OrganoidTracker
Tutorials
Manual tracking and error correction
Automatic tracking
Plugin tutorial
Training the neural network
Jupyter notebook
Working with custom metadata
Segmentation masks editor
For reference
API reference
Batch operations
Custom tracking formats
The data axes editor
Supported image formats
Installation instructions
The scripts
Supported tracking formats
Browse the code
organoid_tracker package
OrganoidTracker
»
Index
Index
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B
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C
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D
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E
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F
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G
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H
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I
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J
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K
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L
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M
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O
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P
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R
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S
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T
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U
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V
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W
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X
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Y
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Z
A
about_the_program() (in module organoid_tracker.gui.action)
AbstractEditor (class in organoid_tracker.visualizer.abstract_editor)
AbstractImageVisualizer (class in organoid_tracker.visualizer.abstract_image_visualizer)
activate() (in module organoid_tracker.visualizer)
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.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_data.PositionData method)
add_spline() (organoid_tracker.core.spline.SplineCollection method)
add_task() (organoid_tracker.gui.threading.Scheduler 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)
addItem() (organoid_tracker.gui.option_choose_dialog.MultipleComboBox method)
addItems() (organoid_tracker.gui.option_choose_dialog.MultipleComboBox method)
all_splines() (organoid_tracker.core.spline.SplineCollection method)
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)
ask_exit() (in module organoid_tracker.gui.action)
ask_save_unsaved_changes() (in module organoid_tracker.gui.action)
attach() (organoid_tracker.visualizer.Visualizer method)
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_index (organoid_tracker.core.beacon_collection.ClosestBeacon attribute)
beacon_position (organoid_tracker.core.beacon_collection.ClosestBeacon attribute)
BeaconCollection (class in organoid_tracker.core.beacon_collection)
BeaconEditor (class in organoid_tracker.visualizer.beacon_editor)
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)
button_home() (organoid_tracker.gui.toolbar.Toolbar method)
button_load_image() (organoid_tracker.gui.toolbar.Toolbar method)
button_load_tracking() (organoid_tracker.gui.toolbar.Toolbar method)
button_save_tracking() (organoid_tracker.gui.toolbar.Toolbar method)
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)
CANCEL (organoid_tracker.gui.dialog.DefaultOption attribute)
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)
CellCompartmentVisualizer (class in organoid_tracker.visualizer.cell_compartment_visualizer)
CellDensityVisualizer (class in organoid_tracker.visualizer.cell_density_visualizer)
CellDivisionVisualizer (class in organoid_tracker.visualizer.cell_division_visualizer)
CellFate (class in organoid_tracker.linking_analysis.cell_fate_finder)
CellFateType (class in organoid_tracker.linking_analysis.cell_fate_finder)
CellFateVisualizer (class in organoid_tracker.visualizer.cell_fate_visualizer)
CellMovementVisualizer (class in organoid_tracker.visualizer.cell_movement_visualizer)
CellSegmentationEditor (class in organoid_tracker.visualizer.cell_segmentation_editor)
CellTrackEndVisualizer (class in organoid_tracker.visualizer.cell_death_visualizer)
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)
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_experiment() (in module organoid_tracker.gui.action)
close_handler() (organoid_tracker.gui.toolbar.Toolbar 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() (organoid_tracker.gui.threading.Task method)
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() (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.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_experiment() (organoid_tracker.gui.worker_job.WorkerJob method)
copy_selected() (organoid_tracker.core.experiment.Experiment method)
corners_split() (in module organoid_tracker.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_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.position_detection_cnn.training_data_creator)
create_image_with_divisions_list() (in module organoid_tracker.division_detection_cnn.training_data_creator)
create_image_with_links_list() (in module organoid_tracker.link_detection_cnn.training_data_creator)
create_image_with_positions_list() (in module organoid_tracker.division_detection_cnn.training_data_creator)
(in module organoid_tracker.position_detection_cnn.training_data_creator)
create_image_with_possible_links_list() (in module organoid_tracker.link_detection_cnn.training_data_creator)
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.position_detection_cnn.peak_calling)
create_run_script() (in module organoid_tracker.util.run_script_creator)
create_time_point_dict() (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)
currentData() (organoid_tracker.gui.option_choose_dialog.MultipleComboBox method)
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_SIZE (organoid_tracker.visualizer.abstract_image_visualizer.AbstractImageVisualizer attribute)
DefaultOption (class in organoid_tracker.gui.dialog)
delete_data() (organoid_tracker.comparison.report.ComparisonReport method)
delete_data_with_name() (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() (organoid_tracker.visualizer.Visualizer method)
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)
display_settings (organoid_tracker.gui.window.Window property)
DisplaySettings (class in organoid_tracker.gui.window)
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)
DivisionScoreVisualizer (class in organoid_tracker.visualizer.division_score_visualizer)
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)
draw_view() (organoid_tracker.visualizer.abstract_image_visualizer.AbstractImageVisualizer method)
(organoid_tracker.visualizer.empty_visualizer.EmptyVisualizer method)
(organoid_tracker.visualizer.lineage_tree_visualizer.LineageTreeVisualizer method)
(organoid_tracker.visualizer.position_list_visualizer.PositionListVisualizer method)
(organoid_tracker.visualizer.Visualizer method)
E
EmptyVisualizer (class in organoid_tracker.visualizer.empty_visualizer)
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)
error_correction_max_time_point (organoid_tracker.gui.window.DisplaySettings attribute)
error_correction_min_time_point (organoid_tracker.gui.window.DisplaySettings attribute)
errored_positions (organoid_tracker.linking_analysis.lineage_error_finder.LineageWithErrors attribute)
ErrorsVisualizer (class in organoid_tracker.visualizer.errors_visualizer)
eventFilter() (organoid_tracker.gui.option_choose_dialog.MultipleComboBox method)
execute_command() (organoid_tracker.gui.gui_experiment.GuiExperiment method)
exists() (organoid_tracker.core.spline.SplineCollection method)
ExitableImageVisualizer (class in organoid_tracker.visualizer.exitable_image_visualizer)
expanded() (organoid_tracker.core.bounding_box.BoundingBox method)
Experiment (class in organoid_tracker.core.experiment)
experiment (organoid_tracker.gui.gui_experiment.SingleGuiTab property)
experiment_select_handler() (organoid_tracker.gui.toolbar.Toolbar method)
export_links() (in module organoid_tracker.guizela_tracker_compatibility.guizela_data_exporter)
export_links_ctc() (in module organoid_tracker.gui.action)
export_links_guizela() (in module organoid_tracker.gui.action)
export_links_trackmate() (in module organoid_tracker.gui.action)
export_positions() (in module organoid_tracker.gui.action)
extra() (organoid_tracker.core.marker.Marker method)
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)
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.link_data.LinkData 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)
find_all_data_of_position() (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)
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_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_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_all_dividing_cells() (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_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
gather_data() (organoid_tracker.gui.worker_job.WorkerJob method)
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)
(organoid_tracker.gui.window.Window 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_all_data() (organoid_tracker.core.global_data.GlobalData method)
get_all_tabs() (organoid_tracker.gui.gui_experiment.GuiExperiment method)
get_beacon_by_index() (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_closest_position() (organoid_tracker.visualizer.Visualizer static 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_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_data.PositionData method)
get_default_status() (organoid_tracker.visualizer.Visualizer 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.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() (in module organoid_tracker.linking_analysis.cell_error_finder)
get_error_marker() (in module organoid_tracker.linking_analysis.linking_markers)
get_experiment() (organoid_tracker.gui.gui_experiment.GuiExperiment method)
(organoid_tracker.gui.window.Window method)
get_extra_menu_options() (organoid_tracker.visualizer.abstract_editor.AbstractEditor method)
(organoid_tracker.visualizer.abstract_image_visualizer.AbstractImageVisualizer method)
(organoid_tracker.visualizer.beacon_editor.BeaconEditor method)
(organoid_tracker.visualizer.cell_segmentation_editor.CellSegmentationEditor method)
(organoid_tracker.visualizer.errors_visualizer.ErrorsVisualizer method)
(organoid_tracker.visualizer.exitable_image_visualizer.ExitableImageVisualizer method)
(organoid_tracker.visualizer.image_offset_editor.ImageOffsetEditor method)
(organoid_tracker.visualizer.lineage_tree_visualizer.LineageTreeVisualizer method)
(organoid_tracker.visualizer.link_and_position_editor.LinkAndPositionEditor method)
(organoid_tracker.visualizer.position_in_rectangle_selector.PositionsInRectangleSelector method)
(organoid_tracker.visualizer.position_list_visualizer.PositionListVisualizer method)
(organoid_tracker.visualizer.spline_editor.SplineEditor method)
(organoid_tracker.visualizer.standard_image_visualizer.StandardImageVisualizer method)
(organoid_tracker.visualizer.track_visualizer.TrackVisualizer method)
(organoid_tracker.visualizer.Visualizer 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_figure() (organoid_tracker.gui.window.Window 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_gui_experiment() (organoid_tracker.gui.window.Window method)
get_highest_track_id() (organoid_tracker.core.links.Links method)
get_icon() (in module organoid_tracker.gui.icon_getter)
get_image() (organoid_tracker.core.images.Images 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)
get_image_slice_2d() (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)
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_message_no_positions() (organoid_tracker.visualizer.cell_death_visualizer.CellTrackEndVisualizer method)
(organoid_tracker.visualizer.cell_division_visualizer.CellDivisionVisualizer method)
(organoid_tracker.visualizer.errors_visualizer.ErrorsVisualizer method)
(organoid_tracker.visualizer.position_list_visualizer.PositionListVisualizer method)
get_message_press_right() (organoid_tracker.visualizer.cell_death_visualizer.CellTrackEndVisualizer method)
(organoid_tracker.visualizer.cell_division_visualizer.CellDivisionVisualizer method)
(organoid_tracker.visualizer.errors_visualizer.ErrorsVisualizer method)
(organoid_tracker.visualizer.position_list_visualizer.PositionListVisualizer 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)
get_nearby() (organoid_tracker.gui.location_map.LocationMap method)
get_next_division() (in module organoid_tracker.linking.cell_division_finder)
get_next_index() (organoid_tracker.core.beacon_collection.BeaconCollection method)
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_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_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_scheduler() (organoid_tracker.gui.window.Window 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.position_list_popup.PositionListPopup method)
(organoid_tracker.text_popup.position_popup.PositionPopup method)
(organoid_tracker.text_popup.text_popup.RichTextPopup method)
(organoid_tracker.visualizer.cell_death_visualizer.CellTrackEndVisualizer method)
(organoid_tracker.visualizer.cell_division_visualizer.CellDivisionVisualizer method)
(organoid_tracker.visualizer.errors_visualizer.ErrorsVisualizer method)
(organoid_tracker.visualizer.position_list_visualizer.PositionListVisualizer 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_undo_redo() (organoid_tracker.gui.window.Window 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_window() (organoid_tracker.visualizer.Visualizer 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_active_tasks() (organoid_tracker.gui.threading.Scheduler method)
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)
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_data.PositionData method)
has_position_data_with_name() (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)
hidePopup() (organoid_tracker.gui.option_choose_dialog.MultipleComboBox method)
highest_z() (organoid_tracker.core.position_collection.PositionCollection method)
home_handler() (organoid_tracker.gui.toolbar.Toolbar method)
I
Image (class in organoid_tracker.core.images)
image_channel (organoid_tracker.gui.window.DisplaySettings attribute)
image_handler() (organoid_tracker.gui.toolbar.Toolbar method)
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)
ImageOffsetEditor (class in organoid_tracker.visualizer.image_offset_editor)
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)
ImageSliceViewer (class in organoid_tracker.visualizer.image_slice_visualizer)
ImageTimings (class in organoid_tracker.core.resolution)
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.division_detection_cnn.training_data_creator)
(in module organoid_tracker.link_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_cancel() (organoid_tracker.gui.dialog.PromptAnswer 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_no() (organoid_tracker.gui.dialog.PromptAnswer method)
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_yes() (organoid_tracker.gui.dialog.PromptAnswer method)
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
KEY_SHOW_IMAGES (organoid_tracker.gui.window.DisplaySettings attribute)
KEY_SHOW_NEXT_IMAGE_ON_TOP (organoid_tracker.gui.window.DisplaySettings attribute)
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)
launch_window() (in module organoid_tracker.gui.launcher)
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)
LineageErrorsVisualizer (class in organoid_tracker.visualizer.lineage_errors_visualizer)
LineageFate (class in organoid_tracker.linking_analysis.lineage_fate_finder)
LineageFateVisualizer (class in organoid_tracker.visualizer.lineage_fate_visualizer)
LineageTreeVisualizer (class in organoid_tracker.visualizer.lineage_tree_visualizer)
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)
LinkAndPositionEditor (class in organoid_tracker.visualizer.link_and_position_editor)
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)
LinkScoreVisualizer (class in organoid_tracker.visualizer.link_score_visualizer)
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_folder() (organoid_tracker.plugin.plugin_manager.PluginManager method)
load_from_czi_file() (in module organoid_tracker.image_loading.czifile_image_loader)
load_from_czi_reader() (in module organoid_tracker.image_loading.czifile_image_loader)
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_handler() (organoid_tracker.gui.toolbar.Toolbar 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_images() (in module organoid_tracker.gui.action)
(in module organoid_tracker.image_loading.general_image_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_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)
load_tracking_data() (in module organoid_tracker.gui.action)
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_LINK_SCORE (organoid_tracker.linking_analysis.errors.Error attribute)
LOW_MOTHER_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)
mainloop() (in module organoid_tracker.gui.launcher)
MainWindow (class in organoid_tracker.gui.launcher)
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_distance_moved_um_per_min (organoid_tracker.core.warning_limits.WarningLimits attribute)
max_intensity_projection (organoid_tracker.gui.window.DisplaySettings attribute)
max_none() (in module organoid_tracker.core)
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)
MAX_Z_DISTANCE (organoid_tracker.visualizer.abstract_image_visualizer.AbstractImageVisualizer 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.link_data.LinkData method)
(organoid_tracker.core.position_data.PositionData 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_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)
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.division_detection_cnn
organoid_tracker.division_detection_cnn.training_data_creator
organoid_tracker.gui
organoid_tracker.gui.action
organoid_tracker.gui.dialog
organoid_tracker.gui.gui_experiment
organoid_tracker.gui.icon_getter
organoid_tracker.gui.image_resolution_dialog
organoid_tracker.gui.image_series_loader_dialog
organoid_tracker.gui.launcher
organoid_tracker.gui.location_map
organoid_tracker.gui.option_choose_dialog
organoid_tracker.gui.threading
organoid_tracker.gui.toolbar
organoid_tracker.gui.undo_redo
organoid_tracker.gui.window
organoid_tracker.gui.worker_job
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.czifile_image_loader
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.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.link_detection_cnn
organoid_tracker.link_detection_cnn.training_data_creator
organoid_tracker.linking
organoid_tracker.linking.cell_division_finder
organoid_tracker.linking.nearby_position_finder
organoid_tracker.linking.nearest_neighbor_linker
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.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.position_detection_cnn
organoid_tracker.position_detection_cnn.peak_calling
organoid_tracker.position_detection_cnn.split_images
organoid_tracker.position_detection_cnn.training_data_creator
organoid_tracker.text_popup
organoid_tracker.text_popup.help_popup
organoid_tracker.text_popup.position_list_popup
organoid_tracker.text_popup.position_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
organoid_tracker.visualizer
organoid_tracker.visualizer.abstract_editor
organoid_tracker.visualizer.abstract_image_visualizer
organoid_tracker.visualizer.beacon_editor
organoid_tracker.visualizer.cell_compartment_visualizer
organoid_tracker.visualizer.cell_death_visualizer
organoid_tracker.visualizer.cell_density_visualizer
organoid_tracker.visualizer.cell_division_visualizer
organoid_tracker.visualizer.cell_fate_visualizer
organoid_tracker.visualizer.cell_movement_visualizer
organoid_tracker.visualizer.cell_segmentation_editor
organoid_tracker.visualizer.debug_image_visualizer
organoid_tracker.visualizer.division_score_visualizer
organoid_tracker.visualizer.empty_visualizer
organoid_tracker.visualizer.errors_visualizer
organoid_tracker.visualizer.exitable_image_visualizer
organoid_tracker.visualizer.image_offset_editor
organoid_tracker.visualizer.image_slice_visualizer
organoid_tracker.visualizer.lineage_errors_visualizer
organoid_tracker.visualizer.lineage_fate_visualizer
organoid_tracker.visualizer.lineage_tree_visualizer
organoid_tracker.visualizer.link_and_position_editor
organoid_tracker.visualizer.link_score_visualizer
organoid_tracker.visualizer.position_in_rectangle_selector
organoid_tracker.visualizer.position_list_visualizer
organoid_tracker.visualizer.spline_editor
organoid_tracker.visualizer.standard_image_visualizer
organoid_tracker.visualizer.track_visualizer
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.link_data.LinkData 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)
MultipleComboBox (class in organoid_tracker.gui.option_choose_dialog)
MultipleComboBox.Delegate (class in organoid_tracker.gui.option_choose_dialog)
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.position_list_popup.PositionListPopup method)
(organoid_tracker.text_popup.position_popup.PositionPopup 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)
nearest_neighbor() (in module organoid_tracker.linking.nearest_neighbor_linker)
needs_saving (organoid_tracker.gui.undo_redo.UndoableAction attribute)
new() (in module organoid_tracker.gui.action)
new_handler() (organoid_tracker.gui.toolbar.Toolbar method)
NO_FUTURE_POSITION (organoid_tracker.linking_analysis.errors.Error 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)
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)
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)
OK (organoid_tracker.gui.dialog.DefaultOption attribute)
on_error() (organoid_tracker.gui.threading.Task method)
(organoid_tracker.gui.worker_job.WorkerJob method)
on_finished() (organoid_tracker.gui.threading.Task method)
(organoid_tracker.gui.worker_job.WorkerJob method)
open_file() (in module organoid_tracker.gui.dialog)
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.division_detection_cnn
module
organoid_tracker.division_detection_cnn.training_data_creator
module
organoid_tracker.gui
module
organoid_tracker.gui.action
module
organoid_tracker.gui.dialog
module
organoid_tracker.gui.gui_experiment
module
organoid_tracker.gui.icon_getter
module
organoid_tracker.gui.image_resolution_dialog
module
organoid_tracker.gui.image_series_loader_dialog
module
organoid_tracker.gui.launcher
module
organoid_tracker.gui.location_map
module
organoid_tracker.gui.option_choose_dialog
module
organoid_tracker.gui.threading
module
organoid_tracker.gui.toolbar
module
organoid_tracker.gui.undo_redo
module
organoid_tracker.gui.window
module
organoid_tracker.gui.worker_job
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.czifile_image_loader
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.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.link_detection_cnn
module
organoid_tracker.link_detection_cnn.training_data_creator
module
organoid_tracker.linking
module
organoid_tracker.linking.cell_division_finder
module
organoid_tracker.linking.nearby_position_finder
module
organoid_tracker.linking.nearest_neighbor_linker
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.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.position_detection_cnn
module
organoid_tracker.position_detection_cnn.peak_calling
module
organoid_tracker.position_detection_cnn.split_images
module
organoid_tracker.position_detection_cnn.training_data_creator
module
organoid_tracker.text_popup
module
organoid_tracker.text_popup.help_popup
module
organoid_tracker.text_popup.position_list_popup
module
organoid_tracker.text_popup.position_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
organoid_tracker.visualizer
module
organoid_tracker.visualizer.abstract_editor
module
organoid_tracker.visualizer.abstract_image_visualizer
module
organoid_tracker.visualizer.beacon_editor
module
organoid_tracker.visualizer.cell_compartment_visualizer
module
organoid_tracker.visualizer.cell_death_visualizer
module
organoid_tracker.visualizer.cell_density_visualizer
module
organoid_tracker.visualizer.cell_division_visualizer
module
organoid_tracker.visualizer.cell_fate_visualizer
module
organoid_tracker.visualizer.cell_movement_visualizer
module
organoid_tracker.visualizer.cell_segmentation_editor
module
organoid_tracker.visualizer.debug_image_visualizer
module
organoid_tracker.visualizer.division_score_visualizer
module
organoid_tracker.visualizer.empty_visualizer
module
organoid_tracker.visualizer.errors_visualizer
module
organoid_tracker.visualizer.exitable_image_visualizer
module
organoid_tracker.visualizer.image_offset_editor
module
organoid_tracker.visualizer.image_slice_visualizer
module
organoid_tracker.visualizer.lineage_errors_visualizer
module
organoid_tracker.visualizer.lineage_fate_visualizer
module
organoid_tracker.visualizer.lineage_tree_visualizer
module
organoid_tracker.visualizer.link_and_position_editor
module
organoid_tracker.visualizer.link_score_visualizer
module
organoid_tracker.visualizer.position_in_rectangle_selector
module
organoid_tracker.visualizer.position_list_visualizer
module
organoid_tracker.visualizer.spline_editor
module
organoid_tracker.visualizer.standard_image_visualizer
module
organoid_tracker.visualizer.track_visualizer
module
OUT_OF_VIEW (organoid_tracker.linking_analysis.linking_markers.EndMarker attribute)
OutsideImageError
P
perform_data_action() (organoid_tracker.gui.window.Window method)
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)
plugin_manager (organoid_tracker.gui.window.Window property)
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)
popup_3d_image() (in module organoid_tracker.visualizer.debug_image_visualizer)
popup_error() (in module organoid_tracker.gui.dialog)
popup_exception() (in module organoid_tracker.gui.dialog)
popup_figure() (in module organoid_tracker.gui.dialog)
popup_manual() (in module organoid_tracker.gui.dialog)
popup_message() (in module organoid_tracker.gui.dialog)
popup_message_cancellable() (in module organoid_tracker.gui.dialog)
popup_resolution_setter() (in module organoid_tracker.gui.image_resolution_dialog)
popup_rich_text() (in module organoid_tracker.gui.dialog)
popup_visualizer() (in module organoid_tracker.gui.dialog)
PopupWindow (class in organoid_tracker.gui.dialog)
pos (organoid_tracker.core.spline.SplinePosition attribute)
Position (class in organoid_tracker.core.position)
position (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)
PositionListPopup (class in organoid_tracker.text_popup.position_list_popup)
PositionListVisualizer (class in organoid_tracker.visualizer.position_list_visualizer)
PositionPopup (class in organoid_tracker.text_popup.position_popup)
positions (organoid_tracker.connection_analysis.cluster_finder.Cluster attribute)
(organoid_tracker.core.experiment.Experiment property)
positions() (organoid_tracker.core.links.LinkingTrack method)
PositionsInRectangleSelector (class in organoid_tracker.visualizer.position_in_rectangle_selector)
postprocess() (in module organoid_tracker.linking_analysis.links_postprocessor)
POTENTIALLY_NOT_A_MOTHER (organoid_tracker.linking_analysis.errors.Error attribute)
POTENTIALLY_SHOULD_BE_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)
prompt_color() (in module organoid_tracker.gui.dialog)
prompt_confirmation() (in module organoid_tracker.gui.dialog)
prompt_directory() (in module organoid_tracker.gui.dialog)
prompt_float() (in module organoid_tracker.gui.dialog)
prompt_image_series() (in module organoid_tracker.gui.image_series_loader_dialog)
prompt_int() (in module organoid_tracker.gui.dialog)
prompt_list() (in module organoid_tracker.gui.option_choose_dialog)
prompt_list_multiple() (in module organoid_tracker.gui.option_choose_dialog)
prompt_load_file() (in module organoid_tracker.gui.dialog)
prompt_load_multiple_files() (in module organoid_tracker.gui.dialog)
prompt_options() (in module organoid_tracker.gui.dialog)
prompt_save_file() (in module organoid_tracker.gui.dialog)
prompt_str() (in module organoid_tracker.gui.dialog)
prompt_yes_no() (in module organoid_tracker.gui.dialog)
prompt_yes_no_cancel() (in module organoid_tracker.gui.dialog)
PromptAnswer (class in organoid_tracker.gui.dialog)
provide_automatic_name() (organoid_tracker.core.Name method)
R
radius_um (organoid_tracker.coordinate_system.spherical_coordinates.SphericalCoordinate attribute)
read_czi_file() (in module organoid_tracker.image_loading.czifile_image_loader)
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_image() (organoid_tracker.visualizer.Visualizer method)
reconstruct_image_3d() (organoid_tracker.visualizer.Visualizer method)
reconstruct_volume() (in module organoid_tracker.position_detection_cnn.peak_calling)
reconstruction() (in module organoid_tracker.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_all() (organoid_tracker.gui.window.Window method)
redraw_data() (organoid_tracker.gui.gui_experiment.GuiExperiment method)
(organoid_tracker.gui.window.Window method)
redraw_image_and_data() (organoid_tracker.gui.gui_experiment.GuiExperiment method)
reference_time_point() (organoid_tracker.core.spline.SplineCollection method)
refresh_all() (organoid_tracker.visualizer.abstract_image_visualizer.AbstractImageVisualizer method)
(organoid_tracker.visualizer.empty_visualizer.EmptyVisualizer method)
(organoid_tracker.visualizer.Visualizer method)
refresh_data() (organoid_tracker.visualizer.abstract_image_visualizer.AbstractImageVisualizer method)
(organoid_tracker.visualizer.empty_visualizer.EmptyVisualizer method)
(organoid_tracker.visualizer.Visualizer method)
register_event_handler() (organoid_tracker.gui.gui_experiment.GuiExperiment method)
(organoid_tracker.gui.window.Window method)
Registry (class in organoid_tracker.plugin.registry)
registry (organoid_tracker.gui.window.Window property)
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_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.link_data.LinkData method)
(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)
(organoid_tracker.core.position_data.PositionData method)
remove_positions() (organoid_tracker.core.experiment.Experiment method)
remove_random_positions() (in module organoid_tracker.link_detection_cnn.training_data_creator)
remove_spline() (organoid_tracker.core.spline.SplineCollection method)
remove_tracks_too_deep() (in module organoid_tracker.linking_analysis.links_postprocessor)
rename_experiment() (in module organoid_tracker.gui.action)
replace_link() (organoid_tracker.core.link_data.LinkData method)
replace_plugin_manager() (organoid_tracker.gui.window.Window method)
replace_position() (organoid_tracker.core.connections.Connections method)
(organoid_tracker.core.links.Links method)
(organoid_tracker.core.position_data.PositionData method)
replace_selected_experiment() (organoid_tracker.gui.gui_experiment.GuiExperiment method)
resizeEvent() (organoid_tracker.gui.option_choose_dialog.MultipleComboBox 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)
run() (organoid_tracker.gui.threading.Scheduler method)
run_async() (organoid_tracker.visualizer.Visualizer method)
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_handler() (organoid_tracker.gui.toolbar.Toolbar method)
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.gui.action)
(in module organoid_tracker.imaging.trackmate_io)
save_tracking_data_of_tab() (in module organoid_tracker.gui.action)
Scheduler (class in organoid_tracker.gui.threading)
search_position (organoid_tracker.core.beacon_collection.ClosestBeacon attribute)
segmentation_channel (organoid_tracker.gui.window.DisplaySettings 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_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_channel_description() (organoid_tracker.core.images.Images method)
set_color() (in module organoid_tracker.linking_analysis.lineage_markers)
set_data() (organoid_tracker.core.global_data.GlobalData method)
set_error_marker() (in module organoid_tracker.linking_analysis.linking_markers)
set_figure_title() (organoid_tracker.gui.window.Window method)
set_image_resolution() (in module organoid_tracker.gui.action)
set_lineage_data() (organoid_tracker.core.links.Links method)
set_link_data() (organoid_tracker.core.link_data.LinkData 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_data.PositionData method)
set_position_type() (in module organoid_tracker.position_analysis.position_markers)
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_status() (organoid_tracker.gui.launcher.MainWindow method)
(organoid_tracker.gui.window.Window 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)
set_window_title() (organoid_tracker.gui.window.Window method)
setup_figure_2d() (in module organoid_tracker.coordinate_system.sphere_representer)
setup_figure_3d() (in module organoid_tracker.coordinate_system.sphere_representer)
setup_menu() (organoid_tracker.gui.window.Window method)
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)
should_show_image_reconstruction() (organoid_tracker.visualizer.Visualizer method)
show() (in module organoid_tracker.visualizer.standard_image_visualizer)
show_errors (organoid_tracker.gui.window.DisplaySettings attribute)
show_images (organoid_tracker.gui.window.DisplaySettings attribute)
show_links_and_connections (organoid_tracker.gui.window.DisplaySettings attribute)
show_manual() (in module organoid_tracker.gui.action)
show_next_time_point (organoid_tracker.gui.window.DisplaySettings attribute)
show_positions (organoid_tracker.gui.window.DisplaySettings attribute)
show_splines (organoid_tracker.gui.window.DisplaySettings attribute)
showPopup() (organoid_tracker.gui.option_choose_dialog.MultipleComboBox method)
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)
sizeHint() (organoid_tracker.gui.option_choose_dialog.MultipleComboBox.Delegate method)
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)
SplineEditor (class in organoid_tracker.visualizer.spline_editor)
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)
StandardImageVisualizer (class in organoid_tracker.visualizer.standard_image_visualizer)
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)
staticMetaObject (organoid_tracker.gui.option_choose_dialog.MultipleComboBox attribute)
(organoid_tracker.gui.option_choose_dialog.MultipleComboBox.Delegate attribute)
(organoid_tracker.gui.toolbar.Toolbar attribute)
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)
submit_job() (in module organoid_tracker.gui.worker_job)
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)
Task (class in organoid_tracker.gui.threading)
theta_degrees (organoid_tracker.coordinate_system.spherical_coordinates.SphericalCoordinate attribute)
ThresholdFilter (class in organoid_tracker.image_loading.builtin_image_filters)
time_point (organoid_tracker.gui.window.DisplaySettings attribute)
(organoid_tracker.image_loading.builtin_image_filters.IntensityPoint 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)
timerEvent() (organoid_tracker.gui.option_choose_dialog.MultipleComboBox method)
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_experiment_list_file_structure() (in module organoid_tracker.gui.action)
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)
toggle_axis() (in module organoid_tracker.gui.action)
TOO_MANY_DAUGHTER_CELLS (organoid_tracker.linking_analysis.errors.Error attribute)
Toolbar (class in organoid_tracker.gui.toolbar)
toolitems (organoid_tracker.gui.toolbar.Toolbar 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)
tracks (organoid_tracker.linking_analysis.lineage_fate_finder.LineageFate attribute)
TrackVisualizer (class in organoid_tracker.visualizer.track_visualizer)
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.GuiExperiment property)
(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)
(organoid_tracker.gui.window.Window 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)
update_selectable_experiments() (organoid_tracker.gui.toolbar.Toolbar method)
update_status() (organoid_tracker.visualizer.Visualizer method)
updateText() (organoid_tracker.gui.option_choose_dialog.MultipleComboBox method)
use_data() (organoid_tracker.gui.worker_job.WorkerJob method)
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)
view_statistics() (in module organoid_tracker.gui.action)
Visualizer (class in organoid_tracker.visualizer)
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)
Window (class in organoid_tracker.gui.window)
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)
WorkerJob (class in organoid_tracker.gui.worker_job)
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)
Y
y (organoid_tracker.core.position.Position attribute)
(organoid_tracker.core.vector.Vector2 attribute)
(organoid_tracker.core.vector.Vector3 attribute)
YOUNG_MOTHER (organoid_tracker.linking_analysis.errors.Error attribute)
Z
z (organoid_tracker.core.position.Position attribute)
(organoid_tracker.core.vector.Vector3 attribute)
(organoid_tracker.gui.window.DisplaySettings 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)