{"name":"napari-brainbow-diagnose","display_name":"Napari Brainbow Diagnose","visibility":"public","icon":"","categories":[],"schema_version":"0.2.0","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 Tooltip","python_name":"napari_brainbow_diagnose._tooltip_pointer:tooltip_pointer_widget","short_title":null,"category":null,"icon":null,"enablement":null},{"id":"napari-brainbow-diagnose.DiagnoseWidget","title":"Diagnose Brainbow Image","python_name":"napari_brainbow_diagnose._widget:DiagnoseWidget","short_title":null,"category":null,"icon":null,"enablement":null}],"readers":null,"writers":null,"widgets":[{"command":"napari-brainbow-diagnose.DiagnoseWidget","display_name":"Diagnose Brainbow Image","autogenerate":false},{"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":"2.1","name":"napari-brainbow-diagnose","version":"0.1.3","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 space.\nBrainbow dataset have unique features that need to be addressed by specialized tools. This plugin aims at visualize and diagnose brainbow dataset.\nIn particular we want to interact with the distribution of the dataset in the channel space.\n\n![demo_gif](https://raw.githubusercontent.com/LaboratoryOpticsBiosciences/napari-brainbow-diagnose/main/docs/demo_napari-brainbow-diagnose.gif)\n\n## Usage\n\nYou can also look at the [demo notebook](docs/demo.ipynb)\nFind all menus under `Plugins > napari-brainbow-diagnose > Diagnose Brainbow Image`\n\n### Choose your dataset\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- Chrom 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### Get Channel Ratio Density of the image\n\nWhen you click on `Compute brainbow image density` you will populate the Hue-Saturation density Wheel.\nThis should allow you to quickly see which ratio is more present in your image. You can see the corresponding ratio according to the \"HS Color wheel\" on the right.\nFor example here on this screenshot we can see that:\n\n- there is a high number of non saturated red-only ratio. (2)\n- there is not a high number of non saturated magenta ratio. (3)\n\n![ratio](https://raw.githubusercontent.com/LaboratoryOpticsBiosciences/napari-brainbow-diagnose/main/docs/ratio_view.png)\n\n### Create a selection of ratio on the channel coordinate system and apply it on the original image\n\n\n![ratio](https://raw.githubusercontent.com/LaboratoryOpticsBiosciences/napari-brainbow-diagnose/main/docs/wheel_to_image_selection.gif)\n\n### Create a selection of pixel in the image and show where they are in the channel coordinate system\n\n![ratio](https://raw.githubusercontent.com/LaboratoryOpticsBiosciences/napari-brainbow-diagnose/main/docs/image_to_wheel_selection.gif)\n## Installation\n\nYou can install `napari-brainbow-diagnose` via [pip]:\n\n    pip install napari-brainbow-diagnose\n\n\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","qtpy","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}