Command line tools

geff

GEFF Command Line Interface

Usage:

 [OPTIONS] COMMAND [ARGS]...

Options:

  --install-completion  Install completion for the current shell.
  --show-completion     Show completion for the current shell, to copy it or
                        customize the installation.

convert-ctc

Convert a CTC data directory to a GEFF file.

Usage:

 convert-ctc [OPTIONS] CTC_PATH GEFF_PATH

Options:

  --segm-path PATH              The path to export the segmentation file, if
                                not provided, it won't be exported.
  --input-image-dir PATH        The path to the input image directory. If not
                                provided, it won't be exported.
  --output-image-path PATH      The path to export the image file, if not
                                provided, it won't be exported.
  --tczyx / --no-tczyx          Expand data to make it (T, C, Z, Y, X)
                                otherwise it's (T,) + Frame shape.  \[default:
                                no-tczyx]
  --overwrite / --no-overwrite  Whether to overwrite the GEFF file if it
                                already exists.  \[default: no-overwrite]
  --zarr-format INTEGER         The version of zarr to write.  \[default: 2]

convert-to-csv

Usage:

 convert-to-csv [OPTIONS] STORE OUTPATH

convert-trackmate-xml

Convert a TrackMate XML file to a GEFF file.

Usage:

 convert-trackmate-xml [OPTIONS] XML_PATH GEFF_PATH

Options:

  --discard-filtered-spots / --no-discard-filtered-spots
                                  True to discard the spots filtered out in
                                  TrackMate, False otherwise.  \[default: no-
                                  discard-filtered-spots]
  --discard-filtered-tracks / --no-discard-filtered-tracks
                                  True to discard the tracks filtered out in
                                  TrackMate, False otherwise.  \[default: no-
                                  discard-filtered-tracks]
  --overwrite / --no-overwrite    Whether to overwrite the GEFF file if it
                                  already exists.  \[default: no-overwrite]
  --zarr-format INTEGER           The version of zarr to write.  \[default: 2]

info

Display information about a GEFF file.

Usage:

 info [OPTIONS] INPUT_PATH

validate

Validate a GEFF file.

Usage:

 validate [OPTIONS] INPUT_PATH

Running command line tools

Without pip-installing geff, you can run the tools as

uvx geff -h # by uv
# or 
pipx geff -h # by pipx

Running command with a developmental build

You can run the command line tool for your local build as

pip install -e .
geff -h