{"name":"napari-brainbow-diagnose","display_name":"Napari Brainbow Diagnose","visibility":"public","icon":"","categories":[],"schema_version":"0.2.1","on_activate":null,"on_deactivate":null,"contributions":{"commands":[{"id":"napari-brainbow-diagnose.make_rgb_cube_data","title":"Load sample data from Napari Brainbow Diagnose","python_name":"napari_brainbow_diagnose._sample_data:make_rgb_cube_data","short_title":null,"category":null,"icon":null,"enablement":null},{"id":"napari-brainbow-diagnose.load_chroms_data_sample","title":"Load chroms data sample from Napari Brainbow Diagnose","python_name":"napari_brainbow_diagnose._sample_data:load_chroms_data_sample","short_title":null,"category":null,"icon":null,"enablement":null},{"id":"napari-brainbow-diagnose.tooltip_pointer_widget","title":"Brainbow 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image","autogenerate":true},{"command":"napari-brainbow-diagnose.compute_all_channel_space","display_name":"RGB features to all channel spaces","autogenerate":true},{"command":"napari-brainbow-diagnose.tooltip_pointer_widget","display_name":"Brainbow Tooltip","autogenerate":false}],"sample_data":[{"command":"napari-brainbow-diagnose.make_rgb_cube_data","key":"unique_id.1","display_name":"RGB Cube"},{"command":"napari-brainbow-diagnose.load_chroms_data_sample","key":"unique_id.2","display_name":"Chroms Cortex Sample"}],"themes":null,"menus":{},"submenus":null,"keybindings":null,"configuration":[]},"package_metadata":{"metadata_version":"2.2","name":"napari-brainbow-diagnose","version":"0.2.0","dynamic":null,"platform":null,"supported_platform":null,"summary":"Visualize and Diagnose brainbow dataset in color space.","description":"# napari-brainbow-diagnose\n\n[![License BSD-3](https://img.shields.io/pypi/l/napari-brainbow-diagnose.svg?color=green)](https://github.com/LaboratoryOpticsBiosciences/napari-brainbow-diagnose/raw/main/LICENSE)\n[![PyPI](https://img.shields.io/pypi/v/napari-brainbow-diagnose.svg?color=green)](https://pypi.org/project/napari-brainbow-diagnose)\n[![Python Version](https://img.shields.io/pypi/pyversions/napari-brainbow-diagnose.svg?color=green)](https://python.org)\n[![tests](https://github.com/LaboratoryOpticsBiosciences/napari-brainbow-diagnose/workflows/tests/badge.svg)](https://github.com/LaboratoryOpticsBiosciences/napari-brainbow-diagnose/actions)\n[![codecov](https://codecov.io/gh/LaboratoryOpticsBiosciences/napari-brainbow-diagnose/branch/main/graph/badge.svg)](https://codecov.io/gh/LaboratoryOpticsBiosciences/napari-brainbow-diagnose)\n[![napari hub](https://img.shields.io/endpoint?url=https://api.napari-hub.org/shields/napari-brainbow-diagnose)](https://napari-hub.org/plugins/napari-brainbow-diagnose)\n\nExplore image in channel coordinate spaces.\n\n\n**Original motivation**: Brainbow dataset have unique features that need to be addressed by specialized tools.\nThis plugin allows you to visualize the distribution of the channel ratio interactively in the image space and channel spaces.\n\nYou can also use this plugin along with the [`napari-cluster-plotter` plugin](https://github.com/BiAPoL/napari-clusters-plotter?tab=readme-ov-file#installation) to interact with individual objects.\n\n![demo_gif](https://raw.githubusercontent.com/LaboratoryOpticsBiosciences/napari-brainbow-diagnose/main/docs/demo_napari-brainbow-diagnose.gif)\n\n## Available Channel space transformation\n\nThe following channel spaces are available:\n\n![image|width=10](https://github.com/user-attachments/assets/0dae9090-da16-4653-b466-a08289e061ea)\n\n\nFrom Cartesian RGB:\n- (a) Maxwell triangle (ternary plot) [illustration](https://en.wikipedia.org/wiki/Ternary_plot)\n- (c) Hue-Saturation wheel [illustration (g)](https://en.wikipedia.org/wiki/File:Hsl-hsv_models.svg)\n- (e) Spherical coordinates (Theta, Phi and Radius) [illustration](https://en.wikipedia.org/wiki/Spherical_coordinate_system)\n- (g,i) Hue-Saturation-Value planes [illustration (b)(f)](https://en.wikipedia.org/wiki/File:Hsl-hsv_models.svg)\n\n## Example Notebooks\n\nYou can use this plugin to visualize channel space of:\n- interactively every voxel in the image (see [demo notebook](docs/demo.ipynb))\n- interactively every object (aka center point) in the image (see [demo notebook](docs/cluster_plotter_compatibility.ipynb)). To use this notebook you need to install [`napari-cluster-plotter` plugin](https://github.com/BiAPoL/napari-clusters-plotter?tab=readme-ov-file#installation).\n- Not interactive in matplotlib to export figures: (see [demo notebook](docs/plot_color_space_matplotlib.ipynb))\n\n## Example Datasets\n\nIf you want to use your dataset, you have to format it such as each channel is in one distinct `napari.Layers`\nYou can open test dataset to try this plugin in `File > Open Sample > napari-brainbow-diagnose`.\n\n- The RGB Cube is an array with shape (3x256x256x256) cube : Great to check how the plugin work when all color are represented\n- ChroMS Cortex Sample is an array with shape (3x256x256x256) #Hugo : Real life brainbow image (Cortex E18 Emx1Cre) !\n\nOnce you have your layers you can use the dropdown and select the corresponding layer. It is advised to match the `red, green, blue` order so the ratio you see on the napari viewer corresponds to the Hue-Saturation Wheel of the plugin.\n\n## Installation\n\nYou can install `napari-brainbow-diagnose` via [pip]:\n\n    pip install napari-brainbow-diagnose\n\nIf you want to use [`napari-cluster-plotter` plugin](https://github.com/BiAPoL/napari-clusters-plotter?tab=readme-ov-file#installation)  you also need to install it manually\n\nTo install latest development version :\n\n    pip install git+https://github.com/LaboratoryOpticsBiosciences/napari-brainbow-diagnose.git\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-brainbow-diagnose\" 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/LaboratoryOpticsBiosciences/napari-brainbow-diagnose/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\n----------------------------------\n\nThis [napari] plugin was generated with [Cookiecutter] using [@napari]'s [cookiecutter-napari-plugin] template.\n\n<!--\nDon't miss the full getting started guide to set up your new package:\nhttps://github.com/napari/cookiecutter-napari-plugin#getting-started\n\nand review the napari docs for plugin developers:\nhttps://napari.org/stable/plugins/index.html\n-->\n","description_content_type":"text/markdown","keywords":null,"home_page":"https://github.com/LaboratoryOpticsBiosciences/napari-brainbow-diagnose","download_url":null,"author":"Clement Caporal","author_email":"clement.caporal@polytechnique.edu","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 :: Scientific/Engineering :: Image Processing"],"requires_dist":["numpy","magicgui","pooch","matplotlib","scikit-image","tox; extra == \"testing\"","pytest; extra == \"testing\"","pytest-cov; extra == \"testing\"","pytest-qt; extra == \"testing\"","pre-commit; extra == \"testing\"","napari; extra == \"testing\"","pyqt5; extra == \"testing\""],"requires_python":">=3.8","requires_external":null,"project_url":["Bug Tracker, https://github.com/LaboratoryOpticsBiosciences/napari-brainbow-diagnose/issues","Documentation, https://github.com/LaboratoryOpticsBiosciences/napari-brainbow-diagnose#README.md","Source Code, https://github.com/LaboratoryOpticsBiosciences/napari-brainbow-diagnose","User Support, https://github.com/LaboratoryOpticsBiosciences/napari-brainbow-diagnose/issues"],"provides_extra":["testing"],"provides_dist":null,"obsoletes_dist":null},"npe1_shim":false}