ultrack

Large-scale cell tracking under segmentation uncertainty.

Zebrafish imaged using DaXi whole embryo tracking.

Basics:

• Quickstart
  • Installation
  • Basic Usage
  • Advanced Features
  • Contribute
  • Support and Feedback
  • Citing
  • License
• Theory
• FAQ

Reference:

• API
  • Core functionalities
    • Tracker
      • Tracker.add_flow()
      • Tracker.link()
      • Tracker.segment()
      • Tracker.solve()
      • Tracker.to_ctc()
      • Tracker.to_napari()
      • Tracker.to_networkx()
      • Tracker.to_pandas()
      • Tracker.to_trackmate()
      • Tracker.to_zarr()
      • Tracker.track()
    • add_flow()
    • link()
    • load_config()
    • segment()
    • solve()
    • to_ctc()
    • to_trackmate()
    • to_tracks_layer()
    • track()
    • tracks_to_zarr()
  • Array utilities
    • array_apply()
    • check_array_chunk()
    • create_zarr()
    • large_chunk_size()
    • validate_and_overwrite_path()
  • Image processing utilities
    • DL models interface
      • Cellpose
      • PlantSeg
      • MicroSAM
      • set_peak_maxima_prompt()
    • Flow
      • add_flow()
      • advenct_field()
      • advenct_field_from_labels()
      • advenct_from_quasi_random()
      • apply_field()
      • flow_field()
      • identity_grid()
      • timelapse_flow()
      • trajectories_to_tracks()
  • Tracks utilities
    • add_track_ids_to_tracks_df()
    • close_tracks_gaps()
    • filter_short_sibling_tracks()
    • get_paths_to_roots()
    • get_subgraph()
    • inv_tracks_df_forest()
    • left_first_search()
    • sort_track_ids()
    • sort_trees_by_length()
    • sort_trees_by_max_radius()
    • split_tracks_df_by_lineage()
    • split_trees()
    • tracks_df_forest()
    • tracks_df_movement()
    • tracks_length()
    • tracks_profile_matrix()
  • Exporting
    • to_ctc()
    • to_networkx()
    • to_trackmate()
    • to_tracks_layer()
    • tracks_layer_to_networkx()
    • tracks_layer_to_trackmate()
    • tracks_to_zarr()
• CLI
  • ultrack create_config
  • ultrack segment
  • ultrack flow
  • ultrack link
  • ultrack solve
  • ultrack export
    • ctc
    • lp
    • trackmate
    • zarr-napari
  • ultrack clear_database