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:
CTC_PATH The path to the directory containing ctc
tracks (man_track.txt or res_track.txt), e.g.
data/01_GT/TRA or data/01_RES \[required]
GEFF_PATH Path to save the output geff, including the
geff directory name (eg.
~/folder/folder/data.zarr/tracks.geff)
\[required]
--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]
convert-trackmate-xml
Convert a TrackMate XML file to a GEFF file.
Usage:
convert-trackmate-xml [OPTIONS] XML_PATH GEFF_PATH
Options:
XML_PATH The path to the TrackMate XML file
\[required]
GEFF_PATH Path to save the output geff, including the
geff directory name (eg.
~/folder/folder/data.zarr/tracks.geff)
\[required]
--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
Options:
INPUT_PATH Path to the GEFF folder, e.g. data.zarr/tracks.geff \[required]
validate
Validate a GEFF file.
Usage:
validate [OPTIONS] INPUT_PATH
Options:
INPUT_PATH Path to the GEFF folder, e.g. data.zarr/tracks.geff \[required]
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