Index

A

accumulate_dac() (in module itasc.contact_analysis.dynamics.kinematics) add_anchor() (in module itasc.tracking_ultrack.validation_state) add_cell() (in module itasc.correction.labels) add_correction() (in module itasc.tracking_ultrack.validation_state) add_corrections() (in module itasc.tracking_ultrack.validation_state) admitted (itasc.tracking_ultrack.atoms.BranchReport attribute) aggregate() (in module itasc.contact_analysis) (in module itasc.contact_analysis.pipeline) (in module itasc.contact_analysis.shape_tables) alpha (itasc.contact_analysis.dynamics.msd.MsdFit attribute) anchor_incident_links_inserted (itasc.tracking_ultrack.db_build.AnnotateAndScoreReport attribute) anchor_links (itasc.tracking_ultrack.corrections.CorrectionDatabaseReport attribute) (itasc.tracking_ultrack.db_build.AnnotateAndScoreReport attribute) anchor_nodes (itasc.tracking_ultrack.corrections.CorrectionDatabaseReport attribute) (itasc.tracking_ultrack.db_build.AnnotateAndScoreReport attribute) anchor_overlaps_pruned (itasc.tracking_ultrack.corrections.CorrectionDatabaseReport attribute) anchor_radius_px (itasc.tracking_ultrack.config.TrackingConfig attribute) anchor_stamp_radius_px (itasc.tracking_ultrack.config.TrackingConfig attribute) anchor_tail_links_annotated (itasc.tracking_ultrack.db_build.AnnotateAndScoreReport attribute) AnchorIncidentLinkReport (class in itasc.tracking_ultrack.corrections) anchors_processed (itasc.tracking_ultrack.corrections.AnchorIncidentLinkReport attribute) AnchorTailLinkReport (class in itasc.tracking_ultrack.corrections) anisotropy (itasc.cellpose.cellpose_runner.NucleusParams attribute) annotate_anchor_tail_links() (in module itasc.tracking_ultrack.corrections) annotate_database_from_corrections() (in module itasc.tracking_ultrack.db_build) AnnotateAndScoreReport (class in itasc.tracking_ultrack.db_build) annotated (itasc.tracking_ultrack.corrections.AnchorTailLinkReport attribute) annotation (itasc.tracking_ultrack.db_query.NodeEdge attribute)

annotation_name() (in module itasc.tracking_ultrack.db_query) appear_weight (itasc.tracking_ultrack.config.TrackingConfig attribute) append_exclusion() (in module itasc.contact_analysis.curation) apply_annotations_and_score() (in module itasc.tracking_ultrack.db_build) apply_corrections_to_database() (in module itasc.tracking_ultrack.corrections) apply_curation() (in module itasc.contact_analysis.curation) apply_post_solve_corrections() (in module itasc.tracking_ultrack.corrections) area (itasc.tracking_ultrack.swap_candidate.SwapCandidate attribute) area_weight (itasc.tracking_ultrack.config.TrackingConfig attribute) as_tuple() (itasc.tracking_ultrack.db_query.UltrackDbPreview method) assemble_cost_field() (in module itasc.segmentation) (in module itasc.segmentation.cell_label_icm) assign_persistent_edge_ids() (in module itasc.contact_analysis.contacts.build) assignments (itasc.tracking_ultrack.extend.ExtendCandidates attribute) (itasc.tracking_ultrack.extend.ExtendResult attribute) atom_adjacency() (in module itasc.tracking_ultrack.atoms) atom_adjacency_weighted() (in module itasc.tracking_ultrack.atoms) atom_min_area (itasc.tracking_ultrack.atoms.AtomParams attribute) (itasc.tracking_ultrack.config.TrackingConfig attribute) atom_overlap_budget (itasc.tracking_ultrack.config.TrackingConfig attribute) atom_union_max_area (itasc.tracking_ultrack.config.TrackingConfig attribute) AtomParams (class in itasc.tracking_ultrack.atoms) AtomUnionDatabaseBuildReport (class in itasc.tracking_ultrack.db_build) author_config() (in module itasc.contact_analysis) (in module itasc.contact_analysis.pipeline) available_fields() (in module itasc.contact_analysis.records) available_quantifiers() (in module itasc.contact_analysis) (in module itasc.contact_analysis.quantifier)

B

balance (itasc.segmentation.cell_divergence_segmentation.CellDivergenceParams attribute) (itasc.segmentation.cell_label_icm.CellLabelICMParams attribute) (itasc.segmentation.CellDivergenceParams attribute) (itasc.segmentation.CellLabelICMParams attribute) balance_strength_to_weights() (in module itasc.segmentation) (in module itasc.segmentation.cell_label_icm) bbox (itasc.tracking_ultrack.extend.ExtendAssignment attribute) (itasc.tracking_ultrack.extend.ExtendResult attribute) (itasc.tracking_ultrack.swap_candidate.SwapCandidate attribute) best_overlapping_label() (in module itasc.correction.labels) bias (itasc.tracking_ultrack.config.TrackingConfig attribute) branch_unions() (in module itasc.tracking_ultrack.atoms) BranchReport (class in itasc.tracking_ultrack.atoms) budget_hit (itasc.tracking_ultrack.atoms.BranchReport attribute) build() (itasc.contact_analysis.quantifier.Quantifier method) (itasc.contact_analysis.quantifiers.cell_dynamics.CellDynamicsQuantifier method) (itasc.contact_analysis.quantifiers.contacts.ContactsQuantifier method) (itasc.contact_analysis.quantifiers.nucleus_dynamics.NucleusDynamicsQuantifier method) build_atom_merge_tree() (in module itasc.tracking_ultrack.atoms)

build_atom_union_database() (in module itasc.tracking_ultrack.db_build) build_catalog() (in module itasc.contact_analysis) (in module itasc.contact_analysis.pipeline) build_contacts() (in module itasc.contact_analysis) (in module itasc.contact_analysis.contacts.build) build_divergence_maps() (in module itasc.cellpose) (in module itasc.cellpose.divergence_maps) build_lineage() (in module itasc.core.lineage) (in module itasc.segmentation) (in module itasc.segmentation.lineage) build_position_contacts() (in module itasc.contact_analysis) (in module itasc.contact_analysis.contacts.build) build_quantities() (in module itasc.contact_analysis) (in module itasc.contact_analysis.pipeline) build_table() (in module itasc.contact_analysis.shape_tables) build_track_dataframe() (in module itasc.cellpose.track_laptrack) build_track_dynamics() (in module itasc.contact_analysis.dynamics) (in module itasc.contact_analysis.dynamics.store) build_ultrack_database() (in module itasc.tracking_ultrack.db_build)

C

can_build() (itasc.contact_analysis.quantifier.Quantifier method) CancelledError, [1], [2], [3], [4] candidate_label (itasc.tracking_ultrack.extend.ExtendAssignment attribute) (itasc.tracking_ultrack.extend.ExtendResult attribute) candidate_partition (itasc.tracking_ultrack.extend.ExtendAssignment attribute) (itasc.tracking_ultrack.extend.ExtendResult attribute) carve_into_selected() (in module itasc.correction.labels) catalog (itasc.contact_analysis.config.RunConfig attribute) (itasc.contact_analysis.RunConfig attribute) catalogue_root() (in module itasc.contact_analysis.shape_tables) cell_density() (in module itasc.contact_analysis.contacts) (in module itasc.contact_analysis.contacts.neighborhood) cell_foreground_from_prob() (in module itasc.cellpose.joint) cell_id (itasc.core.lineage.TrackLane attribute) (itasc.segmentation.lineage.TrackLane attribute) (itasc.segmentation.TrackLane attribute) (itasc.tracking_ultrack.corrections.Correction attribute) (itasc.tracking_ultrack.extend.ExtendAssignment attribute) cell_labels (itasc.contact_analysis.ContactBatchJob attribute) (itasc.contact_analysis.contacts.batch.ContactBatchJob attribute) cell_labels_path (itasc.contact_analysis.quantifier.PositionInputs attribute) cell_neighbor_counts() (in module itasc.contact_analysis.contacts) (in module itasc.contact_analysis.contacts.neighborhood) cell_tracked_labels_path (itasc.contact_analysis.contacts.reader.PositionContactAnalysis attribute) CellDensityQuantifier (class in itasc.contact_analysis.quantifiers.cell_density) CellDivergenceParams (class in itasc.segmentation) (class in itasc.segmentation.cell_divergence_segmentation) CellDivergenceResult (class in itasc.segmentation) (class in itasc.segmentation.cell_divergence_segmentation) CellDynamicsQuantifier (class in itasc.contact_analysis.quantifiers.cell_dynamics) CellForegroundResult (class in itasc.segmentation) (class in itasc.segmentation.cell_divergence_segmentation) CellICMState (class in itasc.segmentation) (class in itasc.segmentation.cell_label_icm) CellLabelICMParams (class in itasc.segmentation) (class in itasc.segmentation.cell_label_icm) CellParams (class in itasc.cellpose.cellpose_runner) cellprob_threshold (itasc.cellpose.cellpose_runner.NucleusParams attribute) cells (itasc.contact_analysis.contacts.reader.PositionContactAnalysis attribute) CellShapeQuantifier (class in itasc.contact_analysis.quantifiers.cell_shape) centroid (itasc.tracking_ultrack.swap_candidate.SwapCandidate attribute) centroid_corrected_iou() (in module itasc.tracking_ultrack.scoring) centroid_corrected_iou_from_coords() (in module itasc.cellpose.retrack) (in module itasc.tracking_ultrack.scoring) circularity() (in module itasc.contact_analysis.shape.core) circularity_weight (itasc.tracking_ultrack.config.TrackingConfig attribute) clean_and_smooth_contours() (in module itasc.segmentation) (in module itasc.segmentation.cell_divergence_segmentation) clean_stranded_pixels() (in module itasc.correction) (in module itasc.correction.labels) collective (itasc.contact_analysis.dynamics.store.TrackDynamics attribute) (itasc.contact_analysis.dynamics.TrackDynamics attribute) COLLECTIVE_COLUMNS (in module itasc.contact_analysis.dynamics.collective) collective_tables() (in module itasc.contact_analysis.dynamics.collective) columns_from_levels() (in module itasc.contact_analysis.catalog) commit_labels() (in module itasc.segmentation) (in module itasc.segmentation.cell_label_icm) commit_state() (in module itasc.core.commit) compute_cell_foreground() (in module itasc.segmentation) (in module itasc.segmentation.cell_divergence_segmentation) compute_drop_frac() (in module itasc.tracking_ultrack.seed_prior) compute_edge_weight() (in module itasc.tracking_ultrack.linking) compute_filtered_contour_maps() (in module itasc.segmentation) (in module itasc.segmentation.contour_filtering) compute_mask_circularity() (in module itasc.tracking_ultrack.seed_prior)

compute_object_shape() (in module itasc.contact_analysis.shape) (in module itasc.contact_analysis.shape.core) compute_object_table() (itasc.contact_analysis.quantifier.Quantifier method) (itasc.contact_analysis.quantifiers.cell_density.CellDensityQuantifier method) (itasc.contact_analysis.quantifiers.cell_dynamics.CellDynamicsQuantifier method) (itasc.contact_analysis.quantifiers.cell_shape.CellShapeQuantifier method) (itasc.contact_analysis.quantifiers.neighbor_count.NeighborCountQuantifier method) (itasc.contact_analysis.quantifiers.nucleus_dynamics.NucleusDynamicsQuantifier method) (itasc.contact_analysis.quantifiers.nucleus_shape.NucleusShapeQuantifier method) (itasc.contact_analysis.quantifiers.shape_relational.ShapeRelationalQuantifier method) (itasc.contact_analysis.quantifiers.signed_contact_length.SignedContactLengthQuantifier method) compute_relational_table() (in module itasc.contact_analysis.shape) (in module itasc.contact_analysis.shape.relational) compute_track_scores() (in module itasc.tracking_ultrack.track_quality) CONFIG_NAME (in module itasc.core.paths) contact_analysis_path (itasc.contact_analysis.quantifier.PositionInputs attribute) CONTACT_ANALYSIS_RELPATH (in module itasc.contact_analysis.catalog) contact_label_for() (in module itasc.contact_analysis.contacts.contact_labels) ContactBatchJob (class in itasc.contact_analysis) (class in itasc.contact_analysis.contacts.batch) ContactBatchResult (class in itasc.contact_analysis) (class in itasc.contact_analysis.contacts.batch) ContactsQuantifier (class in itasc.contact_analysis.quantifiers.contacts) contour_floor (itasc.tracking_ultrack.atoms.AtomParams attribute) (itasc.tracking_ultrack.config.TrackingConfig attribute) contour_from_dp() (in module itasc.cellpose.divergence_maps) contour_memory_filter() (in module itasc.segmentation.contour_filtering) contour_norm_pct (itasc.segmentation.cell_divergence_segmentation.CellDivergenceParams attribute) (itasc.segmentation.CellDivergenceParams attribute) contour_strength (itasc.segmentation.cell_divergence_segmentation.CellDivergenceParams attribute) (itasc.segmentation.CellDivergenceParams attribute) (itasc.tracking_ultrack.atoms.AtomParams attribute) (itasc.tracking_ultrack.config.TrackingConfig attribute) contour_threshold (itasc.segmentation.cell_divergence_segmentation.CellDivergenceParams attribute) (itasc.segmentation.CellDivergenceParams attribute) contour_window (itasc.segmentation.cell_divergence_segmentation.CellDivergenceParams attribute) (itasc.segmentation.CellDivergenceParams attribute) (itasc.tracking_ultrack.atoms.AtomParams attribute) (itasc.tracking_ultrack.config.TrackingConfig attribute) contour_z_reduction (itasc.cellpose.divergence_maps.DivergenceMapsReport attribute) (itasc.cellpose.DivergenceMapsReport attribute) ContourFilterParams (class in itasc.segmentation) (class in itasc.segmentation.contour_filtering) contours_clean (itasc.segmentation.cell_divergence_segmentation.CellDivergenceResult attribute) (itasc.segmentation.CellDivergenceResult attribute) contours_path (itasc.cellpose.divergence_maps.DivergenceMapsReport attribute) (itasc.cellpose.DivergenceMapsReport attribute) contours_raw (itasc.segmentation.cell_divergence_segmentation.CellDivergenceResult attribute) (itasc.segmentation.CellDivergenceResult attribute) coord_x (itasc.contact_analysis.contacts.reader.PositionContactAnalysis property) coord_y (itasc.contact_analysis.contacts.reader.PositionContactAnalysis property) COORDINATE_COLS (in module itasc.cellpose.track_laptrack) coordinates (itasc.contact_analysis.contacts.build.EdgeRecord attribute) corr_curve (itasc.contact_analysis.dynamics.store.TrackDynamics attribute) (itasc.contact_analysis.dynamics.TrackDynamics attribute) CORR_CURVE_COLUMNS (in module itasc.contact_analysis.dynamics.collective) corr_length_um (itasc.contact_analysis.dynamics.store.TrackDynamics attribute) (itasc.contact_analysis.dynamics.TrackDynamics attribute) Correction (class in itasc.tracking_ultrack.corrections) CorrectionDatabaseReport (class in itasc.tracking_ultrack.corrections) corrections_from_validated_tracks() (in module itasc.tracking_ultrack.corrections) cost_field (itasc.segmentation.cell_divergence_segmentation.CellDivergenceResult attribute) (itasc.segmentation.CellDivergenceResult attribute) CURATION_COLUMNS (in module itasc.contact_analysis.curation) cycle_index() (in module itasc.tracking_ultrack.swap_candidate)

D

D_um2_per_s (itasc.contact_analysis.dynamics.msd.MsdFit attribute) dac (itasc.contact_analysis.dynamics.store.TrackDynamics attribute) (itasc.contact_analysis.dynamics.TrackDynamics attribute) DAC_COLUMNS (in module itasc.contact_analysis.dynamics.kinematics) dac_persistence_time_s (itasc.contact_analysis.dynamics.store.TrackDynamics attribute) (itasc.contact_analysis.dynamics.TrackDynamics attribute) database_has_annotations() (in module itasc.tracking_ultrack.solve) DEFAULT_MSD_TRACK_WINDOW (in module itasc.contact_analysis.dynamics.msd) default_output() (itasc.contact_analysis.quantifier.Quantifier method) (itasc.contact_analysis.quantifiers.contacts.ContactsQuantifier method) default_output_name (itasc.contact_analysis.quantifier.Quantifier attribute) (itasc.contact_analysis.quantifiers.cell_dynamics.CellDynamicsQuantifier attribute) (itasc.contact_analysis.quantifiers.contacts.ContactsQuantifier attribute) (itasc.contact_analysis.quantifiers.nucleus_dynamics.NucleusDynamicsQuantifier attribute) DEFAULT_PARAMS (in module itasc.contact_analysis.dynamics.store) describe_axes() (in module itasc.cellpose.shape) DESCRIPTOR_COLUMNS (in module itasc.contact_analysis.shape.core) device_label() (in module itasc.cellpose.cellpose_runner) diameter (itasc.cellpose.cellpose_runner.CellParams attribute) (itasc.cellpose.cellpose_runner.NucleusParams attribute) direction (itasc.tracking_ultrack.db_query.NodeEdge attribute) directional_autocorrelation() (in module itasc.contact_analysis.dynamics.kinematics)

disappear_weight (itasc.tracking_ultrack.config.TrackingConfig attribute) discover_catalog_entries() (in module itasc.contact_analysis.catalog) discover_contact_batch_jobs() (in module itasc.contact_analysis) (in module itasc.contact_analysis.contacts.batch) discovered_level_depth() (in module itasc.contact_analysis.catalog) display_name (itasc.contact_analysis.quantifier.Quantifier attribute) (itasc.contact_analysis.quantifiers.cell_density.CellDensityQuantifier attribute) (itasc.contact_analysis.quantifiers.cell_dynamics.CellDynamicsQuantifier attribute) (itasc.contact_analysis.quantifiers.cell_shape.CellShapeQuantifier attribute) (itasc.contact_analysis.quantifiers.contacts.ContactsQuantifier attribute) (itasc.contact_analysis.quantifiers.neighbor_count.NeighborCountQuantifier attribute) (itasc.contact_analysis.quantifiers.nucleus_dynamics.NucleusDynamicsQuantifier attribute) (itasc.contact_analysis.quantifiers.nucleus_shape.NucleusShapeQuantifier attribute) (itasc.contact_analysis.quantifiers.shape_relational.ShapeRelationalQuantifier attribute) (itasc.contact_analysis.quantifiers.signed_contact_length.SignedContactLengthQuantifier attribute) distance_weight (itasc.tracking_ultrack.config.TrackingConfig attribute) divergence_2d() (in module itasc.cellpose.divergence_maps) DivergenceMapsReport (class in itasc.cellpose) (class in itasc.cellpose.divergence_maps) division_weight (itasc.tracking_ultrack.config.TrackingConfig attribute) do_3d (itasc.cellpose.cellpose_runner.NucleusParams attribute) draw_cell_path() (in module itasc.correction) (in module itasc.correction.labels)

E

edge_id (itasc.contact_analysis.contacts.build.T1Record attribute) edge_label (itasc.contact_analysis.contacts.build.EdgeRecord attribute) EdgeRecord (class in itasc.contact_analysis.contacts.build) edges (itasc.contact_analysis.contacts.reader.PositionContactAnalysis attribute) (itasc.tracking_ultrack.db_query.NodeEdges attribute) empty_curation() (in module itasc.contact_analysis.curation) end (itasc.core.lineage.TrackSegment attribute) (itasc.segmentation.lineage.TrackSegment attribute) (itasc.segmentation.TrackSegment attribute) ensemble_dac() (in module itasc.contact_analysis.dynamics.kinematics) ensemble_msd() (in module itasc.contact_analysis.dynamics.msd) ensure_anchor_incident_links() (in module itasc.tracking_ultrack.corrections) ensure_contacts() (in module itasc.contact_analysis) (in module itasc.contact_analysis.contacts.build) enum_connected_unions() (in module itasc.tracking_ultrack.atoms) erase_cell() (in module itasc.correction) (in module itasc.correction.labels)

error (itasc.contact_analysis.ContactBatchResult attribute) (itasc.contact_analysis.contacts.batch.ContactBatchResult attribute) error() (itasc.core.logging.StageLogger method) expand_label_to_foreground() (in module itasc.correction) (in module itasc.correction.labels) export_tracked_labels() (in module itasc.tracking_ultrack.export) extend_track_from_db() (in module itasc.tracking_ultrack.extend) ExtendAssignment (class in itasc.tracking_ultrack.extend) ExtendCandidates (class in itasc.tracking_ultrack.extend) ExtendResult (class in itasc.tracking_ultrack.extend) extract_atoms_frame() (in module itasc.tracking_ultrack.atoms) extract_atoms_stack() (in module itasc.tracking_ultrack.atoms) extract_atoms_stack_with_maps() (in module itasc.tracking_ultrack.atoms) extract_trajectories() (in module itasc.contact_analysis.dynamics) (in module itasc.contact_analysis.dynamics.trajectories)

F

fake_nodes (itasc.tracking_ultrack.corrections.CorrectionDatabaseReport attribute) (itasc.tracking_ultrack.db_build.AnnotateAndScoreReport attribute) faked (itasc.tracking_ultrack.validation_nodes.ValidationInjectionReport attribute) feature_strength (itasc.segmentation.cell_divergence_segmentation.CellDivergenceParams attribute) (itasc.segmentation.cell_label_icm.CellLabelICMParams attribute) (itasc.segmentation.CellDivergenceParams attribute) (itasc.segmentation.CellLabelICMParams attribute) fg_cutoff (itasc.tracking_ultrack.atoms.AtomParams attribute) (itasc.tracking_ultrack.config.TrackingConfig attribute) fg_mask (itasc.segmentation.cell_label_icm.CellICMState attribute) (itasc.segmentation.CellICMState attribute) fg_strength (itasc.segmentation.cell_divergence_segmentation.CellDivergenceParams attribute) (itasc.segmentation.CellDivergenceParams attribute) (itasc.tracking_ultrack.atoms.AtomParams attribute) (itasc.tracking_ultrack.config.TrackingConfig attribute) fg_threshold (itasc.cellpose.flow_following.FlowFollowingParams attribute) (itasc.segmentation.cell_divergence_segmentation.CellDivergenceParams attribute) (itasc.segmentation.CellDivergenceParams attribute) fg_window (itasc.segmentation.cell_divergence_segmentation.CellDivergenceParams attribute) (itasc.segmentation.CellDivergenceParams attribute) (itasc.tracking_ultrack.atoms.AtomParams attribute) (itasc.tracking_ultrack.config.TrackingConfig attribute) fill_label_holes() (in module itasc.correction) (in module itasc.correction.labels) filter_excluded() (in module itasc.contact_analysis.curation) finalize_hierarchy_nodes() (in module itasc.tracking_ultrack.db_query) first_frame (itasc.core.lineage.TrackLane property) (itasc.segmentation.lineage.TrackLane property) (itasc.segmentation.TrackLane property) fit_msd_power_law() (in module itasc.contact_analysis.dynamics.msd) fit_persistence_time() (in module itasc.contact_analysis.dynamics.kinematics) fix_label_semiholes() (in module itasc.correction) (in module itasc.correction.labels)

flow_follow_frame() (in module itasc.cellpose.flow_following) flow_follow_movie() (in module itasc.cellpose.flow_following) flow_step_scale (itasc.cellpose.flow_following.FlowFollowingParams attribute) flow_threshold (itasc.cellpose.cellpose_runner.NucleusParams attribute) flow_weight (itasc.cellpose.flow_following.FlowFollowingParams attribute) FlowFollowingParams (class in itasc.cellpose.flow_following) foreground_clean (itasc.segmentation.cell_divergence_segmentation.CellDivergenceResult attribute) (itasc.segmentation.cell_divergence_segmentation.CellForegroundResult attribute) (itasc.segmentation.CellDivergenceResult attribute) (itasc.segmentation.CellForegroundResult attribute) foreground_from_prob() (in module itasc.cellpose.divergence_maps) foreground_mask (itasc.segmentation.cell_divergence_segmentation.CellDivergenceResult attribute) (itasc.segmentation.cell_divergence_segmentation.CellForegroundResult attribute) (itasc.segmentation.CellDivergenceResult attribute) (itasc.segmentation.CellForegroundResult attribute) foreground_median_radius (itasc.cellpose.divergence_maps.DivergenceMapsReport attribute) (itasc.cellpose.DivergenceMapsReport attribute) foreground_path (itasc.cellpose.divergence_maps.DivergenceMapsReport attribute) (itasc.cellpose.DivergenceMapsReport attribute) foreground_raw (itasc.segmentation.cell_divergence_segmentation.CellDivergenceResult attribute) (itasc.segmentation.cell_divergence_segmentation.CellForegroundResult attribute) (itasc.segmentation.CellDivergenceResult attribute) (itasc.segmentation.CellForegroundResult attribute) foreground_smoothing_sigma (itasc.cellpose.divergence_maps.DivergenceMapsReport attribute) (itasc.cellpose.DivergenceMapsReport attribute) foreground_z_reduction (itasc.cellpose.divergence_maps.DivergenceMapsReport attribute) (itasc.cellpose.DivergenceMapsReport attribute) frame (itasc.contact_analysis.contacts.build.EdgeRecord attribute) (itasc.contact_analysis.contacts.build.T1Record attribute) frame_view_2d() (in module itasc.correction.labels) frames (itasc.cellpose.divergence_maps.DivergenceMapsReport attribute) (itasc.cellpose.DivergenceMapsReport attribute) (itasc.contact_analysis.dynamics.trajectories.Trajectory attribute) (itasc.contact_analysis.dynamics.Trajectory attribute)

G

gaining_cell_a (itasc.contact_analysis.contacts.build.T1Record property) gaining_cell_b (itasc.contact_analysis.contacts.build.T1Record property) gaining_pair (itasc.contact_analysis.contacts.build.T1Record attribute) gamma (itasc.cellpose.cellpose_runner.CellParams attribute) (itasc.cellpose.cellpose_runner.NucleusParams attribute) gaussian_sigma_space (itasc.segmentation.contour_filtering.ContourFilterParams attribute) (itasc.segmentation.ContourFilterParams attribute)

gaussian_sigma_time (itasc.segmentation.contour_filtering.ContourFilterParams attribute) (itasc.segmentation.ContourFilterParams attribute) get_model() (in module itasc.cellpose.cellpose_runner) greedy_color_classes() (in module itasc.tracking_ultrack.db_query) group_dir (itasc.contact_analysis.ContactBatchJob attribute) (itasc.contact_analysis.contacts.batch.ContactBatchJob attribute)

H

has_gap (itasc.core.lineage.TrackLane property) (itasc.segmentation.lineage.TrackLane property) (itasc.segmentation.TrackLane property)

height (itasc.tracking_ultrack.db_query.HierarchyCutState attribute) HierarchyCutState (class in itasc.tracking_ultrack.db_query) HomemadeAnchorInjectionReport (class in itasc.tracking_ultrack.corrections)

I

imwrite_grayscale() (in module itasc.core.tiff) infer_layout_from_ndim() (in module itasc.cellpose.cellpose_runner) info() (itasc.core.logging.StageLogger method) initialize_icm() (in module itasc.segmentation) (in module itasc.segmentation.cell_label_icm) inject_unmatched_anchor_nodes() (in module itasc.tracking_ultrack.corrections) inject_validated_nodes() (in module itasc.tracking_ultrack.validation_nodes) injected (itasc.tracking_ultrack.corrections.HomemadeAnchorInjectionReport attribute) injected_homemade_anchors (itasc.tracking_ultrack.db_build.AnnotateAndScoreReport attribute) inserted (itasc.tracking_ultrack.corrections.AnchorIncidentLinkReport attribute) (itasc.tracking_ultrack.validation_nodes.ValidationInjectionReport attribute) instantaneous (itasc.contact_analysis.dynamics.store.TrackDynamics attribute) (itasc.contact_analysis.dynamics.TrackDynamics attribute) INSTANTANEOUS_COLUMNS (in module itasc.contact_analysis.dynamics.kinematics) instantaneous_table() (in module itasc.contact_analysis.dynamics.kinematics) invalidate_frame() (in module itasc.tracking_ultrack.validation_state) invalidate_track() (in module itasc.tracking_ultrack.validation_state) iou_weight (itasc.tracking_ultrack.config.TrackingConfig attribute) is_built() (itasc.contact_analysis.quantifier.Quantifier method) is_empty() (itasc.tracking_ultrack.extend.ExtendCandidates method) is_model_loaded() (in module itasc.cellpose.cellpose_runner) is_track_validated() (in module itasc.tracking_ultrack.validation_state) is_validated() (in module itasc.tracking_ultrack.validation_state) itasc.cellpose module itasc.cellpose.cellpose_runner module itasc.cellpose.divergence_maps module itasc.cellpose.flow_following module itasc.cellpose.joint module itasc.cellpose.native_masks module itasc.cellpose.retrack module itasc.cellpose.shape module itasc.cellpose.track_laptrack module itasc.contact_analysis module itasc.contact_analysis.catalog module itasc.contact_analysis.config module itasc.contact_analysis.contacts module itasc.contact_analysis.contacts.batch module itasc.contact_analysis.contacts.build module itasc.contact_analysis.contacts.contact_labels module itasc.contact_analysis.contacts.neighborhood module itasc.contact_analysis.contacts.reader module itasc.contact_analysis.contacts.signed_contact_length module itasc.contact_analysis.curation module itasc.contact_analysis.dynamics module itasc.contact_analysis.dynamics.collective module itasc.contact_analysis.dynamics.kinematics module itasc.contact_analysis.dynamics.msd module itasc.contact_analysis.dynamics.store module itasc.contact_analysis.dynamics.trajectories module itasc.contact_analysis.frame_interval module itasc.contact_analysis.pipeline module itasc.contact_analysis.pixel_size module itasc.contact_analysis.quantifier module itasc.contact_analysis.quantifiers module itasc.contact_analysis.quantifiers.cell_density module itasc.contact_analysis.quantifiers.cell_dynamics module itasc.contact_analysis.quantifiers.cell_shape module itasc.contact_analysis.quantifiers.contacts module itasc.contact_analysis.quantifiers.neighbor_count module

itasc.contact_analysis.quantifiers.nucleus_dynamics module itasc.contact_analysis.quantifiers.nucleus_shape module itasc.contact_analysis.quantifiers.shape_relational module itasc.contact_analysis.quantifiers.signed_contact_length module itasc.contact_analysis.records module itasc.contact_analysis.shape module itasc.contact_analysis.shape.core module itasc.contact_analysis.shape.relational module itasc.contact_analysis.shape_tables module itasc.core module itasc.core.cancellation module itasc.core.commit module itasc.core.imageops module itasc.core.label_store module itasc.core.lineage module itasc.core.logging module itasc.core.paths module itasc.core.tiff module itasc.correction module itasc.correction.labels module itasc.segmentation module itasc.segmentation.cell_divergence_segmentation module itasc.segmentation.cell_label_icm module itasc.segmentation.contour_filtering module itasc.segmentation.lineage module itasc.segmentation.nucleus_segmentation module itasc.tracking_ultrack module itasc.tracking_ultrack.atoms module itasc.tracking_ultrack.config module itasc.tracking_ultrack.corrections module itasc.tracking_ultrack.db_build module itasc.tracking_ultrack.db_query module itasc.tracking_ultrack.export module itasc.tracking_ultrack.extend module itasc.tracking_ultrack.ingest module itasc.tracking_ultrack.linking module itasc.tracking_ultrack.multi_threshold module itasc.tracking_ultrack.reseed module itasc.tracking_ultrack.retracker module itasc.tracking_ultrack.scoring module itasc.tracking_ultrack.seed_prior module itasc.tracking_ultrack.solve module itasc.tracking_ultrack.swap_candidate module itasc.tracking_ultrack.track_quality module itasc.tracking_ultrack.validation_nodes module itasc.tracking_ultrack.validation_state module iter_nucleus_maps_stack() (in module itasc.cellpose.native_masks)

J

job (itasc.contact_analysis.ContactBatchResult attribute) (itasc.contact_analysis.contacts.batch.ContactBatchResult attribute)

joint_segment_track() (in module itasc.cellpose.joint)

K

keys (itasc.contact_analysis.shape_tables.ShapeTableSpec attribute)

kind (itasc.contact_analysis.contacts.build.EdgeRecord attribute) (itasc.tracking_ultrack.corrections.Correction attribute)

L

label_contacts() (in module itasc.contact_analysis.contacts) (in module itasc.contact_analysis.contacts.contact_labels) label_ids (itasc.segmentation.cell_label_icm.CellICMState attribute) (itasc.segmentation.CellICMState attribute) label_to_node_id (itasc.tracking_ultrack.db_query.UltrackDbPreview attribute) labels (itasc.segmentation.cell_divergence_segmentation.CellDivergenceResult attribute) (itasc.segmentation.CellDivergenceResult attribute) (itasc.tracking_ultrack.db_query.UltrackDbPreview attribute) lane_for() (itasc.core.lineage.LineageModel method) (itasc.segmentation.lineage.LineageModel method) (itasc.segmentation.LineageModel method) lanes (itasc.core.lineage.LineageModel attribute) (itasc.segmentation.lineage.LineageModel attribute) (itasc.segmentation.LineageModel attribute) last_frame (itasc.core.lineage.TrackLane property) (itasc.segmentation.lineage.TrackLane property) (itasc.segmentation.TrackLane property) layout_has_time() (in module itasc.cellpose.cellpose_runner) layout_has_z() (in module itasc.cellpose.cellpose_runner) length (itasc.contact_analysis.contacts.build.EdgeRecord attribute) (itasc.core.lineage.TrackSegment property) (itasc.segmentation.lineage.TrackSegment property) (itasc.segmentation.TrackSegment property)

LineageModel (class in itasc.core.lineage) (class in itasc.segmentation) (class in itasc.segmentation.lineage) link_annotation_counts() (in module itasc.tracking_ultrack.db_query) link_function (itasc.tracking_ultrack.config.TrackingConfig attribute) link_n_workers (itasc.tracking_ultrack.config.TrackingConfig attribute) linking_mode (itasc.tracking_ultrack.config.TrackingConfig attribute) list_extend_candidates() (in module itasc.tracking_ultrack.extend) list_swap_candidates() (in module itasc.tracking_ultrack.swap_candidate) load_catalog() (in module itasc.contact_analysis) (in module itasc.contact_analysis.catalog) load_config() (in module itasc.contact_analysis) (in module itasc.contact_analysis.config) location_x (itasc.contact_analysis.contacts.build.T1Record attribute) location_y (itasc.contact_analysis.contacts.build.T1Record attribute) losing_cell_a (itasc.contact_analysis.contacts.build.T1Record property) losing_cell_b (itasc.contact_analysis.contacts.build.T1Record property) losing_pair (itasc.contact_analysis.contacts.build.T1Record attribute)

M

mask_2d (itasc.tracking_ultrack.extend.ExtendAssignment attribute) (itasc.tracking_ultrack.extend.ExtendResult attribute) (itasc.tracking_ultrack.swap_candidate.SwapCandidate attribute) max_area (itasc.tracking_ultrack.config.TrackingConfig attribute) max_assign_radius (itasc.cellpose.flow_following.FlowFollowingParams attribute) max_distance (itasc.tracking_ultrack.config.TrackingConfig attribute) max_iterations (itasc.cellpose.flow_following.FlowFollowingParams attribute) max_neighbors (itasc.tracking_ultrack.config.TrackingConfig attribute) max_segments_per_time (itasc.tracking_ultrack.config.TrackingConfig attribute) median_kernel_space (itasc.segmentation.contour_filtering.ContourFilterParams attribute) (itasc.segmentation.ContourFilterParams attribute) median_kernel_time (itasc.segmentation.contour_filtering.ContourFilterParams attribute) (itasc.segmentation.ContourFilterParams attribute) median_radius (itasc.cellpose.divergence_maps.DivergenceMapsReport attribute) (itasc.cellpose.DivergenceMapsReport attribute) memory_floor (itasc.segmentation.cell_divergence_segmentation.CellDivergenceParams attribute) (itasc.segmentation.CellDivergenceParams attribute) (itasc.segmentation.contour_filtering.ContourFilterParams attribute) (itasc.segmentation.ContourFilterParams attribute) memory_tau (itasc.segmentation.cell_divergence_segmentation.CellDivergenceParams attribute) (itasc.segmentation.CellDivergenceParams attribute) (itasc.segmentation.contour_filtering.ContourFilterParams attribute) (itasc.segmentation.ContourFilterParams attribute) merge_catalog_records() (in module itasc.contact_analysis.catalog) merge_cells() (in module itasc.correction) (in module itasc.correction.labels) merge_validated_into_export() (in module itasc.tracking_ultrack.reseed) midpoint_x (itasc.contact_analysis.contacts.build.EdgeRecord attribute) midpoint_y (itasc.contact_analysis.contacts.build.EdgeRecord attribute) min_area (itasc.tracking_ultrack.config.TrackingConfig attribute) min_area_ratio (itasc.tracking_ultrack.config.TrackingConfig attribute) min_link_iou (itasc.tracking_ultrack.config.TrackingConfig attribute) min_size (itasc.cellpose.cellpose_runner.CellParams attribute) (itasc.cellpose.cellpose_runner.NucleusParams attribute) missing_build_params() (itasc.contact_analysis.quantifier.Quantifier method) model_config (itasc.tracking_ultrack.config.TrackingConfig attribute) module itasc.cellpose itasc.cellpose.cellpose_runner itasc.cellpose.divergence_maps itasc.cellpose.flow_following itasc.cellpose.joint itasc.cellpose.native_masks itasc.cellpose.retrack itasc.cellpose.shape itasc.cellpose.track_laptrack itasc.contact_analysis itasc.contact_analysis.catalog itasc.contact_analysis.config itasc.contact_analysis.contacts itasc.contact_analysis.contacts.batch itasc.contact_analysis.contacts.build itasc.contact_analysis.contacts.contact_labels itasc.contact_analysis.contacts.neighborhood itasc.contact_analysis.contacts.reader itasc.contact_analysis.contacts.signed_contact_length itasc.contact_analysis.curation itasc.contact_analysis.dynamics itasc.contact_analysis.dynamics.collective itasc.contact_analysis.dynamics.kinematics itasc.contact_analysis.dynamics.msd itasc.contact_analysis.dynamics.store itasc.contact_analysis.dynamics.trajectories itasc.contact_analysis.frame_interval itasc.contact_analysis.pipeline itasc.contact_analysis.pixel_size itasc.contact_analysis.quantifier itasc.contact_analysis.quantifiers itasc.contact_analysis.quantifiers.cell_density itasc.contact_analysis.quantifiers.cell_dynamics itasc.contact_analysis.quantifiers.cell_shape itasc.contact_analysis.quantifiers.contacts itasc.contact_analysis.quantifiers.neighbor_count itasc.contact_analysis.quantifiers.nucleus_dynamics itasc.contact_analysis.quantifiers.nucleus_shape itasc.contact_analysis.quantifiers.shape_relational itasc.contact_analysis.quantifiers.signed_contact_length itasc.contact_analysis.records itasc.contact_analysis.shape itasc.contact_analysis.shape.core itasc.contact_analysis.shape.relational itasc.contact_analysis.shape_tables itasc.core itasc.core.cancellation itasc.core.commit itasc.core.imageops itasc.core.label_store itasc.core.lineage itasc.core.logging itasc.core.paths itasc.core.tiff itasc.correction itasc.correction.labels itasc.segmentation itasc.segmentation.cell_divergence_segmentation itasc.segmentation.cell_label_icm itasc.segmentation.contour_filtering itasc.segmentation.lineage itasc.segmentation.nucleus_segmentation itasc.tracking_ultrack itasc.tracking_ultrack.atoms itasc.tracking_ultrack.config itasc.tracking_ultrack.corrections itasc.tracking_ultrack.db_build itasc.tracking_ultrack.db_query itasc.tracking_ultrack.export itasc.tracking_ultrack.extend itasc.tracking_ultrack.ingest itasc.tracking_ultrack.linking itasc.tracking_ultrack.multi_threshold itasc.tracking_ultrack.reseed itasc.tracking_ultrack.retracker itasc.tracking_ultrack.scoring itasc.tracking_ultrack.seed_prior itasc.tracking_ultrack.solve itasc.tracking_ultrack.swap_candidate itasc.tracking_ultrack.track_quality itasc.tracking_ultrack.validation_nodes itasc.tracking_ultrack.validation_state

msd (itasc.contact_analysis.dynamics.store.TrackDynamics attribute) (itasc.contact_analysis.dynamics.TrackDynamics attribute) msd_alpha (itasc.contact_analysis.dynamics.store.TrackDynamics attribute) (itasc.contact_analysis.dynamics.TrackDynamics attribute) MSD_COLUMNS (in module itasc.contact_analysis.dynamics.msd) msd_D_um2_per_s (itasc.contact_analysis.dynamics.store.TrackDynamics attribute) (itasc.contact_analysis.dynamics.TrackDynamics attribute) msd_r2 (itasc.contact_analysis.dynamics.store.TrackDynamics attribute) (itasc.contact_analysis.dynamics.TrackDynamics attribute) MSD_TRACK_COLUMNS (in module itasc.contact_analysis.dynamics.msd) MsdFit (class in itasc.contact_analysis.dynamics.msd)

N

n_frames (itasc.contact_analysis.dynamics.trajectories.Trajectory property) (itasc.contact_analysis.dynamics.Trajectory property) (itasc.core.lineage.LineageModel attribute) (itasc.core.lineage.TrackLane property) (itasc.segmentation.lineage.LineageModel attribute) (itasc.segmentation.lineage.TrackLane property) (itasc.segmentation.LineageModel attribute) (itasc.segmentation.TrackLane property) (itasc.tracking_ultrack.db_build.AtomUnionDatabaseBuildReport attribute) n_gaps (itasc.contact_analysis.dynamics.trajectories.Trajectory property) (itasc.contact_analysis.dynamics.Trajectory property) n_labels (itasc.segmentation.cell_label_icm.CellICMState property) (itasc.segmentation.CellICMState property) n_workers (itasc.segmentation.cell_divergence_segmentation.CellDivergenceParams attribute) (itasc.segmentation.cell_label_icm.CellLabelICMParams attribute) (itasc.segmentation.CellDivergenceParams attribute) (itasc.segmentation.CellLabelICMParams attribute) name (itasc.contact_analysis.shape_tables.ShapeTableSpec attribute) nearest_area_index() (in module itasc.tracking_ultrack.swap_candidate) neighbor_annot (itasc.tracking_ultrack.db_query.NodeEdge attribute) neighbor_id (itasc.tracking_ultrack.db_query.NodeEdge attribute)

neighbor_prob (itasc.tracking_ultrack.db_query.NodeEdge attribute) neighbor_t (itasc.tracking_ultrack.db_query.NodeEdge attribute) NeighborCountQuantifier (class in itasc.contact_analysis.quantifiers.neighbor_count) niter (itasc.cellpose.cellpose_runner.NucleusParams attribute) node_annotation_metadata() (in module itasc.tracking_ultrack.db_query) node_annotations (itasc.tracking_ultrack.db_query.UltrackDbPreview attribute) node_id (itasc.tracking_ultrack.swap_candidate.SwapCandidate attribute) node_id_to_label (itasc.tracking_ultrack.db_query.UltrackDbPreview attribute) node_ids (itasc.tracking_ultrack.db_query.HierarchyCutState attribute) node_mask_and_bbox() (in module itasc.tracking_ultrack.db_query) node_preview_metadata() (in module itasc.tracking_ultrack.db_query) NodeEdge (class in itasc.tracking_ultrack.db_query) NodeEdges (class in itasc.tracking_ultrack.db_query) nuc_tracks (itasc.segmentation.cell_label_icm.CellICMState attribute) (itasc.segmentation.CellICMState attribute) nucleus_labels (itasc.contact_analysis.ContactBatchJob attribute) (itasc.contact_analysis.contacts.batch.ContactBatchJob attribute) nucleus_labels_path (itasc.contact_analysis.quantifier.PositionInputs attribute) nucleus_tracked_labels_path (itasc.contact_analysis.contacts.reader.PositionContactAnalysis attribute) NucleusDynamicsQuantifier (class in itasc.contact_analysis.quantifiers.nucleus_dynamics) NucleusParams (class in itasc.cellpose.cellpose_runner) NucleusShapeQuantifier (class in itasc.contact_analysis.quantifiers.nucleus_shape)

O

object_table() (itasc.contact_analysis.quantifier.Quantifier method) (itasc.contact_analysis.quantifiers.cell_dynamics.CellDynamicsQuantifier method) (itasc.contact_analysis.quantifiers.contacts.ContactsQuantifier method) (itasc.contact_analysis.quantifiers.nucleus_dynamics.NucleusDynamicsQuantifier method) offset_slice_labels() (in module itasc.cellpose.native_masks) out_dir (itasc.contact_analysis.config.RunConfig attribute) (itasc.contact_analysis.RunConfig attribute)

output (itasc.contact_analysis.ContactBatchJob attribute) (itasc.contact_analysis.contacts.batch.ContactBatchJob attribute) output_for_record() (in module itasc.contact_analysis.records) OUTPUT_SUBDIR (in module itasc.contact_analysis.quantifier) overlaps_added (itasc.tracking_ultrack.validation_nodes.ValidationInjectionReport attribute)

P

paint_nodes() (in module itasc.tracking_ultrack.db_query) pair (itasc.contact_analysis.contacts.build.EdgeRecord attribute) params (itasc.contact_analysis.config.RunConfig attribute) (itasc.contact_analysis.RunConfig attribute) params_fingerprint() (in module itasc.tracking_ultrack.atoms) pasted_validated (itasc.tracking_ultrack.corrections.PostSolveCorrectionReport attribute) per_track_msd_fit() (in module itasc.contact_analysis.dynamics) (in module itasc.contact_analysis.dynamics.msd) pixel_size_from_config() (in module itasc.contact_analysis.pixel_size) pixel_size_from_tiff() (in module itasc.contact_analysis.pixel_size) pixel_size_um (itasc.contact_analysis.quantifier.PositionInputs attribute) pooled_corr_length() (in module itasc.contact_analysis.dynamics) (in module itasc.contact_analysis.dynamics.collective)

pos_dir() (in module itasc.core.paths) position_config_path() (in module itasc.core.paths) position_dir (itasc.contact_analysis.quantifier.PositionInputs attribute) position_inputs_from_record() (in module itasc.contact_analysis.records) PositionContactAnalysis (class in itasc.contact_analysis.contacts.reader) PositionInputs (class in itasc.contact_analysis.quantifier) PostSolveCorrectionReport (class in itasc.tracking_ultrack.corrections) power (itasc.tracking_ultrack.config.TrackingConfig attribute) probabilities (itasc.tracking_ultrack.db_query.UltrackDbPreview attribute) produces (itasc.contact_analysis.quantifier.Quantifier attribute) (itasc.contact_analysis.quantifiers.contacts.ContactsQuantifier attribute) promote_labels() (in module itasc.core.commit) PROVENANCE_NAME (in module itasc.contact_analysis.shape_tables) prune_validated_overlaps() (in module itasc.tracking_ultrack.reseed)

Q

quality_exponent (itasc.tracking_ultrack.config.TrackingConfig attribute) quality_order() (in module itasc.tracking_ultrack.track_quality) quality_weight (itasc.tracking_ultrack.config.TrackingConfig attribute) Quantifier (class in itasc.contact_analysis.quantifier) quantities (itasc.contact_analysis.config.RunConfig attribute) (itasc.contact_analysis.RunConfig attribute) quantity_id (itasc.contact_analysis.quantifier.Quantifier attribute) (itasc.contact_analysis.quantifiers.cell_density.CellDensityQuantifier attribute) (itasc.contact_analysis.quantifiers.cell_dynamics.CellDynamicsQuantifier attribute) (itasc.contact_analysis.quantifiers.cell_shape.CellShapeQuantifier attribute) (itasc.contact_analysis.quantifiers.contacts.ContactsQuantifier attribute) (itasc.contact_analysis.quantifiers.neighbor_count.NeighborCountQuantifier attribute) (itasc.contact_analysis.quantifiers.nucleus_dynamics.NucleusDynamicsQuantifier attribute) (itasc.contact_analysis.quantifiers.nucleus_shape.NucleusShapeQuantifier attribute) (itasc.contact_analysis.quantifiers.shape_relational.ShapeRelationalQuantifier attribute) (itasc.contact_analysis.quantifiers.signed_contact_length.SignedContactLengthQuantifier attribute)

quantity_ids (itasc.contact_analysis.shape_tables.ShapeTableSpec attribute) query_connected_nodes() (in module itasc.tracking_ultrack.db_query) query_distinct_heights() (in module itasc.tracking_ultrack.db_query) query_frame_range() (in module itasc.tracking_ultrack.db_query) query_hierarchy_cut_states() (in module itasc.tracking_ultrack.db_query) query_middle_frame() (in module itasc.tracking_ultrack.db_query) query_node_edges() (in module itasc.tracking_ultrack.db_query) query_source_node_ids() (in module itasc.tracking_ultrack.multi_threshold) query_union_color_classes() (in module itasc.tracking_ultrack.db_query) query_union_sizes() (in module itasc.tracking_ultrack.db_query)

R

r2 (itasc.contact_analysis.dynamics.msd.MsdFit attribute) read() (itasc.contact_analysis.quantifier.Quantifier method) (itasc.contact_analysis.quantifiers.cell_dynamics.CellDynamicsQuantifier method) (itasc.contact_analysis.quantifiers.contacts.ContactsQuantifier method) (itasc.contact_analysis.quantifiers.nucleus_dynamics.NucleusDynamicsQuantifier method) read_atoms_params() (in module itasc.tracking_ultrack.atoms) read_corrections() (in module itasc.tracking_ultrack.validation_state) read_curation() (in module itasc.contact_analysis.curation) read_full_tracked_stack() (in module itasc.core.label_store) read_instantaneous_table() (in module itasc.contact_analysis.dynamics) (in module itasc.contact_analysis.dynamics.store) read_label_stack() (in module itasc.contact_analysis.shape.core) read_position_contacts() (in module itasc.contact_analysis.contacts.reader) read_table() (in module itasc.contact_analysis.shape_tables) read_track_dynamics() (in module itasc.contact_analysis.dynamics) (in module itasc.contact_analysis.dynamics.store) read_validated_cells_at_frame() (in module itasc.tracking_ultrack.validation_state) read_validated_frames() (in module itasc.tracking_ultrack.validation_state) read_validated_tracks() (in module itasc.tracking_ultrack.validation_state) record_build_params() (in module itasc.contact_analysis.records) relabel_by_tracks() (in module itasc.cellpose.track_laptrack) relabel_cell() (in module itasc.correction.labels) RELATIONAL_COLUMNS (in module itasc.contact_analysis.shape.relational) relative_levels() (in module itasc.contact_analysis.catalog) remap_validated_tracks() (in module itasc.tracking_ultrack.validation_state) remapped_anchor_tracks (itasc.tracking_ultrack.corrections.PostSolveCorrectionReport attribute) remove_exclusion() (in module itasc.contact_analysis.curation) render_hierarchy_cut() (in module itasc.tracking_ultrack.db_query) render_hierarchy_cut_state() (in module itasc.tracking_ultrack.db_query) render_union_partition() (in module itasc.tracking_ultrack.db_query) required_build_params (itasc.contact_analysis.quantifier.Quantifier attribute) (itasc.contact_analysis.quantifiers.cell_density.CellDensityQuantifier attribute) (itasc.contact_analysis.quantifiers.cell_dynamics.CellDynamicsQuantifier attribute) (itasc.contact_analysis.quantifiers.cell_shape.CellShapeQuantifier attribute) (itasc.contact_analysis.quantifiers.nucleus_dynamics.NucleusDynamicsQuantifier attribute) (itasc.contact_analysis.quantifiers.nucleus_shape.NucleusShapeQuantifier attribute) (itasc.contact_analysis.quantifiers.shape_relational.ShapeRelationalQuantifier attribute)

requires (itasc.contact_analysis.quantifier.Quantifier attribute) (itasc.contact_analysis.quantifiers.cell_density.CellDensityQuantifier attribute) (itasc.contact_analysis.quantifiers.cell_dynamics.CellDynamicsQuantifier attribute) (itasc.contact_analysis.quantifiers.cell_shape.CellShapeQuantifier attribute) (itasc.contact_analysis.quantifiers.contacts.ContactsQuantifier attribute) (itasc.contact_analysis.quantifiers.neighbor_count.NeighborCountQuantifier attribute) (itasc.contact_analysis.quantifiers.nucleus_dynamics.NucleusDynamicsQuantifier attribute) (itasc.contact_analysis.quantifiers.nucleus_shape.NucleusShapeQuantifier attribute) (itasc.contact_analysis.quantifiers.shape_relational.ShapeRelationalQuantifier attribute) (itasc.contact_analysis.quantifiers.signed_contact_length.SignedContactLengthQuantifier attribute) residual() (in module itasc.core.imageops) resolve_pixel_size_um() (in module itasc.contact_analysis.pixel_size) resolve_time_interval_s() (in module itasc.contact_analysis.frame_interval) retrack_frame() (in module itasc.cellpose.retrack) retrack_frame_constrained() (in module itasc.tracking_ultrack.retracker) retrack_stack() (in module itasc.cellpose.retrack) run() (in module itasc.contact_analysis) (in module itasc.contact_analysis.pipeline) run_cell_frame() (in module itasc.cellpose.cellpose_runner) run_cell_masks_frame() (in module itasc.cellpose.native_masks) run_cell_masks_stack() (in module itasc.cellpose.native_masks) run_cell_stack() (in module itasc.cellpose.cellpose_runner) run_contact_batch() (in module itasc.contact_analysis) (in module itasc.contact_analysis.contacts.batch) run_linking() (in module itasc.tracking_ultrack.linking) run_nucleus_frame() (in module itasc.cellpose.cellpose_runner) run_nucleus_maps_frame() (in module itasc.cellpose.native_masks) run_nucleus_masks_frame() (in module itasc.cellpose.native_masks) run_nucleus_masks_stack() (in module itasc.cellpose.native_masks) run_nucleus_stack() (in module itasc.cellpose.cellpose_runner) run_solve() (in module itasc.tracking_ultrack.solve) RunConfig (class in itasc.contact_analysis) (class in itasc.contact_analysis.config)

S

save_catalog() (in module itasc.contact_analysis) (in module itasc.contact_analysis.catalog) scored (itasc.tracking_ultrack.seed_prior.SeedPriorReport attribute) scored_nodes (itasc.tracking_ultrack.db_build.AnnotateAndScoreReport attribute) seed_nodes (itasc.tracking_ultrack.db_build.AnnotateAndScoreReport attribute) SeedPriorReport (class in itasc.tracking_ultrack.seed_prior) seeds (itasc.tracking_ultrack.seed_prior.SeedPriorReport attribute) seg_foreground_threshold (itasc.tracking_ultrack.config.TrackingConfig attribute) seg_max_area (itasc.tracking_ultrack.config.TrackingConfig attribute) seg_min_area (itasc.tracking_ultrack.config.TrackingConfig attribute) seg_min_frontier (itasc.tracking_ultrack.config.TrackingConfig attribute) seg_n_workers (itasc.tracking_ultrack.config.TrackingConfig attribute) seg_ws_hierarchy (itasc.tracking_ultrack.config.TrackingConfig attribute) segment_cells_divergence() (in module itasc.segmentation) (in module itasc.segmentation.cell_divergence_segmentation) segments (itasc.core.lineage.TrackLane attribute) (itasc.segmentation.lineage.TrackLane attribute) (itasc.segmentation.TrackLane attribute) select_quantifiers() (in module itasc.contact_analysis) (in module itasc.contact_analysis.pipeline) selected_annot (itasc.tracking_ultrack.db_query.NodeEdges attribute) selected_id (itasc.tracking_ultrack.db_query.NodeEdges attribute) selected_prob (itasc.tracking_ultrack.db_query.NodeEdges attribute) selected_t (itasc.tracking_ultrack.db_query.NodeEdges attribute) shape (itasc.segmentation.cell_label_icm.CellICMState property) (itasc.segmentation.CellICMState property) shape_table_registry() (in module itasc.contact_analysis.shape_tables) ShapeRelationalQuantifier (class in itasc.contact_analysis.quantifiers.shape_relational) ShapeTableSpec (class in itasc.contact_analysis.shape_tables) shell_width (itasc.cellpose.flow_following.FlowFollowingParams attribute) sigmoid() (in module itasc.cellpose.divergence_maps) signed_central_junction_lengths() (in module itasc.contact_analysis.contacts) (in module itasc.contact_analysis.contacts.signed_contact_length)

SignedContactLengthQuantifier (class in itasc.contact_analysis.quantifiers.signed_contact_length) similarity_score() (in module itasc.cellpose.retrack) (in module itasc.tracking_ultrack.scoring) skipped (itasc.tracking_ultrack.atoms.BranchReport attribute) (itasc.tracking_ultrack.validation_nodes.ValidationInjectionReport attribute) skipped_missing (itasc.tracking_ultrack.validation_nodes.ValidationInjectionReport attribute) skipped_no_anchor (itasc.tracking_ultrack.corrections.AnchorTailLinkReport attribute) skipped_no_link (itasc.tracking_ultrack.corrections.AnchorTailLinkReport attribute) skipped_no_mask (itasc.tracking_ultrack.corrections.HomemadeAnchorInjectionReport attribute) skipped_overflow (itasc.tracking_ultrack.corrections.HomemadeAnchorInjectionReport attribute) smoothing_sigma (itasc.cellpose.divergence_maps.DivergenceMapsReport attribute) (itasc.cellpose.DivergenceMapsReport attribute) solution_gap (itasc.tracking_ultrack.config.TrackingConfig attribute) split_across() (in module itasc.correction) (in module itasc.correction.labels) split_draw() (in module itasc.correction) (in module itasc.correction.labels) StageLogger (class in itasc.core.logging) stamped_anchors (itasc.tracking_ultrack.corrections.PostSolveCorrectionReport attribute) start (itasc.core.lineage.TrackSegment attribute) (itasc.segmentation.lineage.TrackSegment attribute) (itasc.segmentation.TrackSegment attribute) status (itasc.contact_analysis.ContactBatchResult attribute) (itasc.contact_analysis.contacts.batch.ContactBatchResult attribute) (itasc.tracking_ultrack.db_query.UltrackDbPreview attribute) step_directions_by_frame() (in module itasc.contact_analysis.dynamics.kinematics) stitch_z() (in module itasc.cellpose.track_laptrack) summary_text() (in module itasc.tracking_ultrack.db_query) supported_quantities() (in module itasc.contact_analysis.records) swap_labels() (in module itasc.correction) (in module itasc.correction.labels) SwapCandidate (class in itasc.tracking_ultrack.swap_candidate)

T

t (itasc.tracking_ultrack.corrections.Correction attribute) t1_event_id (itasc.contact_analysis.contacts.build.T1Record attribute) t1_events (itasc.contact_analysis.contacts.reader.PositionContactAnalysis attribute) T1Record (class in itasc.contact_analysis.contacts.build) table_for_quantity() (in module itasc.contact_analysis.shape_tables) table_keys (itasc.contact_analysis.quantifier.Quantifier attribute) (itasc.contact_analysis.quantifiers.cell_density.CellDensityQuantifier attribute) (itasc.contact_analysis.quantifiers.cell_dynamics.CellDynamicsQuantifier attribute) (itasc.contact_analysis.quantifiers.cell_shape.CellShapeQuantifier attribute) (itasc.contact_analysis.quantifiers.neighbor_count.NeighborCountQuantifier attribute) (itasc.contact_analysis.quantifiers.nucleus_dynamics.NucleusDynamicsQuantifier attribute) (itasc.contact_analysis.quantifiers.nucleus_shape.NucleusShapeQuantifier attribute) (itasc.contact_analysis.quantifiers.shape_relational.ShapeRelationalQuantifier attribute) (itasc.contact_analysis.quantifiers.signed_contact_length.SignedContactLengthQuantifier attribute) table_path() (in module itasc.contact_analysis.shape_tables) target_frame (itasc.tracking_ultrack.extend.ExtendCandidates attribute) (itasc.tracking_ultrack.extend.ExtendResult attribute) time_interval_from_config() (in module itasc.contact_analysis.frame_interval) time_interval_from_tiff() (in module itasc.contact_analysis.frame_interval) time_interval_s (itasc.contact_analysis.quantifier.PositionInputs attribute) time_limit (itasc.tracking_ultrack.config.TrackingConfig attribute) to_canonical_tzyx() (in module itasc.cellpose.shape) to_tzyx() (in module itasc.cellpose.cellpose_runner)

total_nodes (itasc.tracking_ultrack.db_build.AtomUnionDatabaseBuildReport attribute) total_overlaps (itasc.tracking_ultrack.db_build.AtomUnionDatabaseBuildReport attribute) track_axiswise() (in module itasc.cellpose.track_laptrack) TRACK_COLUMNS (in module itasc.contact_analysis.dynamics.kinematics) track_id (itasc.contact_analysis.dynamics.trajectories.Trajectory attribute) (itasc.contact_analysis.dynamics.Trajectory attribute) track_masks() (in module itasc.cellpose.track_laptrack) track_quality_scores() (in module itasc.tracking_ultrack.track_quality) track_summary_table() (in module itasc.contact_analysis.dynamics.kinematics) TrackDynamics (class in itasc.contact_analysis.dynamics) (class in itasc.contact_analysis.dynamics.store) TrackingConfig (class in itasc.tracking_ultrack.config) TrackLane (class in itasc.core.lineage) (class in itasc.segmentation) (class in itasc.segmentation.lineage) tracks (itasc.contact_analysis.dynamics.store.TrackDynamics attribute) (itasc.contact_analysis.dynamics.TrackDynamics attribute) TrackSegment (class in itasc.core.lineage) (class in itasc.segmentation) (class in itasc.segmentation.lineage) trajectories_from_stack() (in module itasc.contact_analysis.dynamics) (in module itasc.contact_analysis.dynamics.trajectories) Trajectory (class in itasc.contact_analysis.dynamics) (class in itasc.contact_analysis.dynamics.trajectories)

U

UltrackDatabaseBuildReport (class in itasc.tracking_ultrack.db_build) UltrackDbPreview (class in itasc.tracking_ultrack.db_query)

unary_dense (itasc.segmentation.cell_label_icm.CellICMState attribute) (itasc.segmentation.CellICMState attribute) unmatched_anchors (itasc.tracking_ultrack.corrections.CorrectionDatabaseReport attribute)

V

validate_frame() (in module itasc.tracking_ultrack.validation_state)

validate_track() (in module itasc.tracking_ultrack.validation_state) ValidationInjectionReport (class in itasc.tracking_ultrack.validation_nodes)

W

wants_build_params (itasc.contact_analysis.quantifier.Quantifier attribute) (itasc.contact_analysis.quantifiers.cell_density.CellDensityQuantifier attribute) warning() (itasc.core.logging.StageLogger method) weight (itasc.tracking_ultrack.db_query.NodeEdge attribute) (itasc.tracking_ultrack.extend.ExtendAssignment attribute) (itasc.tracking_ultrack.extend.ExtendResult attribute) weight_is_null (itasc.tracking_ultrack.db_query.NodeEdge attribute) window_size (itasc.tracking_ultrack.config.TrackingConfig attribute)

write_atoms_tif() (in module itasc.tracking_ultrack.atoms) write_config() (in module itasc.contact_analysis.config) write_corrections() (in module itasc.tracking_ultrack.validation_state) write_curation() (in module itasc.contact_analysis.curation) write_full_tracked_stack() (in module itasc.core.label_store) write_masks() (in module itasc.cellpose.native_masks) write_outputs() (in module itasc.cellpose.cellpose_runner) write_seed_prior_node_probs() (in module itasc.tracking_ultrack.seed_prior) write_validated_frames() (in module itasc.tracking_ultrack.validation_state)

X

x (itasc.tracking_ultrack.corrections.Correction attribute)

xy (itasc.contact_analysis.dynamics.trajectories.Trajectory attribute) (itasc.contact_analysis.dynamics.Trajectory attribute)

Y

y (itasc.tracking_ultrack.corrections.Correction attribute)