() (organoid_tracker.core.beacon_collection.BeaconCollection method) find_closest_n_positions() (in module organoid_tracker.linking.nearby_position_finder) find_closest_position() (in module organoid_tracker.linking.nearby_position_finder) find_closest_time_point() (organoid_tracker.core.resolution.ImageTimings method) find_clusters() (in module organoid_tracker.connection_analysis.cluster_finder) find_compartment() (in module organoid_tracker.linking_analysis.cell_compartment_finder) find_compartment_ext() (in module organoid_tracker.linking_analysis.cell_compartment_finder) find_connections() (organoid_tracker.core.connections.Connections method) find_death_and_shed_positions() (in module organoid_tracker.linking_analysis.linking_markers) find_death_positions() (in module organoid_tracker.linking_analysis.linking_markers) find_disappeared_positions() (organoid_tracker.core.links.Links method) find_ended_tracks() (in module organoid_tracker.linking_analysis.lineage_end_finder) find_ending_tracks() (organoid_tracker.core.links.Links method) find_error_focus_min_divisions() (in module organoid_tracker.linking_analysis.lineage_error_finder) find_error_focus_tracks() (in module organoid_tracker.linking_analysis.lineage_error_finder) find_errored_positions() (in module organoid_tracker.linking_analysis.linking_markers)

find_errors_in_cell_cycle_lengths() (in module organoid_tracker.linking_analysis.cell_error_finder) find_errors_in_experiment() (in module organoid_tracker.linking_analysis.cell_error_finder) find_errors_in_just_these_positions() (in module organoid_tracker.linking_analysis.cell_error_finder) find_errors_in_positions_links_and_all_dividing_cells() (in module organoid_tracker.linking_analysis.cell_error_finder) find_families() (in module organoid_tracker.linking.cell_division_finder) find_first_position() (organoid_tracker.core.links.LinkingTrack method) find_future_positions_at() (in module organoid_tracker.linking_analysis.particle_movement_finder) find_futures() (organoid_tracker.core.links.Links method) find_last_position() (organoid_tracker.core.links.LinkingTrack method) find_lineage_index_with_crumb() (in module organoid_tracker.linking_analysis.lineage_error_finder) find_links_of() (organoid_tracker.core.links.Links method) find_local_set() (in module organoid_tracker.local_marginalization.local_marginalization_functions) find_mothers() (in module organoid_tracker.linking.cell_division_finder) find_object() (organoid_tracker.gui.location_map.LocationMap method) find_pasts() (organoid_tracker.core.links.Links method) find_position_at_time_point_number() (organoid_tracker.core.links.LinkingTrack method) find_position_in_connected_time_point() (in module organoid_tracker.connection_analysis.connected_position_finder) find_previous_positions() (in module organoid_tracker.linking_analysis.position_connection_finder) find_shed_positions() (in module organoid_tracker.linking_analysis.linking_markers) find_single_beacon() (organoid_tracker.core.beacon_collection.BeaconCollection method) find_single_beacon_of_time_point() (organoid_tracker.core.beacon_collection.BeaconCollection method) find_single_future() (organoid_tracker.core.links.Links method) find_single_past() (organoid_tracker.core.links.Links method) find_starting_tracks() (organoid_tracker.core.links.Links method) find_stimulated_shed_positions() (in module organoid_tracker.linking_analysis.linking_markers) find_time_and_channel_pattern() (in module organoid_tracker.imaging.image_file_name_pattern_finder) find_times_divided() (in module organoid_tracker.linking_analysis.cell_division_counter) finetune_solution() (in module organoid_tracker.linking_analysis.links_postprocessor) first_time_point() (organoid_tracker.core.experiment.Experiment method) (organoid_tracker.core.image_loader.ImageLoader method) (organoid_tracker.core.images.Images method) (organoid_tracker.core.links.LinkingTrack method) (organoid_tracker.core.position_collection.PositionCollection method) (organoid_tracker.core.position_data.PositionData method) (organoid_tracker.core.spline.SplineCollection method) first_time_point_number() (organoid_tracker.comparison.report.ComparisonReport method) (organoid_tracker.core.experiment.Experiment method) (organoid_tracker.core.image_loader.ImageLoader method) (organoid_tracker.core.image_loader.NullImageLoader method) (organoid_tracker.core.images.Images method) (organoid_tracker.core.links.LinkingTrack method) (organoid_tracker.core.position_collection.PositionCollection method) (organoid_tracker.core.position_data.PositionData method) (organoid_tracker.core.spline.SplineCollection method) (organoid_tracker.image_loading.array_image_loader.SingleImageLoader method) (organoid_tracker.image_loading.builtin_merging_image_loaders.ChannelAppendingImageLoader method) (organoid_tracker.image_loading.builtin_merging_image_loaders.ChannelSummingImageLoader method) (organoid_tracker.image_loading.builtin_merging_image_loaders.TimeAppendingImageLoader method) (organoid_tracker.image_loading.folder_image_loader.FolderImageLoader method) flipped() (in module organoid_tracker.imaging.angles) FolderImageLoader (class in organoid_tracker.image_loading.folder_image_loader) from_cartesian() (organoid_tracker.coordinate_system.spherical_coordinates.SphericalCoordinate static method) from_matplotlib() (organoid_tracker.core.Color static method) from_points() (organoid_tracker.imaging.lines.Line3 static method) from_position() (organoid_tracker.core.full_position_snapshot.FullPositionSnapshot static method) from_position_on_axis() (organoid_tracker.core.spline.Spline method) from_rgb() (organoid_tracker.core.Color static method) from_rgb_floats() (organoid_tracker.core.Color static method) from_vector_um() (organoid_tracker.core.position.Position static method) FullPositionSnapshot (class in organoid_tracker.core.full_position_snapshot)

G

GaussianBlurFilter (class in organoid_tracker.image_loading.builtin_image_filters) generate_color_for_lineage_id() (in module organoid_tracker.linking_analysis.lineage_id_creator) get_2d_image_array() (organoid_tracker.core.image_loader.ImageLoader method) (organoid_tracker.core.image_loader.NullImageLoader method) (organoid_tracker.image_loading.array_image_loader.SingleImageLoader method) (organoid_tracker.image_loading.builtin_merging_image_loaders.ChannelAppendingImageLoader method) (organoid_tracker.image_loading.builtin_merging_image_loaders.ChannelSummingImageLoader method) (organoid_tracker.image_loading.builtin_merging_image_loaders.TimeAppendingImageLoader method) (organoid_tracker.image_loading.folder_image_loader.FolderImageLoader method) get_3d_image_array() (organoid_tracker.core.image_loader.ImageLoader method) (organoid_tracker.core.image_loader.NullImageLoader method) (organoid_tracker.image_loading.array_image_loader.SingleImageLoader method) (organoid_tracker.image_loading.builtin_merging_image_loaders.ChannelAppendingImageLoader method) (organoid_tracker.image_loading.builtin_merging_image_loaders.ChannelSummingImageLoader method) (organoid_tracker.image_loading.builtin_merging_image_loaders.TimeAppendingImageLoader method) (organoid_tracker.image_loading.folder_image_loader.FolderImageLoader method) get_active_experiments() (organoid_tracker.gui.gui_experiment.GuiExperiment method) get_active_tabs() (organoid_tracker.gui.gui_experiment.GuiExperiment method) get_age() (in module organoid_tracker.linking_analysis.particle_age_finder) (organoid_tracker.core.links.LinkingTrack method) get_age_at_end_of_track() (in module organoid_tracker.linking_analysis.particle_age_finder) get_age_at_end_of_track_h() (in module organoid_tracker.linking_analysis.particle_age_finder) get_all_data() (organoid_tracker.core.global_data.GlobalData method) get_all_tabs() (organoid_tracker.gui.gui_experiment.GuiExperiment method) get_beacon_type() (organoid_tracker.core.beacon_collection.BeaconCollection method) get_categories() (organoid_tracker.comparison.report.ComparisonReport method) get_category_by_name() (organoid_tracker.comparison.report.ComparisonReport method) get_channel_count() (organoid_tracker.core.image_loader.ImageLoader method) (organoid_tracker.core.image_loader.NullImageLoader method) (organoid_tracker.image_loading.array_image_loader.SingleImageLoader method) (organoid_tracker.image_loading.builtin_merging_image_loaders.ChannelAppendingImageLoader method) (organoid_tracker.image_loading.builtin_merging_image_loaders.ChannelSummingImageLoader method) (organoid_tracker.image_loading.builtin_merging_image_loaders.TimeAppendingImageLoader method) (organoid_tracker.image_loading.folder_image_loader.FolderImageLoader method) get_channel_description() (organoid_tracker.core.images.Images method) get_channels() (organoid_tracker.core.image_loader.ImageLoader method) (organoid_tracker.core.images.Images method) get_color() (in module organoid_tracker.linking_analysis.lineage_markers) get_colormap() (in module organoid_tracker.core.image_coloring) get_commands() (organoid_tracker.plugin.instance.Plugin method) get_connection_data() (organoid_tracker.core.connections.Connections method) get_cumulative_timings_array_m() (organoid_tracker.core.resolution.ImageTimings method) get_data() (organoid_tracker.core.global_data.GlobalData method) get_data_names_and_types() (organoid_tracker.core.position_collection.PositionCollection method) (organoid_tracker.core.position_data.PositionData method) get_density_mm1() (in module organoid_tracker.position_analysis.cell_density_calculator) get_direction_marker() (organoid_tracker.core.spline.Spline method) get_display_name() (organoid_tracker.linking_analysis.errors.Error method) (organoid_tracker.linking_analysis.linking_markers.EndMarker method) (organoid_tracker.linking_analysis.linking_markers.StartMarker method) get_division_count_in_lineage() (in module organoid_tracker.linking_analysis.lineage_division_counter) get_duration_in_time_points() (organoid_tracker.core.links.LinkingTrack method) get_entries() (organoid_tracker.comparison.report.ComparisonReport method) get_error_marker() (in module organoid_tracker.linking_analysis.linking_markers) get_experiment() (organoid_tracker.gui.gui_experiment.GuiExperiment method) get_fate() (in module organoid_tracker.linking_analysis.cell_fate_finder) get_fate_ext() (in module organoid_tracker.linking_analysis.cell_fate_finder) get_file_loaders() (organoid_tracker.plugin.instance.Plugin method) get_file_patterns() (organoid_tracker.imaging.file_loader.FileLoader method) get_flow_to_next() (in module organoid_tracker.linking_analysis.particle_flow_calculator) get_flow_to_previous() (in module organoid_tracker.linking_analysis.particle_flow_calculator) get_flows_and_energies() (in module organoid_tracker.local_marginalization.local_marginalization_functions) get_highest_track_id() (organoid_tracker.core.links.Links method) get_image() (organoid_tracker.core.images.Images method) get_image_offset() (organoid_tracker.neural_network.position_detection_cnn.training_data_creator.ImageWithPositions method) get_image_size_zyx() (organoid_tracker.core.image_loader.ImageLoader method) (organoid_tracker.core.image_loader.NullImageLoader method) (organoid_tracker.image_loading.array_image_loader.SingleImageLoader method) (organoid_tracker.image_loading.builtin_merging_image_loaders.ChannelAppendingImageLoader method) (organoid_tracker.image_loading.builtin_merging_image_loaders.ChannelSummingImageLoader method) (organoid_tracker.image_loading.builtin_merging_image_loaders.TimeAppendingImageLoader method) (organoid_tracker.image_loading.folder_image_loader.FolderImageLoader method) (organoid_tracker.neural_network.position_detection_cnn.training_data_creator.ImageWithPositions method) get_image_slice_2d() (organoid_tracker.core.images.Image method) (organoid_tracker.core.images.Images method) get_image_stack() (organoid_tracker.core.experiment.Experiment method) (organoid_tracker.core.images.Images method) get_intensity_gradient() (in module organoid_tracker.position_analysis.intensity_gradient_calculator) get_intensity_keys() (in module organoid_tracker.position_analysis.intensity_calculator) get_interpolation_2d() (organoid_tracker.core.spline.Spline method) get_interpolation_3d() (organoid_tracker.core.spline.Spline method) get_lineage_data() (organoid_tracker.core.links.Links method) get_lineage_fate() (in module organoid_tracker.linking_analysis.lineage_fate_finder) get_lineage_id() (in module organoid_tracker.linking_analysis.lineage_id_creator) get_link_data() (organoid_tracker.core.link_data.LinkData method) (organoid_tracker.core.links.Links method) get_location_counts() (organoid_tracker.image_loading.nd2file_image_loader.Nd2File method) get_marker_by_save_name() (organoid_tracker.gui.gui_experiment.GuiExperiment method) (organoid_tracker.plugin.registry.Registry method) get_marker_name() (organoid_tracker.core.spline.SplineCollection method) get_marker_names() (organoid_tracker.core.spline.SplineCollection method)

get_markers() (organoid_tracker.plugin.instance.Plugin method) get_mask_array() (organoid_tracker.core.mask.Mask method) get_mean_at() (organoid_tracker.util.moving_average.MovingAverage method) get_menu_items() (organoid_tracker.plugin.instance.Plugin method) get_message() (organoid_tracker.linking_analysis.errors.Error method) get_min_division_count_in_lineage() (in module organoid_tracker.linking_analysis.lineage_division_counter) get_mother_score() (in module organoid_tracker.linking_analysis.linking_markers) get_name() (organoid_tracker.core.image_filters.ImageFilter method) (organoid_tracker.core.Name method) (organoid_tracker.image_loading.builtin_image_filters.GaussianBlurFilter method) (organoid_tracker.image_loading.builtin_image_filters.InterpolatedMinMaxFilter method) (organoid_tracker.image_loading.builtin_image_filters.MultiplyPixelsFilter method) (organoid_tracker.image_loading.builtin_image_filters.ThresholdFilter method) (organoid_tracker.imaging.file_loader.FileLoader method) get_nearby() (organoid_tracker.gui.location_map.LocationMap method) get_next_division() (in module organoid_tracker.linking.cell_division_finder) get_next_time_point() (organoid_tracker.core.experiment.Experiment method) get_next_tracks() (organoid_tracker.core.links.LinkingTrack method) get_normalized_intensity() (in module organoid_tracker.position_analysis.intensity_calculator) (in module organoid_tracker.position_analysis.position_markers) get_normalized_intensity_over_time() (in module organoid_tracker.position_analysis.intensity_calculator) get_number_of_cells_at_end() (in module organoid_tracker.linking_analysis.lineage_division_counter) get_offset() (organoid_tracker.core.spline.Spline method) get_open_tab() (organoid_tracker.gui.gui_experiment.GuiExperiment method) get_or_default() (organoid_tracker.config.ConfigFile method) get_or_prompt() (organoid_tracker.config.ConfigFile method) get_original_track_id() (in module organoid_tracker.linking_analysis.lineage_id_creator) get_plugin_count() (organoid_tracker.plugin.plugin_manager.PluginManager method) get_plugins() (organoid_tracker.plugin.plugin_manager.PluginManager method) get_point_exact() (organoid_tracker.image_loading.builtin_image_filters.InterpolatedMinMaxFilter method) get_points_2d() (organoid_tracker.core.spline.Spline method) get_points_3d() (organoid_tracker.core.spline.Spline method) get_pos() (organoid_tracker.guizela_tracker_compatibility.track_lib.Track method) (organoid_tracker.guizela_tracker_compatibility.track_lib_v2.Track method) (organoid_tracker.guizela_tracker_compatibility.track_lib_v3.Track method) (organoid_tracker.guizela_tracker_compatibility.track_lib_v4.Track method) get_position_at_time_point() (organoid_tracker.core.links.Links method) get_position_data() (organoid_tracker.core.position_collection.PositionCollection method) (organoid_tracker.core.position_data.PositionData method) get_position_flags() (in module organoid_tracker.position_analysis.position_markers) get_position_near_time_point() (organoid_tracker.core.links.Links method) get_position_type() (in module organoid_tracker.linking_analysis.linking_markers) (in module organoid_tracker.position_analysis.position_markers) get_position_types() (in module organoid_tracker.position_analysis.position_markers) get_positions() (organoid_tracker.comparison.report.ComparisonReport method) get_positions_of_type() (in module organoid_tracker.position_analysis.position_markers) get_previous_division() (in module organoid_tracker.linking.cell_division_finder) get_previous_time_point() (organoid_tracker.core.experiment.Experiment method) get_previous_tracks() (organoid_tracker.core.links.LinkingTrack method) get_problematic_lineages() (in module organoid_tracker.linking_analysis.lineage_error_finder) get_production() (organoid_tracker.position_analysis.intensity_calculator.IntensityOverTime method) get_raw_intensity() (in module organoid_tracker.position_analysis.intensity_calculator) (in module organoid_tracker.position_analysis.position_markers) get_registered_file_loaders() (organoid_tracker.plugin.registry.Registry method) get_registered_markers() (organoid_tracker.gui.gui_experiment.GuiExperiment method) (organoid_tracker.plugin.registry.Registry method) get_registry() (organoid_tracker.plugin.plugin_manager.PluginManager method) get_root_folder() (organoid_tracker.text_popup.help_popup.HelpPopup method) (organoid_tracker.text_popup.text_popup.RichTextPopup method) get_save_name() (organoid_tracker.core.Name method) get_segmentation_colormap() (in module organoid_tracker.core.image_coloring) get_selectable_experiments() (organoid_tracker.gui.gui_experiment.GuiExperiment method) get_series_display_names() (in module organoid_tracker.image_loading.liffile_image_loader) get_severity() (organoid_tracker.linking_analysis.errors.Error method) get_size_zyx() (organoid_tracker.core.bounding_box.BoundingBox method) get_spline() (organoid_tracker.core.spline.SplineCollection method) get_time_h_since_start() (organoid_tracker.core.resolution.ImageTimings method) get_time_m_since_previous() (organoid_tracker.core.resolution.ImageTimings method) get_time_m_since_start() (organoid_tracker.core.resolution.ImageTimings method) get_time_point() (organoid_tracker.core.experiment.Experiment method) get_title() (organoid_tracker.text_popup.help_popup.HelpPopup method) (organoid_tracker.text_popup.text_popup.RichTextPopup method) get_track() (organoid_tracker.core.links.Links method) get_track_by_id() (organoid_tracker.core.links.Links method) get_track_end_marker() (in module organoid_tracker.linking_analysis.linking_markers) get_track_id() (organoid_tracker.core.links.Links method) get_track_start_marker() (in module organoid_tracker.linking_analysis.linking_markers) get_type() (organoid_tracker.imaging.file_loader.FileLoader method) get_undo_redo() (organoid_tracker.gui.gui_experiment.GuiExperiment method) get_unmerged_image_loader() (organoid_tracker.image_loading.builtin_merging_image_loaders.ChannelSummingImageLoader method) get_user_folders() (organoid_tracker.plugin.plugin_manager.PluginManager method) get_x_positions_and_means() (organoid_tracker.util.moving_average.LinesAverage method) (organoid_tracker.util.moving_average.MovingAverage method) (organoid_tracker.util.moving_average.PlotAverage method) get_z() (organoid_tracker.core.spline.Spline method) global_data (organoid_tracker.core.experiment.Experiment property) GlobalData (class in organoid_tracker.core.global_data) GOES_INTO_VIEW (organoid_tracker.linking_analysis.linking_markers.StartMarker attribute) goto_position() (organoid_tracker.gui.gui_experiment.GuiExperiment method) green (organoid_tracker.core.Color property) GuiExperiment (class in organoid_tracker.gui.gui_experiment)

H

has_beacons() (organoid_tracker.core.beacon_collection.BeaconCollection method) has_connections() (organoid_tracker.core.connections.Connections method) has_filters() (organoid_tracker.core.image_filters.ImageFilters method) has_full_neighbors() (organoid_tracker.core.connections.Connections method) has_global_data() (organoid_tracker.core.global_data.GlobalData method) has_images() (organoid_tracker.core.image_loader.ImageLoader method) has_link_data() (organoid_tracker.core.link_data.LinkData method) (organoid_tracker.core.links.Links method) has_links() (organoid_tracker.core.links.Links method) has_mother_scores() (in module organoid_tracker.linking_analysis.linking_markers) has_name() (organoid_tracker.core.Name method) has_neighbor_that() (in module organoid_tracker.connection_analysis.connected_position_finder)

has_position_data() (organoid_tracker.core.position_collection.PositionCollection method) (organoid_tracker.core.position_data.PositionData method) has_position_data_with_name() (organoid_tracker.core.position_collection.PositionCollection method) (organoid_tracker.core.position_data.PositionData method) has_positions() (organoid_tracker.core.position_collection.PositionCollection method) has_shapes() (in module organoid_tracker.linking_analysis.linking_markers) has_splines() (organoid_tracker.core.spline.SplineCollection method) has_timings() (organoid_tracker.core.images.Images method) has_unsaved_changes() (organoid_tracker.gui.undo_redo.UndoRedo method) has_zero_volume() (organoid_tracker.core.mask.Mask method) HelpPopup (class in organoid_tracker.text_popup.help_popup) highest_z() (organoid_tracker.core.position_collection.PositionCollection method)

I

Image (class in organoid_tracker.core.images) IMAGE (organoid_tracker.imaging.file_loader.FileLoaderType attribute) image_loader() (organoid_tracker.core.images.Images method) image_to_8bit() (in module organoid_tracker.util.bits) ImageChannel (class in organoid_tracker.core.image_loader) ImageFilter (class in organoid_tracker.core.image_filters) ImageFilters (class in organoid_tracker.core.image_filters) ImageLoader (class in organoid_tracker.core.image_loader) ImageOffsets (class in organoid_tracker.core.images) ImageResolution (class in organoid_tracker.core.resolution) Images (class in organoid_tracker.core.images) images (organoid_tracker.core.experiment.Experiment property) ImageTimings (class in organoid_tracker.core.resolution) ImageWithPositions (class in organoid_tracker.neural_network.position_detection_cnn.training_data_creator) INDEX (organoid_tracker.text_popup.text_popup.RichTextPopup attribute) index_one (organoid_tracker.core.image_loader.ImageChannel property) index_zero (organoid_tracker.core.image_loader.ImageChannel attribute) inside_image() (in module organoid_tracker.neural_network.division_detection_cnn.training_data_creator) IntensityOverTime (class in organoid_tracker.position_analysis.intensity_calculator) IntensityPoint (class in organoid_tracker.image_loading.builtin_image_filters) interpolate() (organoid_tracker.core.position.Position method) (organoid_tracker.guizela_tracker_compatibility.axis_lib_v2.Axis method)

interpolate_point() (organoid_tracker.image_loading.builtin_image_filters.InterpolatedMinMaxFilter method) interpolated (organoid_tracker.guizela_tracker_compatibility.axis_lib_v2.Axis attribute) InterpolatedMinMaxFilter (class in organoid_tracker.image_loading.builtin_image_filters) inverse (organoid_tracker.gui.undo_redo.ReversedAction attribute) is_automatic() (organoid_tracker.core.Name method) is_axis() (organoid_tracker.core.spline.SplineCollection method) is_black() (organoid_tracker.core.Color method) is_connected() (organoid_tracker.core.connections.Connections method) is_error_suppressed() (in module organoid_tracker.linking_analysis.linking_markers) is_incomplete() (organoid_tracker.core.resolution.ImageResolution method) is_inside_image() (organoid_tracker.core.images.Images method) is_live() (in module organoid_tracker.linking_analysis.linking_markers) is_none() (organoid_tracker.util.xml_wrapper.XmlWrapper method) is_selected() (organoid_tracker.gui.gui_experiment.GuiExperiment method) is_shed() (organoid_tracker.linking_analysis.linking_markers.EndMarker static method) is_simple_multiplication() (organoid_tracker.core.resolution.ImageTimings method) is_time_point_number_in_range() (organoid_tracker.core.links.LinkingTrack method) is_uncertain() (in module organoid_tracker.linking_analysis.linking_markers) is_zero() (organoid_tracker.core.position.Position method) items() (organoid_tracker.core.image_filters.ImageFilters method) iterate_to_future() (organoid_tracker.core.links.Links method) iterate_to_past() (organoid_tracker.core.links.Links method)

J

JUST_MOVING (organoid_tracker.linking_analysis.cell_fate_finder.CellFateType attribute)

just_position() (organoid_tracker.core.full_position_snapshot.FullPositionSnapshot static method)

K

KNOWN_EVENTS (organoid_tracker.gui.gui_experiment.GuiExperiment attribute)

L

last_save_file (organoid_tracker.core.experiment.Experiment attribute) last_time_point() (organoid_tracker.core.experiment.Experiment method) (organoid_tracker.core.image_loader.ImageLoader method) (organoid_tracker.core.images.Images method) (organoid_tracker.core.links.LinkingTrack method) (organoid_tracker.core.position_collection.PositionCollection method) (organoid_tracker.core.position_data.PositionData method) (organoid_tracker.core.spline.SplineCollection method) last_time_point_number() (organoid_tracker.comparison.report.ComparisonReport method) (organoid_tracker.core.experiment.Experiment method) (organoid_tracker.core.image_loader.ImageLoader method) (organoid_tracker.core.image_loader.NullImageLoader method) (organoid_tracker.core.images.Images method) (organoid_tracker.core.links.LinkingTrack method) (organoid_tracker.core.position_collection.PositionCollection method) (organoid_tracker.core.position_data.PositionData method) (organoid_tracker.core.spline.SplineCollection method) (organoid_tracker.image_loading.array_image_loader.SingleImageLoader method) (organoid_tracker.image_loading.builtin_merging_image_loaders.ChannelAppendingImageLoader method) (organoid_tracker.image_loading.builtin_merging_image_loaders.ChannelSummingImageLoader method) (organoid_tracker.image_loading.builtin_merging_image_loaders.TimeAppendingImageLoader method) (organoid_tracker.image_loading.folder_image_loader.FolderImageLoader method) latitude_degrees() (organoid_tracker.coordinate_system.spherical_coordinates.SphericalCoordinate method) length() (organoid_tracker.core.spline.Spline method) (organoid_tracker.core.vector.Vector2 method) (organoid_tracker.core.vector.Vector3 method) limit_to_time() (organoid_tracker.core.resolution.ImageTimings method) limit_x (organoid_tracker.core.images.Image property) limit_y (organoid_tracker.core.images.Image property) limit_z (organoid_tracker.core.images.Image property) Line3 (class in organoid_tracker.imaging.lines) line_infinite() (in module organoid_tracker.util.mpl_helper) LineageDrawing (class in organoid_tracker.linking_analysis.lineage_drawing) LineageFate (class in organoid_tracker.linking_analysis.lineage_fate_finder) LineageWithErrors (class in organoid_tracker.linking_analysis.lineage_error_finder) LinesAverage (class in organoid_tracker.util.moving_average) link_data (organoid_tracker.core.experiment.Experiment property)

LinkData (class in organoid_tracker.core.link_data) LinkingTrack (class in organoid_tracker.core.links) Links (class in organoid_tracker.core.links) links (organoid_tracker.core.experiment.Experiment property) (organoid_tracker.core.full_position_snapshot.FullPositionSnapshot attribute) LinksReport (class in organoid_tracker.comparison.links_comparison) load_axes_list() (in module organoid_tracker.guizela_tracker_compatibility.axis_lib_v2) load_data_file() (in module organoid_tracker.imaging.ctc_io) (in module organoid_tracker.imaging.io) (in module organoid_tracker.imaging.trackmate_io) load_experiment_list_file() (in module organoid_tracker.imaging.list_io) load_file_interactive() (organoid_tracker.imaging.file_loader.FileLoader method) load_folder() (organoid_tracker.plugin.plugin_manager.PluginManager method) load_from_lif_file() (in module organoid_tracker.image_loading.liffile_image_loader) load_from_lif_reader() (in module organoid_tracker.image_loading.liffile_image_loader) load_from_tif_file() (in module organoid_tracker.image_loading.merged_tiff_image_loader) load_image() (organoid_tracker.neural_network.position_detection_cnn.training_data_creator.ImageWithPositions method) load_image_series() (in module organoid_tracker.image_loading.nd2file_image_loader) load_image_series_from_config() (in module organoid_tracker.image_loading.nd2file_image_loader) load_image_time_stack() (organoid_tracker.neural_network.position_detection_cnn.training_data_creator.ImageWithPositions method) load_images() (in module organoid_tracker.image_loading.general_image_loader) (in module organoid_tracker.neural_network.position_detection_cnn.image_with_positions_to_tensor_loader) load_images_from_dictionary() (in module organoid_tracker.image_loading.general_image_loader) load_images_from_folder() (in module organoid_tracker.image_loading.folder_image_loader) load_images_with_divisions() (in module organoid_tracker.neural_network.division_detection_cnn.image_with_divisions_to_tensor_loader) load_images_with_positions() (in module organoid_tracker.neural_network.division_detection_cnn.image_with_divisions_to_tensor_loader) (in module organoid_tracker.neural_network.position_detection_cnn.image_with_positions_to_tensor_loader) load_plugin() (in module organoid_tracker.plugin.plugin_loader) load_positions_and_shapes_from_json() (in module organoid_tracker.imaging.io) load_report() (in module organoid_tracker.comparison.report_json_io) load_track_list() (in module organoid_tracker.guizela_tracker_compatibility.track_lib) LoadInto (class in organoid_tracker.imaging.file_loader) local_marginalization() (in module organoid_tracker.local_marginalization.local_marginalization_functions) LocationMap (class in organoid_tracker.gui.location_map) longitude_degrees() (organoid_tracker.coordinate_system.spherical_coordinates.SphericalCoordinate method) LOW_DIVISION_SCORE (organoid_tracker.linking_analysis.errors.Error attribute) LOW_LINK_SCORE (organoid_tracker.linking_analysis.errors.Error attribute) lowest_z() (organoid_tracker.core.position_collection.PositionCollection method)

M

made_value_changes (organoid_tracker.config.ConfigFile attribute) make_nearby_positions_graph() (in module organoid_tracker.linking.nearby_position_finder) marginalization() (in module organoid_tracker.local_marginalization.local_marginalization_functions) mark_everything_saved() (organoid_tracker.gui.undo_redo.UndoRedo method) mark_unsaved_changes() (organoid_tracker.gui.undo_redo.UndoRedo method) Marker (class in organoid_tracker.core.marker) Mask (class in organoid_tracker.core.mask) max() (organoid_tracker.core.images.Image method) max_distance_moved_um_per_min (organoid_tracker.core.warning_limits.WarningLimits attribute) max_none() (in module organoid_tracker.core) max_time_point (organoid_tracker.core.warning_limits.WarningLimits attribute) max_time_point_number() (organoid_tracker.core.links.LinkingTrack method) (organoid_tracker.core.resolution.ImageTimings method) max_x (organoid_tracker.core.bounding_box.BoundingBox attribute) max_y (organoid_tracker.core.bounding_box.BoundingBox attribute) max_z (organoid_tracker.core.bounding_box.BoundingBox attribute) mean (organoid_tracker.position_analysis.intensity_calculator.IntensityOverTime property) mean_stderr (organoid_tracker.position_analysis.intensity_calculator.IntensityOverTime property) mean_values (organoid_tracker.util.moving_average.MovingAverage attribute) merge() (organoid_tracker.core.experiment.Experiment method) merge_data() (organoid_tracker.core.global_data.GlobalData method) (organoid_tracker.core.links.Links method) (organoid_tracker.core.position_collection.PositionCollection method) (organoid_tracker.core.position_data.PositionData method) merge_link_meta_data() (organoid_tracker.core.links.Links method) min_marginal_probability (organoid_tracker.core.warning_limits.WarningLimits attribute) min_none() (in module organoid_tracker.core) min_probability (organoid_tracker.core.warning_limits.WarningLimits attribute) min_time_between_divisions_h (organoid_tracker.core.warning_limits.WarningLimits attribute) min_time_point (organoid_tracker.core.warning_limits.WarningLimits attribute) min_time_point_number() (organoid_tracker.core.links.LinkingTrack method) (organoid_tracker.core.resolution.ImageTimings method) min_x (organoid_tracker.core.bounding_box.BoundingBox attribute) (organoid_tracker.core.images.Image property) min_y (organoid_tracker.core.bounding_box.BoundingBox attribute) (organoid_tracker.core.images.Image property) min_z (organoid_tracker.core.bounding_box.BoundingBox attribute) (organoid_tracker.core.images.Image property) minimal_marginalization() (in module organoid_tracker.local_marginalization.local_marginalization_functions) mirrored() (in module organoid_tracker.imaging.angles) MISSED_DIVISION (organoid_tracker.linking_analysis.errors.Error attribute) module organoid_tracker organoid_tracker.comparison organoid_tracker.comparison.lineage_comparison organoid_tracker.comparison.links_comparison organoid_tracker.comparison.positions_comparison organoid_tracker.comparison.report organoid_tracker.comparison.report_csv_io organoid_tracker.comparison.report_json_io organoid_tracker.config organoid_tracker.connecting organoid_tracker.connecting.connector_by_distance organoid_tracker.connecting.connector_using_angles organoid_tracker.connection_analysis organoid_tracker.connection_analysis.cluster_finder organoid_tracker.connection_analysis.connected_position_finder organoid_tracker.coordinate_system organoid_tracker.coordinate_system.orientation_spline_adder organoid_tracker.coordinate_system.sphere_representer organoid_tracker.coordinate_system.spherical_coordinates organoid_tracker.core organoid_tracker.core.beacon_collection organoid_tracker.core.bounding_box organoid_tracker.core.concurrent organoid_tracker.core.connections organoid_tracker.core.experiment organoid_tracker.core.full_position_snapshot organoid_tracker.core.global_data organoid_tracker.core.image_coloring organoid_tracker.core.image_filters organoid_tracker.core.image_loader organoid_tracker.core.images organoid_tracker.core.link_data organoid_tracker.core.links organoid_tracker.core.marker organoid_tracker.core.mask organoid_tracker.core.position organoid_tracker.core.position_collection organoid_tracker.core.position_data organoid_tracker.core.resolution organoid_tracker.core.spline organoid_tracker.core.typing organoid_tracker.core.vector organoid_tracker.core.warning_limits organoid_tracker.gui organoid_tracker.gui.gui_experiment organoid_tracker.gui.location_map organoid_tracker.gui.progress_bar organoid_tracker.gui.undo_redo organoid_tracker.guizela_tracker_compatibility organoid_tracker.guizela_tracker_compatibility.axis_lib organoid_tracker.guizela_tracker_compatibility.axis_lib_v2 organoid_tracker.guizela_tracker_compatibility.cell_type_converter organoid_tracker.guizela_tracker_compatibility.guizela_data_exporter organoid_tracker.guizela_tracker_compatibility.guizela_data_importer organoid_tracker.guizela_tracker_compatibility.track_lib organoid_tracker.guizela_tracker_compatibility.track_lib_v2 organoid_tracker.guizela_tracker_compatibility.track_lib_v3 organoid_tracker.guizela_tracker_compatibility.track_lib_v4 organoid_tracker.image_loading organoid_tracker.image_loading.array_image_loader organoid_tracker.image_loading.builtin_image_filters organoid_tracker.image_loading.builtin_merging_image_loaders organoid_tracker.image_loading.folder_image_loader organoid_tracker.image_loading.general_image_loader organoid_tracker.image_loading.liffile_image_loader organoid_tracker.image_loading.merged_tiff_image_loader organoid_tracker.image_loading.nd2file_image_loader organoid_tracker.imaging organoid_tracker.imaging.angles organoid_tracker.imaging.cropper organoid_tracker.imaging.ctc_io organoid_tracker.imaging.depth_colored_image_creator organoid_tracker.imaging.file_loader organoid_tracker.imaging.image_adder organoid_tracker.imaging.image_file_name_pattern_finder organoid_tracker.imaging.io organoid_tracker.imaging.lines organoid_tracker.imaging.list_io organoid_tracker.imaging.trackmate_io organoid_tracker.linking organoid_tracker.linking.cell_division_finder organoid_tracker.linking.nearby_position_finder organoid_tracker.linking_analysis organoid_tracker.linking_analysis.cell_compartment_finder organoid_tracker.linking_analysis.cell_division_counter organoid_tracker.linking_analysis.cell_error_finder organoid_tracker.linking_analysis.cell_fate_finder organoid_tracker.linking_analysis.cell_nearby_death_counter organoid_tracker.linking_analysis.errors organoid_tracker.linking_analysis.lineage_division_counter organoid_tracker.linking_analysis.lineage_drawing organoid_tracker.linking_analysis.lineage_end_finder organoid_tracker.linking_analysis.lineage_error_finder organoid_tracker.linking_analysis.lineage_fate_finder organoid_tracker.linking_analysis.lineage_id_creator organoid_tracker.linking_analysis.lineage_markers organoid_tracker.linking_analysis.linking_markers organoid_tracker.linking_analysis.links_filter organoid_tracker.linking_analysis.links_postprocessor organoid_tracker.linking_analysis.particle_age_finder organoid_tracker.linking_analysis.particle_flow_calculator organoid_tracker.linking_analysis.particle_movement_finder organoid_tracker.linking_analysis.particle_rotation_calculator organoid_tracker.linking_analysis.position_connection_finder organoid_tracker.linking_analysis.track_positions_finder organoid_tracker.local_marginalization organoid_tracker.local_marginalization.local_marginalization_functions organoid_tracker.local_marginalization.tree_drawing organoid_tracker.neural_network organoid_tracker.neural_network.division_detection_cnn organoid_tracker.neural_network.division_detection_cnn.image_with_divisions_to_tensor_loader organoid_tracker.neural_network.division_detection_cnn.training_data_creator organoid_tracker.neural_network.link_detection_cnn organoid_tracker.neural_network.position_detection_cnn organoid_tracker.neural_network.position_detection_cnn.image_with_positions_to_tensor_loader organoid_tracker.neural_network.position_detection_cnn.peak_calling organoid_tracker.neural_network.position_detection_cnn.split_images organoid_tracker.neural_network.position_detection_cnn.training_data_creator organoid_tracker.plugin organoid_tracker.plugin.instance organoid_tracker.plugin.plugin_loader organoid_tracker.plugin.plugin_manager organoid_tracker.plugin.registry organoid_tracker.position_analysis organoid_tracker.position_analysis.cell_density_calculator organoid_tracker.position_analysis.intensity_calculator organoid_tracker.position_analysis.intensity_gradient_calculator organoid_tracker.position_analysis.position_markers organoid_tracker.position_detection organoid_tracker.position_detection.position_mover organoid_tracker.text_popup organoid_tracker.text_popup.help_popup organoid_tracker.text_popup.text_popup organoid_tracker.util organoid_tracker.util.bits organoid_tracker.util.moving_average organoid_tracker.util.mpl_helper organoid_tracker.util.mpl_helper_3d organoid_tracker.util.run_script_creator organoid_tracker.util.xml_wrapper

mother (organoid_tracker.linking.cell_division_finder.Family attribute) move() (organoid_tracker.core.beacon_collection.BeaconCollection method) move_in_time() (organoid_tracker.core.beacon_collection.BeaconCollection method) (organoid_tracker.core.connections.Connections method) (organoid_tracker.core.experiment.Experiment method) (organoid_tracker.core.images.ImageOffsets method) (organoid_tracker.core.images.Images method) (organoid_tracker.core.links.Links method) (organoid_tracker.core.position_collection.PositionCollection method) (organoid_tracker.core.position_data.PositionData method) (organoid_tracker.core.resolution.ImageTimings method) (organoid_tracker.core.spline.SplineCollection method) move_points() (organoid_tracker.core.spline.Spline method) move_position() (organoid_tracker.core.experiment.Experiment method) (organoid_tracker.core.position_collection.PositionCollection method) MOVED_TOO_FAST (organoid_tracker.linking_analysis.errors.Error attribute) MovingAverage (class in organoid_tracker.util.moving_average) mpl_color (organoid_tracker.core.marker.Marker property) multiply() (organoid_tracker.core.vector.Vector2 method) (organoid_tracker.core.vector.Vector3 method) (organoid_tracker.position_analysis.intensity_calculator.IntensityOverTime method) MultiplyPixelsFilter (class in organoid_tracker.image_loading.builtin_image_filters)

N

Name (class in organoid_tracker.core) name (organoid_tracker.comparison.report.Category property) (organoid_tracker.core.experiment.Experiment property) navigate() (organoid_tracker.text_popup.help_popup.HelpPopup method) (organoid_tracker.text_popup.text_popup.RichTextPopup method) Nd2File (class in organoid_tracker.image_loading.nd2file_image_loader) nearby_z() (organoid_tracker.core.position_collection.PositionCollection method) NearbyDeaths (class in organoid_tracker.linking_analysis.cell_nearby_death_counter) needs_saving (organoid_tracker.gui.undo_redo.UndoableAction attribute)

next_experiment() (organoid_tracker.imaging.file_loader.LoadInto method) NO_OP (organoid_tracker.gui.progress_bar.ProgressBar attribute) NO_PAST_POSITION (organoid_tracker.linking_analysis.errors.Error attribute) noise_limit (organoid_tracker.image_loading.builtin_image_filters.ThresholdFilter attribute) NON_DIVIDING (organoid_tracker.linking_analysis.cell_compartment_finder.CellCompartment attribute) normalized() (organoid_tracker.core.vector.Vector2 method) (organoid_tracker.core.vector.Vector3 method) NullImageLoader (class in organoid_tracker.core.image_loader) NumpyToJsonEncoder (class in organoid_tracker.imaging.io)

O

of_channel() (organoid_tracker.core.image_filters.ImageFilters method) of_time_point() (organoid_tracker.core.beacon_collection.BeaconCollection method) (organoid_tracker.core.connections.Connections method) (organoid_tracker.core.images.ImageOffsets method) (organoid_tracker.core.links.Links method) (organoid_tracker.core.position_collection.PositionCollection method) (organoid_tracker.core.spline.SplineCollection method) of_time_point_and_z() (organoid_tracker.core.position_collection.PositionCollection method) of_time_point_with_data() (organoid_tracker.core.connections.Connections method) of_time_point_with_type() (organoid_tracker.core.beacon_collection.BeaconCollection method) offset (organoid_tracker.core.images.Image property) offset_x (organoid_tracker.core.mask.Mask property) offset_y (organoid_tracker.core.mask.Mask property) offset_z (organoid_tracker.core.mask.Mask property) offsets (organoid_tracker.core.images.Images property) organoid_tracker module organoid_tracker.comparison module organoid_tracker.comparison.lineage_comparison module organoid_tracker.comparison.links_comparison module organoid_tracker.comparison.positions_comparison module organoid_tracker.comparison.report module organoid_tracker.comparison.report_csv_io module organoid_tracker.comparison.report_json_io module organoid_tracker.config module organoid_tracker.connecting module organoid_tracker.connecting.connector_by_distance module organoid_tracker.connecting.connector_using_angles module organoid_tracker.connection_analysis module organoid_tracker.connection_analysis.cluster_finder module organoid_tracker.connection_analysis.connected_position_finder module organoid_tracker.coordinate_system module organoid_tracker.coordinate_system.orientation_spline_adder module organoid_tracker.coordinate_system.sphere_representer module organoid_tracker.coordinate_system.spherical_coordinates module organoid_tracker.core module organoid_tracker.core.beacon_collection module organoid_tracker.core.bounding_box module organoid_tracker.core.concurrent module organoid_tracker.core.connections module organoid_tracker.core.experiment module organoid_tracker.core.full_position_snapshot module organoid_tracker.core.global_data module organoid_tracker.core.image_coloring module organoid_tracker.core.image_filters module organoid_tracker.core.image_loader module organoid_tracker.core.images module organoid_tracker.core.link_data module organoid_tracker.core.links module organoid_tracker.core.marker module organoid_tracker.core.mask module organoid_tracker.core.position module organoid_tracker.core.position_collection module organoid_tracker.core.position_data module organoid_tracker.core.resolution module organoid_tracker.core.spline module organoid_tracker.core.typing module organoid_tracker.core.vector module organoid_tracker.core.warning_limits module organoid_tracker.gui module organoid_tracker.gui.gui_experiment module organoid_tracker.gui.location_map module organoid_tracker.gui.progress_bar module organoid_tracker.gui.undo_redo module organoid_tracker.guizela_tracker_compatibility module organoid_tracker.guizela_tracker_compatibility.axis_lib module organoid_tracker.guizela_tracker_compatibility.axis_lib_v2 module organoid_tracker.guizela_tracker_compatibility.cell_type_converter module organoid_tracker.guizela_tracker_compatibility.guizela_data_exporter module organoid_tracker.guizela_tracker_compatibility.guizela_data_importer module organoid_tracker.guizela_tracker_compatibility.track_lib module organoid_tracker.guizela_tracker_compatibility.track_lib_v2 module organoid_tracker.guizela_tracker_compatibility.track_lib_v3 module organoid_tracker.guizela_tracker_compatibility.track_lib_v4 module organoid_tracker.image_loading module organoid_tracker.image_loading.array_image_loader module organoid_tracker.image_loading.builtin_image_filters module organoid_tracker.image_loading.builtin_merging_image_loaders module organoid_tracker.image_loading.folder_image_loader module organoid_tracker.image_loading.general_image_loader module organoid_tracker.image_loading.liffile_image_loader module organoid_tracker.image_loading.merged_tiff_image_loader module organoid_tracker.image_loading.nd2file_image_loader module

organoid_tracker.imaging module organoid_tracker.imaging.angles module organoid_tracker.imaging.cropper module organoid_tracker.imaging.ctc_io module organoid_tracker.imaging.depth_colored_image_creator module organoid_tracker.imaging.file_loader module organoid_tracker.imaging.image_adder module organoid_tracker.imaging.image_file_name_pattern_finder module organoid_tracker.imaging.io module organoid_tracker.imaging.lines module organoid_tracker.imaging.list_io module organoid_tracker.imaging.trackmate_io module organoid_tracker.linking module organoid_tracker.linking.cell_division_finder module organoid_tracker.linking.nearby_position_finder module organoid_tracker.linking_analysis module organoid_tracker.linking_analysis.cell_compartment_finder module organoid_tracker.linking_analysis.cell_division_counter module organoid_tracker.linking_analysis.cell_error_finder module organoid_tracker.linking_analysis.cell_fate_finder module organoid_tracker.linking_analysis.cell_nearby_death_counter module organoid_tracker.linking_analysis.errors module organoid_tracker.linking_analysis.lineage_division_counter module organoid_tracker.linking_analysis.lineage_drawing module organoid_tracker.linking_analysis.lineage_end_finder module organoid_tracker.linking_analysis.lineage_error_finder module organoid_tracker.linking_analysis.lineage_fate_finder module organoid_tracker.linking_analysis.lineage_id_creator module organoid_tracker.linking_analysis.lineage_markers module organoid_tracker.linking_analysis.linking_markers module organoid_tracker.linking_analysis.links_filter module organoid_tracker.linking_analysis.links_postprocessor module organoid_tracker.linking_analysis.particle_age_finder module organoid_tracker.linking_analysis.particle_flow_calculator module organoid_tracker.linking_analysis.particle_movement_finder module organoid_tracker.linking_analysis.particle_rotation_calculator module organoid_tracker.linking_analysis.position_connection_finder module organoid_tracker.linking_analysis.track_positions_finder module organoid_tracker.local_marginalization module organoid_tracker.local_marginalization.local_marginalization_functions module organoid_tracker.local_marginalization.tree_drawing module organoid_tracker.neural_network module organoid_tracker.neural_network.division_detection_cnn module organoid_tracker.neural_network.division_detection_cnn.image_with_divisions_to_tensor_loader module organoid_tracker.neural_network.division_detection_cnn.training_data_creator module organoid_tracker.neural_network.link_detection_cnn module organoid_tracker.neural_network.position_detection_cnn module organoid_tracker.neural_network.position_detection_cnn.image_with_positions_to_tensor_loader module organoid_tracker.neural_network.position_detection_cnn.peak_calling module organoid_tracker.neural_network.position_detection_cnn.split_images module organoid_tracker.neural_network.position_detection_cnn.training_data_creator module organoid_tracker.plugin module organoid_tracker.plugin.instance module organoid_tracker.plugin.plugin_loader module organoid_tracker.plugin.plugin_manager module organoid_tracker.plugin.registry module organoid_tracker.position_analysis module organoid_tracker.position_analysis.cell_density_calculator module organoid_tracker.position_analysis.intensity_calculator module organoid_tracker.position_analysis.intensity_gradient_calculator module organoid_tracker.position_analysis.position_markers module organoid_tracker.position_detection module organoid_tracker.position_detection.position_mover module organoid_tracker.text_popup module organoid_tracker.text_popup.help_popup module organoid_tracker.text_popup.text_popup module organoid_tracker.util module organoid_tracker.util.bits module organoid_tracker.util.moving_average module organoid_tracker.util.mpl_helper module organoid_tracker.util.mpl_helper_3d module organoid_tracker.util.run_script_creator module organoid_tracker.util.xml_wrapper module OUT_OF_VIEW (organoid_tracker.linking_analysis.linking_markers.EndMarker attribute) OutsideImageError

P

perform_intensity_normalization() (in module organoid_tracker.position_analysis.intensity_calculator) phi_degrees (organoid_tracker.coordinate_system.spherical_coordinates.SphericalCoordinate attribute) pinpoint_divisions() (in module organoid_tracker.linking_analysis.links_postprocessor) pixel_size_x_um (organoid_tracker.core.resolution.ImageResolution property) pixel_size_y_um (organoid_tracker.core.resolution.ImageResolution property) pixel_size_z_um (organoid_tracker.core.resolution.ImageResolution property) pixel_size_zyx_um (organoid_tracker.core.resolution.ImageResolution attribute) PIXELS (organoid_tracker.core.resolution.ImageResolution attribute) plot() (organoid_tracker.util.moving_average.LinesAverage method) (organoid_tracker.util.moving_average.MovingAverage method) (organoid_tracker.util.moving_average.PlotAverage method) plot_multicolor() (in module organoid_tracker.util.mpl_helper) PlotAverage (class in organoid_tracker.util.moving_average) Plugin (class in organoid_tracker.plugin.instance) PluginManager (class in organoid_tracker.plugin.plugin_manager) point (organoid_tracker.imaging.lines.Line3 attribute) point_on_line_2_nearest_to_line_1() (in module organoid_tracker.imaging.lines) points (organoid_tracker.image_loading.builtin_image_filters.InterpolatedMinMaxFilter attribute) pos (organoid_tracker.core.spline.SplinePosition attribute)

Position (class in organoid_tracker.core.position) position (organoid_tracker.core.beacon_collection.Beacon attribute) (organoid_tracker.core.full_position_snapshot.FullPositionSnapshot attribute) position_data (organoid_tracker.core.experiment.Experiment property) (organoid_tracker.core.full_position_snapshot.FullPositionSnapshot attribute) position_with_links() (organoid_tracker.core.full_position_snapshot.FullPositionSnapshot static method) PositionCollection (class in organoid_tracker.core.position_collection) PositionData (class in organoid_tracker.core.position_data) positions (organoid_tracker.connection_analysis.cluster_finder.Cluster attribute) (organoid_tracker.core.experiment.Experiment property) positions() (organoid_tracker.core.links.LinkingTrack method) postprocess() (in module organoid_tracker.linking_analysis.links_postprocessor) POTENTIALLY_NOT_A_MOTHER (organoid_tracker.linking_analysis.errors.Error attribute) POTENTIALLY_WRONG_DAUGHTERS (organoid_tracker.linking_analysis.errors.Error attribute) precision (organoid_tracker.comparison.report.Statistics attribute) precision_overall (organoid_tracker.comparison.report.Statistics attribute) prob_to_energy() (in module organoid_tracker.local_marginalization.local_marginalization_functions) program_closing() (organoid_tracker.gui.gui_experiment.GuiExperiment method) ProgressBar (class in organoid_tracker.gui.progress_bar) provide_automatic_name() (organoid_tracker.core.Name method)

R

radius_um (organoid_tracker.coordinate_system.spherical_coordinates.SphericalCoordinate attribute) range() (organoid_tracker.core.TimePoint static method) read_xml() (in module organoid_tracker.util.xml_wrapper) recall (organoid_tracker.comparison.report.Statistics attribute) recall_overall (organoid_tracker.comparison.report.Statistics attribute) reconstruct_volume() (in module organoid_tracker.neural_network.position_detection_cnn.peak_calling) reconstruction() (in module organoid_tracker.neural_network.position_detection_cnn.split_images) recorded_parameters() (organoid_tracker.comparison.report.ComparisonReport method) red (organoid_tracker.core.Color property) redo() (organoid_tracker.gui.undo_redo.UndoRedo method) redraw_data() (organoid_tracker.gui.gui_experiment.GuiExperiment method) redraw_image_and_data() (organoid_tracker.gui.gui_experiment.GuiExperiment method) reference_time_point() (organoid_tracker.core.spline.SplineCollection method) register_event_handler() (organoid_tracker.gui.gui_experiment.GuiExperiment method) Registry (class in organoid_tracker.plugin.registry) reload() (organoid_tracker.plugin.instance.Plugin method) reload_plugins() (organoid_tracker.plugin.plugin_manager.PluginManager method) remove() (organoid_tracker.core.beacon_collection.BeaconCollection method) (organoid_tracker.core.concurrent.ConcurrentSet method) remove_all_links() (organoid_tracker.core.links.Links method) remove_axis_from_axes_list() (in module organoid_tracker.guizela_tracker_compatibility.axis_lib_v2) remove_connection() (organoid_tracker.core.connections.Connections method)

remove_connections_of_position() (organoid_tracker.core.connections.Connections method) remove_error_marker() (in module organoid_tracker.linking_analysis.linking_markers) remove_experiment() (organoid_tracker.gui.gui_experiment.GuiExperiment method) remove_intensities() (in module organoid_tracker.position_analysis.intensity_calculator) remove_intensity_normalization() (in module organoid_tracker.position_analysis.intensity_calculator) remove_link() (organoid_tracker.core.links.Links method) remove_links_of_position() (organoid_tracker.core.links.Links method) remove_point() (organoid_tracker.core.spline.Spline method) remove_position() (organoid_tracker.core.experiment.Experiment method) remove_positions() (organoid_tracker.core.experiment.Experiment method) remove_spline() (organoid_tracker.core.spline.SplineCollection method) remove_tracks_too_deep() (in module organoid_tracker.linking_analysis.links_postprocessor) replace_link() (organoid_tracker.core.link_data.LinkData method) replace_position() (organoid_tracker.core.connections.Connections method) (organoid_tracker.core.links.Links method) replace_selected_experiment() (organoid_tracker.gui.gui_experiment.GuiExperiment method) resolution (organoid_tracker.core.beacon_collection.ClosestBeacon attribute) resolution() (organoid_tracker.core.images.Images method) restore() (organoid_tracker.core.full_position_snapshot.FullPositionSnapshot method) restore_axes_limits() (in module organoid_tracker.util.mpl_helper) ReversedAction (class in organoid_tracker.gui.undo_redo) RichTextPopup (class in organoid_tracker.text_popup.text_popup) right_hand_rule() (in module organoid_tracker.imaging.angles)

S

save() (organoid_tracker.config.ConfigFile method) save_3d_image_array() (organoid_tracker.core.image_loader.ImageLoader method) (organoid_tracker.core.images.Images method) (organoid_tracker.image_loading.builtin_merging_image_loaders.ChannelAppendingImageLoader method) (organoid_tracker.image_loading.builtin_merging_image_loaders.ChannelSummingImageLoader method) (organoid_tracker.image_loading.folder_image_loader.FolderImageLoader method) save_and_exit_if_changed() (organoid_tracker.config.ConfigFile method) save_axes_list() (in module organoid_tracker.guizela_tracker_compatibility.axis_lib_v2) save_data_files() (in module organoid_tracker.imaging.ctc_io) save_data_to_json() (in module organoid_tracker.imaging.io) save_experiment_list_file() (in module organoid_tracker.imaging.list_io) save_name (organoid_tracker.core.marker.Marker property) save_positions_to_json() (in module organoid_tracker.imaging.io) save_report() (in module organoid_tracker.comparison.report_json_io) save_report_time_statistics() (in module organoid_tracker.comparison.report_csv_io) save_track_list() (in module organoid_tracker.guizela_tracker_compatibility.track_lib) save_tracking_data() (in module organoid_tracker.imaging.trackmate_io) search_position (organoid_tracker.core.beacon_collection.ClosestBeacon attribute) select_experiment() (organoid_tracker.gui.gui_experiment.GuiExperiment method) serialize_to_config() (organoid_tracker.core.image_loader.ImageLoader method) (organoid_tracker.core.image_loader.NullImageLoader method) (organoid_tracker.image_loading.array_image_loader.SingleImageLoader method) (organoid_tracker.image_loading.builtin_merging_image_loaders.ChannelAppendingImageLoader method) (organoid_tracker.image_loading.builtin_merging_image_loaders.ChannelSummingImageLoader method) (organoid_tracker.image_loading.builtin_merging_image_loaders.TimeAppendingImageLoader method) (organoid_tracker.image_loading.folder_image_loader.FolderImageLoader method) serialize_to_dictionary() (organoid_tracker.core.image_loader.ImageLoader method) (organoid_tracker.image_loading.builtin_merging_image_loaders.ChannelAppendingImageLoader method) (organoid_tracker.image_loading.builtin_merging_image_loaders.ChannelSummingImageLoader method) (organoid_tracker.image_loading.builtin_merging_image_loaders.TimeAppendingImageLoader method) set() (organoid_tracker.config.ConfigFile method) (organoid_tracker.gui.location_map.LocationMap method) set_area() (organoid_tracker.gui.location_map.LocationMap method) set_beacon_type() (organoid_tracker.core.beacon_collection.BeaconCollection method) set_bounds() (organoid_tracker.core.mask.Mask method) set_bounds_around() (organoid_tracker.core.mask.Mask method) set_bounds_exact() (organoid_tracker.core.mask.Mask method) set_busy() (organoid_tracker.gui.progress_bar.ProgressBar method) set_channel_description() (organoid_tracker.core.images.Images method) set_color() (in module organoid_tracker.linking_analysis.lineage_markers) set_connection_data() (organoid_tracker.core.connections.Connections method) set_data() (organoid_tracker.core.global_data.GlobalData method) set_error() (organoid_tracker.gui.progress_bar.ProgressBar method) set_error_marker() (in module organoid_tracker.linking_analysis.linking_markers) set_lineage_data() (organoid_tracker.core.links.Links method) set_link_data() (organoid_tracker.core.link_data.LinkData method) (organoid_tracker.core.links.Links method) set_marker() (organoid_tracker.core.spline.SplineCollection method) set_marker_name() (organoid_tracker.core.spline.SplineCollection method) set_mother_score() (in module organoid_tracker.linking_analysis.linking_markers)

set_name() (organoid_tracker.core.Name method) set_offset() (organoid_tracker.core.spline.Spline method) set_pixel() (organoid_tracker.core.images.Image method) set_point() (organoid_tracker.image_loading.builtin_image_filters.InterpolatedMinMaxFilter method) set_position_data() (organoid_tracker.core.position_collection.PositionCollection method) (organoid_tracker.core.position_data.PositionData method) set_position_type() (in module organoid_tracker.position_analysis.position_markers) set_progress() (organoid_tracker.gui.progress_bar.ProgressBar method) set_raw_intensities() (in module organoid_tracker.position_analysis.intensity_calculator) (in module organoid_tracker.position_analysis.position_markers) set_resolution() (organoid_tracker.core.images.Images method) set_timings() (organoid_tracker.core.images.Images method) set_track_end_marker() (in module organoid_tracker.linking_analysis.linking_markers) set_track_start_marker() (in module organoid_tracker.linking_analysis.linking_markers) set_uncertain() (in module organoid_tracker.linking_analysis.linking_markers) setup_figure_2d() (in module organoid_tracker.coordinate_system.sphere_representer) setup_figure_3d() (in module organoid_tracker.coordinate_system.sphere_representer) Severity (class in organoid_tracker.linking_analysis.errors) shape_x (organoid_tracker.core.images.Image property) shape_y (organoid_tracker.core.images.Image property) shape_z (organoid_tracker.core.images.Image property) SHED (organoid_tracker.linking_analysis.linking_markers.EndMarker attribute) SHED_OUTSIDE (organoid_tracker.linking_analysis.linking_markers.EndMarker attribute) sheds (organoid_tracker.linking_analysis.lineage_fate_finder.LineageFate attribute) SHORT_CELL_CYCLE (organoid_tracker.linking_analysis.errors.Error attribute) SHRUNK_A_LOT (organoid_tracker.linking_analysis.errors.Error attribute) SingleGuiTab (class in organoid_tracker.gui.gui_experiment) SingleImageLoader (class in organoid_tracker.image_loading.array_image_loader) slope (organoid_tracker.position_analysis.intensity_calculator.IntensityOverTime property) slope_stderr (organoid_tracker.position_analysis.intensity_calculator.IntensityOverTime property) sort_tracks_by_x() (organoid_tracker.core.links.Links method) SphereRepresentation (class in organoid_tracker.coordinate_system.sphere_representer) SphericalCoordinate (class in organoid_tracker.coordinate_system.spherical_coordinates) Spline (class in organoid_tracker.core.spline) spline (organoid_tracker.core.spline.SplinePosition attribute) spline_id (organoid_tracker.core.spline.SplinePosition attribute) SplineCollection (class in organoid_tracker.core.spline) SplinePosition (class in organoid_tracker.core.spline) splines (organoid_tracker.core.experiment.Experiment attribute) stamp_image() (organoid_tracker.core.mask.Mask method) standard_deviation_values (organoid_tracker.util.moving_average.MovingAverage attribute) start (organoid_tracker.linking_analysis.lineage_error_finder.LineageWithErrors attribute) starting_tracks (organoid_tracker.linking_analysis.lineage_drawing.LineageDrawing attribute) StartMarker (class in organoid_tracker.linking_analysis.linking_markers) Statistics (class in organoid_tracker.comparison.report) STIMULATED_SHED (organoid_tracker.linking_analysis.linking_markers.EndMarker attribute) store_axes_limits() (in module organoid_tracker.util.mpl_helper) sum() (organoid_tracker.core.vector.Vector3 static method) summary (organoid_tracker.comparison.report.ComparisonReport attribute) suppress_error_marker() (in module organoid_tracker.linking_analysis.linking_markers)

T

t (organoid_tracker.guizela_tracker_compatibility.axis_lib_v2.Axis attribute) theta_degrees (organoid_tracker.coordinate_system.spherical_coordinates.SphericalCoordinate attribute) ThresholdFilter (class in organoid_tracker.image_loading.builtin_image_filters) time_point (organoid_tracker.core.spline.SplinePosition attribute) (organoid_tracker.image_loading.builtin_image_filters.IntensityPoint attribute) (organoid_tracker.neural_network.position_detection_cnn.training_data_creator.ImageWithPositions attribute) time_point() (organoid_tracker.core.position.Position method) time_point_interval_h (organoid_tracker.core.resolution.ImageResolution property) time_point_interval_m (organoid_tracker.core.resolution.ImageResolution attribute) time_point_number() (organoid_tracker.core.position.Position method) (organoid_tracker.core.TimePoint method) time_points() (organoid_tracker.comparison.report.ComparisonReport method) (organoid_tracker.core.beacon_collection.BeaconCollection method) (organoid_tracker.core.connections.Connections method) (organoid_tracker.core.experiment.Experiment method) (organoid_tracker.core.images.Images method) (organoid_tracker.core.position_collection.PositionCollection method) (organoid_tracker.core.spline.SplineCollection method) time_points_remaining (organoid_tracker.linking_analysis.cell_fate_finder.CellFate attribute) TimeAppendingImageLoader (class in organoid_tracker.image_loading.builtin_merging_image_loaders) TimePoint (class in organoid_tracker.core) timings() (organoid_tracker.core.images.Images method) title (organoid_tracker.comparison.report.ComparisonReport attribute) (organoid_tracker.core.UserError attribute)

to_cartesian() (organoid_tracker.coordinate_system.spherical_coordinates.SphericalCoordinate method) to_dict() (organoid_tracker.core.warning_limits.WarningLimits method) to_dict_key() (organoid_tracker.core.position.Position method) to_html_hex() (organoid_tracker.core.Color method) to_list() (organoid_tracker.core.images.ImageOffsets method) to_networkx_graph() (organoid_tracker.core.connections.Connections method) to_position_on_axis() (organoid_tracker.core.spline.Spline method) to_position_on_original_axis() (organoid_tracker.core.spline.SplineCollection method) to_position_on_spline() (organoid_tracker.core.spline.SplineCollection method) to_rgb() (organoid_tracker.core.Color method) to_rgb_floats() (organoid_tracker.core.Color method) to_rgba_floats() (organoid_tracker.core.Color method) to_vector3() (organoid_tracker.core.vector.Vector2 method) to_vector_um() (organoid_tracker.core.position.Position method) TOO_MANY_DAUGHTER_CELLS (organoid_tracker.linking_analysis.errors.Error attribute) Track (class in organoid_tracker.guizela_tracker_compatibility.track_lib) (class in organoid_tracker.guizela_tracker_compatibility.track_lib_v2) (class in organoid_tracker.guizela_tracker_compatibility.track_lib_v3) (class in organoid_tracker.guizela_tracker_compatibility.track_lib_v4) TRACK_END (organoid_tracker.linking_analysis.errors.Error attribute) TRACKING (organoid_tracker.imaging.file_loader.FileLoaderType attribute) tracks (organoid_tracker.linking_analysis.lineage_fate_finder.LineageFate attribute) translate() (organoid_tracker.imaging.lines.Line3 method) true_positives (organoid_tracker.comparison.report.Statistics attribute) type (organoid_tracker.linking_analysis.cell_fate_finder.CellFate attribute)

U

uncached() (organoid_tracker.core.image_loader.ImageLoader method) (organoid_tracker.image_loading.builtin_merging_image_loaders.ChannelAppendingImageLoader method) (organoid_tracker.image_loading.builtin_merging_image_loaders.TimeAppendingImageLoader method) UNCERTAIN_POSITION (organoid_tracker.linking_analysis.errors.Error attribute) undo() (organoid_tracker.gui.undo_redo.CombinedAction method) (organoid_tracker.gui.undo_redo.ReversedAction method) (organoid_tracker.gui.undo_redo.UndoableAction method) (organoid_tracker.gui.undo_redo.UndoRedo method) undo_redo (organoid_tracker.gui.gui_experiment.SingleGuiTab property) UndoableAction (class in organoid_tracker.gui.undo_redo) UndoRedo (class in organoid_tracker.gui.undo_redo)

UNKNOWN (organoid_tracker.linking_analysis.cell_compartment_finder.CellCompartment attribute) (organoid_tracker.linking_analysis.cell_fate_finder.CellFateType attribute) unregister_event_handlers() (organoid_tracker.gui.gui_experiment.GuiExperiment method) unregister_folder() (organoid_tracker.plugin.plugin_manager.PluginManager method) unsuppress_error_marker() (in module organoid_tracker.linking_analysis.linking_markers) UNSURE (organoid_tracker.linking_analysis.linking_markers.StartMarker attribute) update_for_changed_positions() (organoid_tracker.core.spline.SplineCollection method) update_offset() (organoid_tracker.core.images.ImageOffsets method) update_offset_for_positions() (organoid_tracker.core.spline.Spline method) update_positions_for_changed_offsets() (in module organoid_tracker.position_detection.position_mover) use_image_loader_from() (organoid_tracker.core.images.Images method) UserError

V

value_at() (organoid_tracker.core.images.Image method) value_float() (organoid_tracker.util.xml_wrapper.XmlWrapper method)

value_str() (organoid_tracker.util.xml_wrapper.XmlWrapper method) Vector2 (class in organoid_tracker.core.vector) Vector3 (class in organoid_tracker.core.vector)

W

WARNING (organoid_tracker.linking_analysis.errors.Severity attribute) warning_limits (organoid_tracker.core.experiment.Experiment property) WarningLimits (class in organoid_tracker.core.warning_limits) white() (organoid_tracker.core.Color static method) WILL_DIE (organoid_tracker.linking_analysis.cell_fate_finder.CellFateType attribute) WILL_DIVIDE (organoid_tracker.linking_analysis.cell_fate_finder.CellFateType attribute)

will_divide() (organoid_tracker.core.links.LinkingTrack method) WILL_SHED (organoid_tracker.linking_analysis.cell_fate_finder.CellFateType attribute) with_colormap() (organoid_tracker.core.images.ChannelDescription method) with_offset() (organoid_tracker.core.position.Position method) with_time_point() (organoid_tracker.core.position.Position method) with_time_point_number() (organoid_tracker.core.position.Position method)

X

x (organoid_tracker.core.position.Position attribute) (organoid_tracker.core.vector.Vector2 attribute) (organoid_tracker.core.vector.Vector3 attribute) (organoid_tracker.guizela_tracker_compatibility.axis_lib_v2.Axis attribute)

x_axis_numbers (organoid_tracker.comparison.report.Statistics attribute) x_label (organoid_tracker.comparison.report.Statistics attribute) x_values (organoid_tracker.util.moving_average.MovingAverage attribute) XmlWrapper (class in organoid_tracker.util.xml_wrapper) xyz_positions (organoid_tracker.neural_network.position_detection_cnn.training_data_creator.ImageWithPositions attribute)

Y

y (organoid_tracker.core.position.Position attribute) (organoid_tracker.core.vector.Vector2 attribute) (organoid_tracker.core.vector.Vector3 attribute)

Z

z (organoid_tracker.core.position.Position attribute) (organoid_tracker.core.vector.Vector3 attribute) (organoid_tracker.image_loading.builtin_image_filters.IntensityPoint attribute)

ZERO (organoid_tracker.core.vector.Vector2 attribute) (organoid_tracker.core.vector.Vector3 attribute) zeros_like() (organoid_tracker.core.images.Image static method)