Index

Symbols

--api-results-path ultrack-server command line option --batch-index ultrack-link command line option ultrack-segment command line option ultrack-solve command line option --channel-axis ultrack-flow command line option ultrack-link command line option --config ultrack-clear_database command line option ultrack-data_summary command line option ultrack-export-ctc command line option ultrack-export-lp command line option ultrack-export-trackmate command line option ultrack-export-zarr-napari command line option ultrack-flow command line option ultrack-link command line option ultrack-segment command line option ultrack-server command line option ultrack-solve command line option --contours-layer ultrack-segment command line option --dilation-iters ultrack-export-ctc command line option --first-frame-path ultrack-export-ctc command line option --foreground-layer ultrack-segment command line option --host ultrack-server command line option --image-path ultrack-export-zarr-napari command line option --insertion-throttle-rate ultrack-segment command line option --layer-key ultrack-estimate_params command line option --margin ultrack-export-ctc command line option --measure ultrack-export-zarr-napari command line option --output-directory ultrack-data_summary command line option ultrack-estimate_params command line option ultrack-export-ctc command line option ultrack-export-zarr-napari command line option ultrack-labels_to_contours command line option --output-path ultrack-export-lp command line option ultrack-export-trackmate command line option --overwrite ultrack-export-ctc command line option ultrack-export-lp command line option ultrack-export-trackmate command line option ultrack-export-zarr-napari command line option ultrack-labels_to_contours command line option ultrack-link command line option ultrack-segment command line option ultrack-solve command line option --port ultrack-server command line option --reader-plugin ultrack-estimate_params command line option ultrack-export-zarr-napari command line option ultrack-flow command line option ultrack-labels_to_contours command line option ultrack-link command line option ultrack-segment command line option --scale ultrack-export-ctc command line option

--sigma ultrack-labels_to_contours command line option --stitch-tracks ultrack-export-ctc command line option --timelapse ultrack-estimate_params command line option -b ultrack-link command line option ultrack-segment command line option ultrack-solve command line option -cfg ultrack-clear_database command line option ultrack-data_summary command line option ultrack-export-ctc command line option ultrack-export-lp command line option ultrack-export-trackmate command line option ultrack-export-zarr-napari command line option ultrack-flow command line option ultrack-link command line option ultrack-segment command line option ultrack-server command line option ultrack-solve command line option -cha ultrack-flow command line option ultrack-link command line option -cl ultrack-segment command line option -di ultrack-export-ctc command line option -fl ultrack-segment command line option -i ultrack-export-zarr-napari command line option -l ultrack-estimate_params command line option -ma ultrack-export-ctc command line option -nt ultrack-estimate_params command line option -o ultrack-data_summary command line option ultrack-estimate_params command line option ultrack-export-ctc command line option ultrack-export-lp command line option ultrack-export-trackmate command line option ultrack-export-zarr-napari command line option ultrack-labels_to_contours command line option -ow ultrack-export-ctc command line option ultrack-export-lp command line option ultrack-export-trackmate command line option ultrack-export-zarr-napari command line option ultrack-labels_to_contours command line option ultrack-link command line option ultrack-segment command line option ultrack-solve command line option -r ultrack-estimate_params command line option ultrack-export-zarr-napari command line option ultrack-flow command line option ultrack-labels_to_contours command line option ultrack-link command line option ultrack-segment command line option -s ultrack-export-ctc command line option ultrack-labels_to_contours command line option -t ultrack-estimate_params command line option

_

__call__() (ultrack.imgproc.PlantSeg method) (ultrack.imgproc.sam.MicroSAM method)

A

add_flow() (in module ultrack) (in module ultrack.imgproc.flow) (ultrack.Tracker method) add_links() (ultrack.Tracker method) add_new_node() (in module ultrack) add_nodes_prob() (ultrack.Tracker method) add_track_ids_to_tracks_df() (in module ultrack.tracks) address (ultrack.config.DataConfig attribute), [1]

advenct_field() (in module ultrack.imgproc.flow) advenct_field_from_labels() (in module ultrack.imgproc.flow) advenct_from_quasi_random() (in module ultrack.imgproc.flow) anisotropy_penalization (ultrack.config.SegmentationConfig attribute), [1] appear_weight (ultrack.config.TrackingConfig attribute), [1] apply_field() (in module ultrack.imgproc.flow) array_apply() (in module ultrack.utils.array) assert_same_length() (in module ultrack.utils.array)

B

bias (ultrack.config.TrackingConfig attribute), [1]

C

check_array_chunk() (in module ultrack.utils.array)

close_tracks_gaps() (in module ultrack.tracks) create_zarr() (in module ultrack.utils.array)

D

data_config (ultrack.config.MainConfig attribute), [1] database (ultrack.config.DataConfig attribute), [1] database_path (ultrack.config.DataConfig property), [1] detect_foreground() (in module ultrack.imgproc)

dict() (ultrack.config.DataConfig method), [1] (ultrack.config.SegmentationConfig method), [1] disappear_weight (ultrack.config.TrackingConfig attribute), [1] distance_weight (ultrack.config.LinkingConfig attribute), [1] division_weight (ultrack.config.TrackingConfig attribute), [1]

E

ExperimentStatus (class in ultrack.api.database)

export_by_extension() (ultrack.Tracker method) export_tracks_by_extension() (in module ultrack)

F

filter_short_sibling_tracks() (in module ultrack.tracks)

flow_field() (in module ultrack.imgproc.flow)

G

get_nodes_features() (ultrack.Tracker method)

get_paths_to_roots() (in module ultrack.tracks) get_subgraph() (in module ultrack.tracks)

I

identity_grid() (in module ultrack.imgproc.flow)

inv_tracks_df_forest() (in module ultrack.tracks) inverted_edt() (in module ultrack.imgproc)

L

labels_to_contours() (in module ultrack.utils) large_chunk_size() (in module ultrack.utils.array) left_first_search() (in module ultrack.tracks) link() (in module ultrack) (ultrack.Tracker method)

link_function (ultrack.config.TrackingConfig attribute), [1] linking_config (ultrack.config.MainConfig attribute), [1] load_config() (in module ultrack)

M

max_area (ultrack.config.SegmentationConfig attribute), [1] max_distance (ultrack.config.LinkingConfig attribute), [1] max_neighbors (ultrack.config.LinkingConfig attribute), [1] max_noise (ultrack.config.SegmentationConfig attribute), [1] metadata (ultrack.config.DataConfig property), [1] metadata_add() (ultrack.config.DataConfig method), [1] method (ultrack.config.TrackingConfig attribute), [1] MicroSAM (class in ultrack.imgproc.sam) min_area (ultrack.config.SegmentationConfig attribute), [1] min_frontier (ultrack.config.SegmentationConfig attribute), [1]

MODE ultrack-clear_database command line option module ultrack ultrack.core.export ultrack.imgproc ultrack.imgproc.flow ultrack.imgproc.sam ultrack.tracks ultrack.utils.array

N

n_threads (ultrack.config.TrackingConfig attribute), [1] n_workers (ultrack.config.DataConfig attribute), [1] (ultrack.config.LinkingConfig attribute), [1] (ultrack.config.SegmentationConfig attribute), [1]

normalize() (in module ultrack.imgproc)

O

OUTPUT_PATH ultrack-create_config command line option

overlap_size (ultrack.config.TrackingConfig attribute), [1]

P

PATHS ultrack-estimate_params command line option ultrack-flow command line option ultrack-labels_to_contours command line option ultrack-link command line option ultrack-segment command line option

PlantSeg (class in ultrack.imgproc) power (ultrack.config.TrackingConfig attribute), [1]

R

register_timelapse() (in module ultrack.imgproc)

robust_invert() (in module ultrack.imgproc)

S

segment() (in module ultrack) (ultrack.Tracker method) segmentation_config (ultrack.config.MainConfig attribute), [1] set_peak_maxima_prompt() (in module ultrack.imgproc.sam) solution_gap (ultrack.config.TrackingConfig attribute), [1] solve() (in module ultrack) (ultrack.Tracker method)

sort_track_ids() (in module ultrack.tracks) sort_trees_by_length() (in module ultrack.tracks) sort_trees_by_max_radius() (in module ultrack.tracks) split_tracks_df_by_lineage() (in module ultrack.tracks) split_trees() (in module ultrack.tracks)

T

threshold (ultrack.config.SegmentationConfig attribute), [1] time_limit (ultrack.config.TrackingConfig attribute), [1] timelapse_flow() (in module ultrack.imgproc.flow) to_ctc() (in module ultrack) (in module ultrack.core.export) (ultrack.Tracker method) to_networkx() (in module ultrack.core.export) (ultrack.Tracker method) to_pandas() (ultrack.Tracker method) to_sqlalchemy() (ultrack.api.database.Experiment method) to_trackmate() (in module ultrack) (in module ultrack.core.export) (ultrack.Tracker method) to_tracks_layer() (in module ultrack) (in module ultrack.core.export) (ultrack.Tracker method)

to_zarr() (ultrack.Tracker method) track() (in module ultrack) (ultrack.Tracker method) Tracker (class in ultrack) tracking_config (ultrack.config.MainConfig attribute), [1] tracks_df_forest() (in module ultrack.tracks) tracks_df_movement() (in module ultrack.tracks) tracks_layer_to_networkx() (in module ultrack.core.export) tracks_layer_to_trackmate() (in module ultrack.core.export) tracks_length() (in module ultrack.tracks) tracks_profile_matrix() (in module ultrack.tracks) tracks_properties() (in module ultrack.imgproc) tracks_to_zarr() (in module ultrack) (in module ultrack.core.export) trajectories_to_tracks() (in module ultrack.imgproc.flow)

U

ultrack module ultrack-clear_database command line option --config -cfg MODE ultrack-create_config command line option OUTPUT_PATH ultrack-data_summary command line option --config --output-directory -cfg -o ultrack-estimate_params command line option --layer-key --output-directory --reader-plugin --timelapse -l -nt -o -r -t PATHS ultrack-export-ctc command line option --config --dilation-iters --first-frame-path --margin --output-directory --overwrite --scale --stitch-tracks -cfg -di -ma -o -ow -s ultrack-export-lp command line option --config --output-path --overwrite -cfg -o -ow ultrack-export-trackmate command line option --config --output-path --overwrite -cfg -o -ow ultrack-export-zarr-napari command line option --config --image-path --measure --output-directory --overwrite --reader-plugin -cfg -i -o -ow -r ultrack-flow command line option --channel-axis --config --reader-plugin -cfg -cha -r PATHS

ultrack-labels_to_contours command line option --output-directory --overwrite --reader-plugin --sigma -o -ow -r -s PATHS ultrack-link command line option --batch-index --channel-axis --config --overwrite --reader-plugin -b -cfg -cha -ow -r PATHS ultrack-segment command line option --batch-index --config --contours-layer --foreground-layer --insertion-throttle-rate --overwrite --reader-plugin -b -cfg -cl -fl -ow -r PATHS ultrack-server command line option --api-results-path --config --host --port -cfg ultrack-solve command line option --batch-index --config --overwrite -b -cfg -ow ultrack.core.export module ultrack.imgproc module ultrack.imgproc.flow module ultrack.imgproc.sam module ultrack.tracks module ultrack.utils.array module

V

validate_and_overwrite_path() (in module ultrack.utils.array)

W

window_size (ultrack.config.TrackingConfig attribute), [1]

working_dir (ultrack.config.DataConfig attribute), [1] ws_hierarchy (ultrack.config.SegmentationConfig attribute), [1]

Z

z_score_threshold (ultrack.config.LinkingConfig attribute), [1]