Geff IO

A reader and writer for the graph exchange file format (geff)

This napari plugin was generated with copier using the napari-plugin-template.

Installation

You can install napari-geff via pip:

pip install napari-geff

If napari is not already installed, you can install napari-geff with napari and Qt via:

pip install "napari-geff[all]"

Usage

napari-geff supports loading directed graphs stored as GEFF files into napari as Tracks layers, and saving them back out to GEFF format.

To use napari-geff after installation, simply drag a GEFF file into the viewer and select GEFF IO from the plugin selection dialog, if required. The file will be loaded as a Tracks layer.

Any node properties defined on your graph will be stored as features on your tracks layer. Edge properties will be available under layer.metadata['edge_properties'] as a dictionary, but cannot currently be displayed or used for visualization in napari.

If your file contains image or labels related objects as per the GEFF spec, these will also be loaded alongside your Tracks layer.

If you wish to open your geff file into layers programmatically, you can do so using the viewer.open method:

import napari
path = 'path/to/top_level_zarr.zarr/my-geff-group/

viewer = napari.Viewer()
layers = viewer.open(path, plugin='napari-geff')

Contributing

Contributions are very welcome. Tests can be run with tox, please ensure the coverage at least stays the same before you submit a pull request.

License

Distributed under the terms of the BSD-3 license, "napari-geff" is free and open source software

Acknowledgements

The data in docs/examples/cell_segmentation_data are generated by cropping and resizing images in https://osf.io/ysaq2/, which is distributed with Creative Commons Attribution 4.0 International. See 10.1038/sdata.2018.237 for details.

Issues

If you encounter any problems, please [file an issue] along with a detailed description.