{"name":"napari-sketchpose","display_name":"Sketchpose","visibility":"public","icon":"","categories":[],"schema_version":"0.2.0","on_activate":null,"on_deactivate":null,"contributions":{"commands":[{"id":"napari-sketchpose.get_reader","title":"Open data with Sketchpose","python_name":"napari_sketchpose._reader:napari_get_reader","short_title":null,"category":null,"icon":null,"enablement":null},{"id":"napari-sketchpose.write_multiple","title":"Save multi-layer data with Sketchpose","python_name":"napari_sketchpose._writer:write_multiple","short_title":null,"category":null,"icon":null,"enablement":null},{"id":"napari-sketchpose.write_single_image","title":"Save image data with Sketchpose","python_name":"napari_sketchpose._writer:write_single_image","short_title":null,"category":null,"icon":null,"enablement":null},{"id":"napari-sketchpose.make_sample_data","title":"Load sample data from Sketchpose","python_name":"napari_sketchpose._sample_data:make_sample_data","short_title":null,"category":null,"icon":null,"enablement":null},{"id":"napari-sketchpose.make_qwidget","title":"Make example QWidget","python_name":"napari_sketchpose._widget:Dessin","short_title":null,"category":null,"icon":null,"enablement":null},{"id":"napari-sketchpose.make_magic_widget","title":"Make example magic widget","python_name":"napari_sketchpose._widget:example_magic_widget","short_title":null,"category":null,"icon":null,"enablement":null},{"id":"napari-sketchpose.make_func_widget","title":"Make example function widget","python_name":"napari_sketchpose._widget:example_function_widget","short_title":null,"category":null,"icon":null,"enablement":null}],"readers":[{"command":"napari-sketchpose.get_reader","filename_patterns":["*.npy"],"accepts_directories":false}],"writers":[{"command":"napari-sketchpose.write_multiple","layer_types":["image*","labels*"],"filename_extensions":[],"display_name":""},{"command":"napari-sketchpose.write_single_image","layer_types":["image"],"filename_extensions":[".npy"],"display_name":""}],"widgets":[{"command":"napari-sketchpose.make_qwidget","display_name":"Sketchpose","autogenerate":false}],"sample_data":[{"command":"napari-sketchpose.make_sample_data","key":"unique_id.1","display_name":"Sketchpose"}],"themes":null,"menus":{},"submenus":null,"keybindings":null,"configuration":[]},"package_metadata":{"metadata_version":"2.1","name":"napari-sketchpose","version":"0.1.8","dynamic":null,"platform":null,"supported_platform":null,"summary":"A segmentation plugin to adapt Omnipose implementation to partial labelling.","description":"# napari-sketchpose\n\n[![License GNU GPL v3.0](https://img.shields.io/pypi/l/napari-sketchpose.svg?color=green)](https://github.com/koopa31/napari-sketchpose/raw/main/LICENSE)\n[![PyPI](https://img.shields.io/pypi/v/napari-sketchpose.svg?color=green)](https://pypi.org/project/napari-sketchpose)\n[![Python Version](https://img.shields.io/pypi/pyversions/napari-sketchpose.svg?color=green)](https://python.org)\n[![tests](https://github.com/koopa31/napari-sketchpose/workflows/tests/badge.svg)](https://github.com/koopa31/napari-sketchpose/actions)\n[![codecov](https://codecov.io/gh/koopa31/napari-sketchpose/branch/main/graph/badge.svg)](https://codecov.io/gh/koopa31/napari-sketchpose)\n[![napari hub](https://img.shields.io/endpoint?url=https://api.napari-hub.org/shields/napari-sketchpose)](https://napari-hub.org/plugins/napari-sketchpose)\n\nA plugin to adapt the Omnipose implementation to frugal labeling. It aims to facilitate the training from scratch or the \nuse of transfer learning with little data, by not needing to draw entire cells, but a few squiggles instead (see GIF below).\n\n\nIf you use this plugin please cite the [paper](https://hal.science/hal-04330824): \n\nClément Cazorla, Nathanaël Munier, Renaud Morin, Pierre Weiss. Sketchpose: Learning to Segment\nCells with Partial Annotations. 2023. ffhal-04330824f\n\n```bibtex\n@unpublished{cazorla:hal-04330824,\n      TITLE = {{Sketchpose: Learning to Segment Cells with Partial Annotations}},\n      AUTHOR = {Cazorla, Cl{\\'e}ment and Munier, Nathana{\\\"e}l and Morin, Renaud and Weiss, Pierre},\n      URL = {https://hal.science/hal-04330824},\n      NOTE = {working paper or preprint},\n      YEAR = {2023},\n      MONTH = Dec,\n      KEYWORDS = {Cellpose -Segmentation -Frugal learning -Napari -Deep learning -Distance map},\n      PDF = {https://hal.science/hal-04330824/file/sketchpose_hal.pdf},\n      HAL_ID = {hal-04330824},\n      HAL_VERSION = {v1},\n    }\n\n```\n\n\n![](https://bitbucket.org/koopa31/napari-sketchpose/raw/b691817e9e20a3c1c2bc69277579f6fb9b26354e/images/frugalpose.gif)\nImage Credit: Eduard Muzhevskyi\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\n## Installation\n\n\n\nFirst, we advise you to create a conda environment in Python 3.10, in which you will run Napari:\n\n    conda create -n sketchpose_env python=3.10\n    conda activate sketchpose_env\n    conda install pip\n    python -m pip install \"napari[all]\" --upgrade\n\nYou can install `napari_sketchpose` via [pip]:\n\n    pip install napari_sketchpose\n\nWARNING:\n\nFor Windows users, CUDA version of PyTorch may not be installed properly. When the plugin starts for the first time, it checks whether\nCUDA version is installed. If not, it tries to install it using light-the-torch library. If this does not work, you should re-install \nCUDA torch and torchvision versions manually, otherwise the plugin will not work properly.\n\n## Tutorial\n\nWe strongly recommend reading the [documentation] to get the most out of the plugin.\nA step-by-step tutorial illustrated with GIFs will guide you through the various stages.\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 [GNU GPL v3.0] license,\n\"napari-sketchpose\" 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[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[documentation]: https://sketchpose-doc.readthedocs.io/en/latest/\n","description_content_type":"text/markdown","keywords":null,"home_page":null,"download_url":null,"author":"Clément Cazorla","author_email":"clement.cazorla31@gmail.com","maintainer":null,"maintainer_email":null,"license":"GPL-3.0-only","classifier":["Development Status :: 2 - Pre-Alpha","Framework :: napari","Intended Audience :: Developers","License :: OSI Approved :: GNU General Public License v3 (GPLv3)","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","cellpose-omni ==0.9.1","omnipose ==0.4.4","pyqtgraph ==0.13.3","matplotlib","light-the-torch","tox ; extra == 'testing'","pytest ; extra == 'testing'","pytest-cov ; extra == 'testing'","pytest-qt ; extra == 'testing'","napari ; extra == 'testing'","pyqt5 ; extra == 'testing'"],"requires_python":">=3.8","requires_external":null,"project_url":["Bug Tracker, https://bitbucket.org/koopa31/napari-sketchpose/issues?status=new&status=open&status=submitted&is_spam=!spam","Documentation, https://sketchpose-doc.readthedocs.io/en/latest/","Source Code, https://bitbucket.org/koopa31/napari-sketchpose/src/master","User Support, https://bitbucket.org/koopa31/napari-sketchpose/issues?status=new&status=open&status=submitted&is_spam=!spam"],"provides_extra":["testing"],"provides_dist":null,"obsoletes_dist":null},"npe1_shim":false}