{"name":"napari-geff","display_name":"Geff IO","visibility":"public","icon":"","categories":[],"schema_version":"0.2.1","on_activate":null,"on_deactivate":null,"contributions":{"commands":[{"id":"napari-geff.get_reader","title":"Open data with Geff IO","python_name":"napari_geff._reader:get_geff_reader","short_title":null,"category":null,"icon":null,"enablement":null},{"id":"napari-geff.write","title":"Save data with Geff IO","python_name":"napari_geff._writer:write_tracks","short_title":null,"category":null,"icon":null,"enablement":null},{"id":"napari-geff.sample_data","title":"Load sample data","python_name":"napari_geff.data.load_sample_data:load_sample_data","short_title":null,"category":null,"icon":null,"enablement":null},{"id":"napari-geff.sample_data_3d","title":"Load 3D sample data","python_name":"napari_geff.data.load_sample_data:load_sample_data_3d","short_title":null,"category":null,"icon":null,"enablement":null}],"readers":[{"command":"napari-geff.get_reader","filename_patterns":["*"],"accepts_directories":true}],"writers":[{"command":"napari-geff.write","layer_types":["tracks"],"filename_extensions":[],"display_name":""}],"widgets":null,"sample_data":[{"command":"napari-geff.sample_data","key":"napari-geff.sample_data","display_name":"Sample tracks data, w masks and images"},{"command":"napari-geff.sample_data_3d","key":"napari-geff.sample_data_3d","display_name":"Sample tracks data, 3D"}],"themes":null,"menus":{},"submenus":null,"keybindings":null,"configuration":[]},"package_metadata":{"metadata_version":"2.4","name":"napari-geff","version":"0.0.4","dynamic":["license-file"],"platform":null,"supported_platform":null,"summary":"A reader and writer for the graph exchange file format (geff)","description":"# napari-geff\n\n[![License BSD-3](https://img.shields.io/pypi/l/napari-geff.svg?color=green)](https://github.com/live-image-tracking-tools/napari-geff/raw/main/LICENSE)\n[![PyPI](https://img.shields.io/pypi/v/napari-geff.svg?color=green)](https://pypi.org/project/napari-geff)\n[![Python Version](https://img.shields.io/pypi/pyversions/napari-geff.svg?color=green)](https://python.org)\n[![tests](https://github.com/live-image-tracking-tools/napari-geff/workflows/tests/badge.svg)](https://github.com/live-image-tracking-tools/napari-geff/actions)\n[![codecov](https://codecov.io/gh/live-image-tracking-tools/napari-geff/branch/main/graph/badge.svg)](https://codecov.io/gh/live-image-tracking-tools/napari-geff)\n[![napari hub](https://img.shields.io/endpoint?url=https://api.napari-hub.org/shields/napari-geff)](https://napari-hub.org/plugins/napari-geff)\n[![npe2](https://img.shields.io/badge/plugin-npe2-blue?link=https://napari.org/stable/plugins/index.html)](https://napari.org/stable/plugins/index.html)\n[![Copier](https://img.shields.io/endpoint?url=https://raw.githubusercontent.com/copier-org/copier/master/img/badge/badge-grayscale-inverted-border-purple.json)](https://github.com/copier-org/copier)\n\nA reader and writer for the graph exchange file format (geff)\n\n----------------------------------\n\nThis [napari] plugin was generated with [copier] using the [napari-plugin-template].\n\n<!--\nDon't miss the full getting started guide to set up your new package:\nhttps://github.com/napari/napari-plugin-template#getting-started\n\nand review the napari docs for plugin developers:\nhttps://napari.org/stable/plugins/index.html\n-->\n\n![geff-read](https://github.com/user-attachments/assets/bd3d510e-a9c8-490a-b499-47093f15105d)\n\n\n## Installation\n\nYou can install `napari-geff` via [pip]:\n\n```\npip install napari-geff\n```\n\nIf napari is not already installed, you can install `napari-geff` with napari and Qt via:\n\n```\npip install \"napari-geff[all]\"\n```\n\n## Usage\n\n`napari-geff` supports loading directed graphs stored as [GEFF](https://live-image-tracking-tools.github.io/geff/latest/) files into\n`napari` as `Tracks` layers, and saving them back out to GEFF format.\n\nTo use `napari-geff` after installation, simply drag a GEFF file into the viewer and select `GEFF IO` from the\nplugin selection dialog, if required. The file will be loaded as a `Tracks` layer.\n\nAny node properties defined on your graph will be stored as features on your tracks layer. Edge properties\nwill be available under `layer.metadata['edge_properties']` as a dictionary, but cannot currently be displayed\nor used for visualization in `napari`.\n\nIf your file contains `image` or `labels` related objects as per the GEFF\n[spec](https://live-image-tracking-tools.github.io/geff/v0.4.0/specification/#geff_related_objects),\nthese will also be loaded alongside your `Tracks` layer.\n\nIf you wish to open your geff file into layers **programmatically**, you can do so using the `viewer.open` method:\n\n```python\nimport napari\npath = 'path/to/top_level_zarr.zarr/my-geff-group/\n\nviewer = napari.Viewer()\nlayers = viewer.open(path, plugin='napari-geff')\n```\n\n\n## Contributing\n\nContributions are very welcome. Tests can be run with [tox], please ensure\nthe coverage at least stays the same before you submit a pull request.\n\n## License\n\nDistributed under the terms of the [BSD-3] license,\n\"napari-geff\" is free and open source software\n\n## Acknowledgements\n\nThe data in docs/examples/cell\\_segmentation\\_data are generated by cropping and resizing images in [https://osf.io/ysaq2/](https://osf.io/ysaq2/), which is distributed with [Creative Commons Attribution 4.0 International](https://creativecommons.org/licenses/by/4.0/legalcode). See [10.1038/sdata.2018.237](https://doi.org/10.1038/sdata.2018.237) for details.\n\n\n\n## Issues\n\nIf you encounter any problems, please [file an issue] along with a detailed description.\n\n[napari]: https://github.com/napari/napari\n[copier]: https://copier.readthedocs.io/en/stable/\n[@napari]: https://github.com/napari\n[MIT]: http://opensource.org/licenses/MIT\n[BSD-3]: http://opensource.org/licenses/BSD-3-Clause\n[GNU GPL v3.0]: http://www.gnu.org/licenses/gpl-3.0.txt\n[GNU LGPL v3.0]: http://www.gnu.org/licenses/lgpl-3.0.txt\n[Apache Software License 2.0]: http://www.apache.org/licenses/LICENSE-2.0\n[Mozilla Public License 2.0]: https://www.mozilla.org/media/MPL/2.0/index.txt\n[napari-plugin-template]: https://github.com/napari/napari-plugin-template\n\n[napari]: https://github.com/napari/napari\n[tox]: https://tox.readthedocs.io/en/latest/\n[pip]: https://pypi.org/project/pip/\n[PyPI]: https://pypi.org/\n","description_content_type":"text/markdown","keywords":null,"home_page":null,"download_url":null,"author":"Live Image Tracking Tools (LITT) team","author_email":null,"maintainer":null,"maintainer_email":null,"license":"Copyright (c) 2025, Live Image Tracking Tools (LITT) team\nAll rights reserved.\n\nRedistribution and use in source and binary forms, with or without\nmodification, are permitted provided that the following conditions are met:\n\n* Redistributions of source code must retain the above copyright notice, this\n  list of conditions and the following disclaimer.\n\n* Redistributions in binary form must reproduce the above copyright notice,\n  this list of conditions and the following disclaimer in the documentation\n  and/or other materials provided with the distribution.\n\n* Neither the name of copyright holder nor the names of its\n  contributors may be used to endorse or promote products derived from\n  this software without specific prior written permission.\n\nTHIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS \"AS IS\"\nAND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE\nIMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE\nDISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE\nFOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL\nDAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR\nSERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER\nCAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,\nOR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE\nOF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.\n","classifier":["Development Status :: 2 - Pre-Alpha","Framework :: napari","Intended Audience :: Developers","License :: OSI Approved :: BSD License","Operating System :: OS Independent","Programming Language :: Python","Programming Language :: Python :: 3","Programming Language :: Python :: 3 :: Only","Programming Language :: Python :: 3.10","Programming Language :: Python :: 3.11","Programming Language :: Python :: 3.12","Programming Language :: Python :: 3.13","Topic :: Scientific/Engineering :: Image Processing"],"requires_dist":["numpy","magicgui","qtpy","scikit-image","geff>=1.1.1","pandas","napari[all]; extra == \"all\"","tox; extra == \"testing\"","pytest; extra == \"testing\"","pytest-cov; extra == \"testing\"","pytest-qt; extra == \"testing\"","napari[qt]; extra == \"testing\""],"requires_python":">=3.10","requires_external":null,"project_url":null,"provides_extra":["all","testing"],"provides_dist":null,"obsoletes_dist":null},"npe1_shim":false}