{"name":"napari-ctc-io","display_name":"Read CTC format","visibility":"public","icon":"","categories":["Visualization","Utilities"],"schema_version":"0.2.1","on_activate":null,"on_deactivate":null,"contributions":{"commands":[{"id":"napari-ctc-io.read_ctc","title":"Open CTC TRA/RES data","python_name":"napari_ctc_io._reader:napari_get_reader","short_title":null,"category":null,"icon":null,"enablement":null},{"id":"napari-ctc-io.write_multiple","title":"Save masks + tracks to CTC format","python_name":"napari_ctc_io._writer:write_multiple","short_title":null,"category":null,"icon":null,"enablement":null}],"readers":[{"command":"napari-ctc-io.read_ctc","filename_patterns":["TRA","*RES"],"accepts_directories":true}],"writers":[{"command":"napari-ctc-io.write_multiple","layer_types":["labels","tracks"],"filename_extensions":[],"display_name":""}],"widgets":null,"sample_data":null,"themes":null,"menus":{},"submenus":null,"keybindings":null,"configuration":[]},"package_metadata":{"metadata_version":"2.1","name":"napari-ctc-io","version":"0.2.1","dynamic":null,"platform":null,"supported_platform":null,"summary":"Drag and drop/write tracks from/to the Cell Tracking Challenge (CTC) format.","description":"# napari-ctc-io\n\n[![PyPI](https://img.shields.io/pypi/v/napari-ctc-io.svg?color=green)](https://pypi.org/project/napari-ctc-io)\n[![tests](https://github.com/bentaculum/napari-ctc-io/workflows/tests/badge.svg)](https://github.com/bentaculum/napari-ctc-io/actions)\n[![codecov](https://codecov.io/gh/bentaculum/napari-ctc-io/branch/main/graph/badge.svg)](https://codecov.io/gh/bentaculum/napari-ctc-io)\n[![napari hub](https://img.shields.io/endpoint?url=https://api.napari-hub.org/shields/napari-ctc-io)](https://napari-hub.org/plugins/napari-ctc-io)\n\n- Drag and drop annotations/results in the [Cell Tracking Challenge (CTC) format](https://celltrackingchallenge.net) into napari.\n\n  Works for `TRA`, `RES`, etc. folders, which contain a time sequence of segmentations in `tiff` format, and a corresponding tracklet file `*.txt`.\n- Write tracked cells (`labels` layer & corresponding `tracks` layer) to CTC format (see usage below).\n\n\nhttps://github.com/bentaculum/napari-ctc-io/assets/8866751/197c9ea2-4115-4829-851a-4b77eb843bf2\n\n\n## Installation\n\nYou can install `napari-ctc-io` via [pip]:\n\n    pip install napari-ctc-io\n\n\n\nTo install latest development version :\n\n\n    pip install git+https://github.com/bentaculum/napari-ctc-io.git\n\n## Usage of writer in widget\n\n```python\ndef _save(self, event=None):\n    pm = npe2.PluginManager.instance()\n\n    outdir = \"TRA\"\n    writer_contrib = pm.get_writer(\n        outdir,\n        [\"labels\", \"tracks\"],\n        \"napari-ctc-io\",\n    )[0]\n\n    save_layers(\n        path=outdir,\n        layers=[\n            self._viewer.layers[\"masks_tracked\"],\n            self._viewer.layers[\"tracks\"],\n        ],\n        plugin=\"napari-ctc-io\",\n        _writer=writer_contrib,\n    )\n```\n\n\n## Contributing\n\nContributions are very welcome. Tests can be run with [tox].\n\n## License\n\nDistributed under the terms of the [BSD-3] license,\n`napari-ctc-io` is free and open source software.\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[Cookiecutter]: https://github.com/audreyr/cookiecutter\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[cookiecutter-napari-plugin]: https://github.com/napari/cookiecutter-napari-plugin\n\n[file an issue]: https://github.com/bentaculum/napari-ctc-io/issues\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":"https://github.com/bentaculum/napari-ctc-io","download_url":null,"author":"Benjamin Gallusser","author_email":"benjamin.gallusser@epfl.ch","maintainer":null,"maintainer_email":null,"license":"BSD-3-Clause","classifier":["Development Status :: 3 - Alpha","Framework :: napari","License :: OSI Approved :: BSD License","Operating System :: OS Independent","Programming Language :: Python","Programming Language :: Python :: 3","Programming Language :: Python :: 3 :: Only","Programming Language :: Python :: 3.9","Programming Language :: Python :: 3.10","Programming Language :: Python :: 3.11","Topic :: Scientific/Engineering :: Image Processing"],"requires_dist":["napari","numpy","scikit-image","tifffile","pandas","imagecodecs","tox; extra == \"testing\"","pytest; extra == \"testing\"","pytest-cov; extra == \"testing\""],"requires_python":">=3.9","requires_external":null,"project_url":["Bug Tracker, https://github.com/bentaculum/napari-ctc-io/issues","Documentation, https://github.com/bentaculum/napari-ctc-io#README.md","Source Code, https://github.com/bentaculum/napari-ctc-io","User Support, https://github.com/bentaculum/napari-ctc-io/issues"],"provides_extra":["testing"],"provides_dist":null,"obsoletes_dist":null},"npe1_shim":false}