Supported tracking formats

The program itself uses .aut files. This is the only file format that saves all data, including positions, position shape, errors and warnings, data axes, etc. You can also import/export from other formats, but beware that data will be lost in the conversion process.

The TrackMate format saves positions, links and the resolution. Other data is lost. Cell merges are included. Importing works by opening a TrackMate XML file, exporting can be done in the File -> Export links menu.
The Cell Tracking Challenge track format is described at https://celltrackingchallenge.net/. You can export your data using the File -> Export links menu option, and you can import your data simply by loading the man_track.txt file. OrganoidTracker only exports the positions and links. Cell merges (like in the skin) are not supported, as this file format only allows one single parent for each cell track.
The Paraview CSV format just consists of a bunch of CSV files. Use File -> Export positions to export the positions with or without extra data like cell density and track id. You’ll be asked to select a folder to export everything to. After exporting you’ll find a help file in that folder with instructions on how to import your files in Paraview. If you choose to export the positions with metadata, you’ll also get a JSON file with a colormap, so that you can color the cells by lineage in Paraview.
For other formats you will need to write an importer yourself. Instructions can be found at the custom tracking formats page.

If you’re writing a Python script for data analysis, I recommend looking at the API to see how you can interact with the data files. If you’re using another programming language, you can load the .aut file as a JSON file.

Some details of AUT tracking format

AUT files are simply JSON files, and the format is mostly self-explanatory. However, for storing the position and links two varations exist.

There is the older “v1” format, in use from 2018-2024. You can recognize these files by the "version": "v1" entry in the root of the file. It stored positions and links, plus their metadata, in a kind of cumbersome and duplicative way:

// Old format
"positions": {
 "1": [[56.4, 54.1, 4], ...],
 ...
},
"links": { // Links i nthe d3js graph format
    "directed": false,
    "multigraph": false,
    "graph": {},
    "nodes": [
      // All positions again, so that we follow the d3js format
      // Difference with above is that we now also list position metadata
      // Note how "_time_point_number" and the metadata keys are repeated over and over,
      // further bloating file size
      {"id": {"x": 136.92842303555807, "y": 186.91887053353733, "z": 12.0,
        "_time_point_number": 1, "blah": ...}},
      {"id": {"x": 157.02603447837174, "y": 184.34746761541615, "z": 12.0,
        "_time_point_number": 1, "blah": ...}}
      ...
    ],
    "links": [
       // All individual links
       // The save format doesn't know about tracks, so those are reconstructed when loading tracking data
       {
         "source": {"x": 132.0952578173535, "y": 249.18141069746628, "z": 12.0, "_time_point_number": 1},
         "target": {"x": 125.84057341732412, "y": 253.73027207930585, "z": 12.0, "_time_point_number": 2},
         "blah": ...  // Link metadata
       },
       ...
    ]
}

There is also the newer “v2” format, in use from 2025 onwards. You can recognize these files by the "version": "v2" entry in the root of the file. It directly stores tracks, and also stores metadata in a more efficient way, without repeating the metadata keys over and over:

// New format
"positions": [
  { // Holds all positions and metadata for a single time point
    "time_point": 0,
    "coords_xyz_px": [[56.4, 54.1, 4], ...],
    "position_meta": { // Position meta now stored among the positions (instead of in the links graph)
       "blah": [...]  // One entry per position, null if not defined
    }
  },
  ...
]
"tracks": [
  { // Holds all positions and metadata for a single track

    // Coords of mother cell, in time point 17. Usually one entry, multiple in case of cell merges
    "coords_xyz_px_before": [[52.4, 51.1, 3]],  
    "time_point_start": 18,  // Time point of first position of track, 18 in this case
    // Coords of all positions, first for time point 18, then time point 19, etc.
    "coords_xyz_px": [[56.4, 54.1, 4], [58.4, 55.1, 4], ...],  
    "link_meta": { // Link metadata
       "blah": [...],
       ...
    },
    "link_meta_before": { // Link metadata for the links connecting this track to the previous track(s)
       "blah": [...],
       ...
    },
    
    // Metadata for the entire lineage (so also daughter tracks), only defined for tracks without a previous track
    "lineage_meta": { 
        "blah": ...  
    }
  },
  ...
],