{"name":"phenome-gui","display_name":"PhenoMe GUI","visibility":"public","icon":null,"categories":[],"schema_version":"0.3.0","on_activate":null,"on_deactivate":null,"contributions":{"commands":[{"id":"phenome-gui.make_phenome_widget","title":"Make the PhenoMe widget","python_name":"phenome_gui._widget:PhenoMeWidget","short_title":null,"category":null,"icon":null,"enablement":null}],"readers":null,"writers":null,"widgets":[{"command":"phenome-gui.make_phenome_widget","display_name":"PhenoMe","autogenerate":false,"default_dock_area":"right","tabify":false}],"sample_data":null,"themes":null,"menus":{},"submenus":null,"keybindings":null,"configurations":{}},"package_metadata":{"metadata_version":"2.4","name":"phenome-gui","version":"0.3.0","dynamic":null,"platform":null,"supported_platform":null,"summary":"GUI integration of the PhenoMe phenotyping framework","description":"# PhenoMe GUI - A napari plugin\n\n[![License MIT](https://img.shields.io/pypi/l/phenome-gui.svg?color=green)](https://github.com/PhenoMe-Ecosystem/PhenoMe-napari-GUI/blob/main/LICENSE)\n[![PyPI](https://img.shields.io/pypi/v/phenome-gui.svg?color=green)](https://pypi.org/project/phenome-gui)\n[![napari hub](https://img.shields.io/endpoint?url=https://api.napari-hub.org/shields/phenome-gui)](https://napari-hub.org/plugins/phenome-gui)\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\nGUI integration of the [PhenoMe] phenotyping framework as a plugin for the [napari] image viewer.\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## Installation\n\nIf you you already have napari installed, this plugin can be installed directly from the napari hub. Otherwise, follow these instructions to install napari:\n\nhttps://napari.org/stable/getting_started/installation.html\n\nYou can also install `phenome-gui` in your napari environment via [pip]:\n\n```bash\npip install phenome-gui\n```\n\nIf napari is not already installed, you can install `phenome-gui` with napari and Qt via:\n\n```bash\npip install \"napari[all]\" phenome-gui\n```\n\n## Usage\n\nThis napari plugin integrates the [PhenoMe] phenotyping pipeline in a user-friendly graphical interface. To summarize, PhenoMe is a framework for phenotyping biological image data using embeddings extracted using vision models and physical properties. \n\nAs a first step, take a look at the [tutorial](docs/TUTORIAL.md) for a simple step-by-step explanation.\n\nA [manual](docs/MANUAL.md) is provided for more specific explanations about every functionality.\n\nThis plugin allows users to easily execute the PhenoMe pipeline in a guided manner, following the three main steps:\n\n1. **Data loading:** Point to the folders containing the images to analyse\n2. **Image processing:** Extract the embeddings and properties from the images\n3. **Analysis:** Explore the resulting embeddings\n\nFor in-depth information about the inner workings of the plugin, see the [PhenoMe] documentation.\n\n## License\n\nDistributed under the terms of the [MIT] license,\n\"phenome-gui\" 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[copier]: https://copier.readthedocs.io/en/stable/\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[PhenoMe]: https://github.com/AAitorG/PhenoMe/tree/main\n\n[tox]: https://tox.readthedocs.io/en/latest/\n[pip]: https://pypi.org/project/pip/\n[PyPI]: https://pypi.org/\n[uv]:  https://docs.astral.sh/uv/\n","description_content_type":"text/markdown","keywords":null,"home_page":null,"download_url":null,"author":"PREDIS","author_email":null,"maintainer":null,"maintainer_email":null,"license":null,"classifier":["Development Status :: 2 - Pre-Alpha","Framework :: napari","Intended Audience :: Science/Research","Operating System :: OS Independent","Programming Language :: Python","Programming Language :: Python :: 3","Programming Language :: Python :: 3 :: Only","Programming Language :: Python :: 3.12","Programming Language :: Python :: 3.13","Programming Language :: Python :: 3.14","Topic :: Scientific/Engineering :: Image Processing"],"requires_dist":["numpy","magicgui","qtpy","scikit-image","phenome>=1.5.1","timm>=1.0","pydantic>=2","pyqtgraph>=0.14.0","superqt","colorcet>=3.2.1","napari[all] ; extra == 'all'"],"requires_python":">=3.12","requires_external":null,"project_url":null,"provides_extra":["all"],"provides_dist":null,"obsoletes_dist":null},"npe1_shim":false}