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Conversion to GEFF

If you already have tracking data stored in another format, we have some functions for converting data to GEFF.

Cell Tracking Challenge (CTC)

To use the geff cli to convert CTC data to GEFF, see the docs for geff convert-ctc.

To use the geff python API, see the docs for ctc_tiffs_to_zarr and from_ctc_to_geff.

Trackmate XML

Note

Conversion from TrackMate XML to GEFF is currently NOT lossless, but we are working on it.
The output GEFF is missing:

  • for each spot, the coordinates of its ROI (segmentation)
  • for each track, the value of its features (e.g., TRACK_DISPLACEMENT, TRACK_MEAN_SPEED)

To convert a Trackmat XML file to GEFF using the geff cli, see the docs for geff convert-trackmate-xml.

To use the geff python API, see the docs for from_trackmate_xml_to_geff.

AceTree

An example of how to convert AceTree data to a GEFF is available here.