{"name":"napari-griottes","display_name":"Griottes","visibility":"public","icon":"","categories":[],"schema_version":"0.2.0","on_activate":null,"on_deactivate":null,"contributions":{"commands":[{"id":"napari-griottes.get_reader","title":"Open data with Griottes","python_name":"napari_griottes._reader:napari_get_reader","short_title":null,"category":null,"icon":null,"enablement":null},{"id":"napari-griottes.save_graph","title":"Save graph with Griottes","python_name":"napari_griottes._writer:save_graph_to_json","short_title":null,"category":null,"icon":null,"enablement":null},{"id":"napari-griottes.save_graph_widget","title":"Save graph","python_name":"napari_griottes._widget:save_graph","short_title":null,"category":null,"icon":null,"enablement":null},{"id":"napari-griottes.make_zebrafish_data","title":"Load zebrafish sample data from Griottes","python_name":"napari_griottes._sample_data:make_zebrafish_data","short_title":null,"category":null,"icon":null,"enablement":null},{"id":"napari-griottes.make_cell_properties","title":"Load zebrafish cell properties Griottes","python_name":"napari_griottes._sample_data:make_cell_properties","short_title":null,"category":null,"icon":null,"enablement":null},{"id":"napari-griottes.make_graph","title":"Make graph","python_name":"napari_griottes._widget:make_graph","short_title":null,"category":null,"icon":null,"enablement":null}],"readers":[{"command":"napari-griottes.get_reader","filename_patterns":["*.json","*.npy","*.tif","*.tiff","*.csv","*.griottes"],"accepts_directories":false}],"writers":[{"command":"napari-griottes.save_graph","layer_types":["shapes","vectors"],"filename_extensions":[".json"],"display_name":""}],"widgets":[{"command":"napari-griottes.make_graph","display_name":"Make graph","autogenerate":false},{"command":"napari-griottes.save_graph_widget","display_name":"Save graph","autogenerate":false}],"sample_data":[{"command":"napari-griottes.make_cell_properties","key":"csv","display_name":"Cell properties table 3D"},{"command":"napari-griottes.make_zebrafish_data","key":"zebra","display_name":"Zebrafish 2D with labels"}],"themes":null,"menus":{},"submenus":null,"keybindings":null,"configuration":[]},"package_metadata":{"metadata_version":"2.1","name":"napari-griottes","version":"0.4.1","dynamic":null,"platform":null,"supported_platform":null,"summary":"Create graphs","description":"# napari-griottes\n\n[![License](https://img.shields.io/pypi/l/napari-griottes.svg?color=green)](https://github.com/BaroudLab/napari-griottes/raw/main/LICENSE)\n[![PyPI](https://img.shields.io/pypi/v/napari-griottes.svg?color=green)](https://pypi.org/project/napari-griottes)\n[![Python Version](https://img.shields.io/pypi/pyversions/napari-griottes.svg?color=green)](https://python.org)\n[![tests](https://github.com/BaroudLab/napari-griottes/workflows/tests/badge.svg)](https://github.com/BaroudLab/napari-griottes/actions)\n[![codecov](https://codecov.io/gh/BaroudLab/napari-griottes/branch/main/graph/badge.svg)](https://codecov.io/gh/BaroudLab/napari-griottes)\n\n[![napari hub](https://img.shields.io/endpoint?url=https://api.napari-hub.org/shields/napari-griottes)](https://napari-hub.org/plugins/napari-griottes)\n\n\n\nUse [🍒  `Griottes` 🍒](https://github.com/BaroudLab/Griottes) in napari!\n\n----------------------------------\n\n\n\nhttps://user-images.githubusercontent.com/11408456/224119160-c381091d-8275-449e-9cf4-679ab474acd2.mp4\n\n\n\n\n## Installation\n\nInstall from napari\n\n![image](https://user-images.githubusercontent.com/11408456/224108834-f484ba37-50f4-415e-bdfb-509c6c5b88c4.png)\n\n\nYou can install `napari-griottes` via [pip]:\n\n    pip install napari-griottes\n\n\n\nTo install latest development version :\n\n    pip install git+https://github.com/BaroudLab/napari-griottes.git\n\n\n\n## Usage\n\n### Starting with labels:\n\n1. Open the plugin in Plugins/napari-griottes\n2. Make sure the layer with labels is selected\n3. Click Run once to get centers\n4. Click Run second time to get graph\n5. Select the right kind of graph in the drop-down menu\n6. Adjust the distance\n7. Adjust thickness\n\n![Screenshot from three labels geometric contact mp4](https://user-images.githubusercontent.com/11408456/167371516-05db2ba5-cdfc-47c4-a488-8f46afd0ae5b.png)\n\n\n\nhttps://user-images.githubusercontent.com/11408456/167825581-47c39884-34cf-4b5c-ad84-a4572217559d.mp4\n\n\n\n### Starting with Segmented cells\n\n1. Open sample data: File / Open Sample / napari-griottes / Zebrafish 2D with labels\n2. Select the top layer and covert it to labels (right click - Convert to labels)\n3. Run the plugin once to get the centers of labels\n4. Run the plugin twice to get the connections\n5. Proceed with graph creation\n\n\n![Screenshot from cells graphs mp4](https://user-images.githubusercontent.com/11408456/167372895-3c9036b9-af50-4575-bcf3-1805eb261bd7.png)\n\n\n\n\nhttps://user-images.githubusercontent.com/11408456/168237170-b43afd5a-26a4-4cdc-bc42-d3f46f138536.mp4\n\n\n### Saving and recovering the graph\n\nAny graph you see in napari can be saved in .json format.\n1. Select he layers with connections\n2. Click File/Save Selected Layer\n3. Choose Griottes in drop-down menu\n4. Save\n\nIn order to recover a previously saved graph in napari, you can simply drag-n-drop your file into napari, or use file open fialog.\n\n\n\nhttps://user-images.githubusercontent.com/11408456/167845853-e7071199-3f58-4d11-8d7b-c1358a150e6b.mp4\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-griottes\" 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/BaroudLab/napari-griottes/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/aaristov/napari-griottes","download_url":null,"author":"Andrey Aristov","author_email":"aaristov@pasteur.fr","maintainer":null,"maintainer_email":null,"license":"BSD-3-Clause","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 :: 3.8","Programming Language :: Python :: 3.9","Programming Language :: Python :: 3.10","Topic :: Software Development :: Testing"],"requires_dist":["griottes","networkx","numpy","pandas (<2)"],"requires_python":">=3.8","requires_external":null,"project_url":["Bug Tracker, https://github.com/aaristov/napari-griottes/issues","Documentation, https://github.com/aaristov/napari-griottes#README.md","Source Code, https://github.com/aaristov/napari-griottes","User Support, https://github.com/aaristov/napari-griottes/issues"],"provides_extra":null,"provides_dist":null,"obsoletes_dist":null},"npe1_shim":false}