{"name":"featureforest","display_name":"Feature Forest","visibility":"public","icon":"","categories":["Annotation","Segmentation"],"schema_version":"0.2.1","on_activate":null,"on_deactivate":null,"contributions":{"commands":[{"id":"featureforest.make_feature_extractor_widget","title":"Make feature extractor widget","python_name":"featureforest:FeatureExtractorWidget","short_title":null,"category":null,"icon":null,"enablement":null},{"id":"featureforest.make_segmentation_widget","title":"Make segmentation widget","python_name":"featureforest:SegmentationWidget","short_title":null,"category":null,"icon":null,"enablement":null}],"readers":null,"writers":null,"widgets":[{"command":"featureforest.make_feature_extractor_widget","display_name":"Feature Extractor","autogenerate":false},{"command":"featureforest.make_segmentation_widget","display_name":"Segmentation Widget","autogenerate":false}],"sample_data":null,"themes":null,"menus":{},"submenus":null,"keybindings":null,"configuration":[]},"package_metadata":{"metadata_version":"2.4","name":"featureforest","version":"0.1.2","dynamic":null,"platform":null,"supported_platform":null,"summary":"A napari plugin for segmentation using vision transformer features","description":"# Feature Forest\n\n[![License BSD-3](https://img.shields.io/pypi/l/featureforest.svg?color=green)](https://github.com/juglab/featureforest/blob/main/LICENSE)\n[![PyPI](https://img.shields.io/pypi/v/featureforest.svg?color=green)](https://pypi.org/project/featureforest)\n![PyPI - Downloads](https://img.shields.io/pypi/dm/featureforest)\n[![Python Version](https://img.shields.io/pypi/pyversions/featureforest.svg?color=green)](https://python.org)\n[![tests](https://github.com/juglab/featureforest/workflows/tests/badge.svg)](https://github.com/juglab/featureforest/actions)\n[![codecov](https://codecov.io/gh/juglab/featureforest/branch/main/graph/badge.svg)](https://codecov.io/gh/juglab/featureforest)\n[![napari hub](https://img.shields.io/endpoint?url=https://api.napari-hub.org/shields/featureforest)](https://napari-hub.org/plugins/featureforest)\n<!--[![Downloads](https://pepy.tech/badge/featureforest)](https://pepy.tech/project/featureforest)-->\n\n**A napari plugin for making image annotation using feature space of vision transformers and random forest classifier.**  \nWe developed a *napari* plugin to train a *Random Forest* model using extracted features of vision foundation models and just a few scribble labels provided by the user as input. This approach can do the segmentation of desired objects almost as well as manual segmentations but in a much shorter time with less manual effort.  \n\n----------------------------------\n\n## Documentation\nYou can check the documentation [here](https://juglab.github.io/featureforest/) (⚠️ work in progress!).  \n\n## Installation\nWe provided `install.sh` for Linux & Mac OS users, and `install.bat` for Windows users.  \nFirst you need to clone the repo:  \n```bash\ngit clone https://github.com/juglab/featureforest\ncd ./featureforest\n```\nNow run the installation script:  \n```bash\n# Linux or Mac OS\nsh ./install.sh\n```\n```bash\n# Windows\n./install.bat\n```\n\nFor developers that want to contribute to FeatureForest, you need to use this command to install the `dev` dependencies:  \n```bash\npip install -U \"featureforest[dev]\"\n```\nAnd make sure you have `pre-commit` installed in your environment, before committing changes:  \n```bash\npre-commit install\n```\n\nFor more detailed installation guide, check out [here](https://juglab.github.io/featureforest/install/).\n\n\n## Cite us\n\nSeifi, Mehdi, Damian Dalle Nogare, Juan Battagliotti, Vera Galinova, Ananya Kediga Rao, AI4Life Horizon Europe Programme Consortium, Johan Decelle, Florian Jug, and Joran Deschamps. \"FeatureForest: the power of foundation models, the usability of random forests.\" bioRxiv (2024): 2024-12. [DOI: 10.1101/2024.12.12.628025](https://www.biorxiv.org/content/10.1101/2024.12.12.628025v1.full)\n\n\n## License\n\nDistributed under the terms of the [BSD-3] license,\n\"featureforest\" is free and open source software.  \n\n## Issues\n\nIf you encounter any problems, please [file an issue](https://github.com/juglab/featureforest/issues/new) 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[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[conda]: https://conda.io/projects/conda/en/latest/index.html\n[mamba]: https://mamba.readthedocs.io/en/latest/installation/mamba-installation.html\n","description_content_type":"text/markdown","keywords":null,"home_page":null,"download_url":null,"author":null,"author_email":"Mehdi Seifi <mehdi.seifi@fht.org>, Vera Galinova <vera.galinova@fht.org>","maintainer":null,"maintainer_email":null,"license":"BSD-3-Clause","classifier":["Development Status :: 3 - Alpha","Framework :: napari","License :: OSI Approved :: BSD License","Programming Language :: Python :: 3","Programming Language :: Python :: 3.10","Programming Language :: Python :: 3.11","Programming Language :: Python :: 3.12","Topic :: Scientific/Engineering :: Image Processing"],"requires_dist":["h5py","iopath>=0.1.10","magicgui","matplotlib","napari[all]","numpy<2.2","opencv-python","pims","pooch","pynrrd","qtpy","scikit-image","scikit-learn","scipy","tifffile","timm","torch>=2.5.1","torchvision>=0.20.1","tqdm>=4.66.1","mkdocs-material; extra == 'dev'","pre-commit; extra == 'dev'","pytest; extra == 'dev'","pytest-cov; extra == 'dev'","sybil; extra == 'dev'","tox; extra == 'dev'","tox-gh-actions; extra == 'dev'"],"requires_python":">=3.10","requires_external":null,"project_url":["homepage, https://featureforest.github.io/","repository, https://github.com/juglab/featureforest"],"provides_extra":["dev"],"provides_dist":null,"obsoletes_dist":null},"npe1_shim":false}