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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.

DataFrames / CSV

To convert pandas DataFrames to a GEFF store, use dataframes_to_geff. The node DataFrame must have an ID column (default "id") and the edge DataFrame must have source and target columns (default "source" and "target"). All other columns become node or edge properties.

To convert CSV files directly, use csv_to_geff. The CSVs are expected to have a header row and a pandas-style index column.

To convert in the other direction, use geff_to_dataframes or geff_to_csv.

AceTree

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