{"name":"cellpose-napari","display_name":"cellpose-napari","visibility":"public","icon":"","categories":[],"schema_version":"0.1.0","on_activate":null,"on_deactivate":null,"contributions":{"commands":[{"id":"cellpose-napari.widget_wrapper","title":"Create cellpose","python_name":"cellpose_napari._dock_widget:widget_wrapper","short_title":null,"category":null,"icon":null,"enablement":null},{"id":"cellpose-napari.data.rgb_3D","title":"Generate RGB 3D sample","python_name":"cellpose_napari._sample_data:rgb_3D.tif","short_title":null,"category":null,"icon":null,"enablement":null},{"id":"cellpose-napari.data.rgb_2D","title":"Generate RGB 2D sample","python_name":"cellpose_napari._sample_data:rgb_2D.png","short_title":null,"category":null,"icon":null,"enablement":null}],"readers":null,"writers":null,"widgets":[{"command":"cellpose-napari.widget_wrapper","display_name":"cellpose","autogenerate":false}],"sample_data":[{"command":"cellpose-napari.data.rgb_3D","key":"rgb_3D","display_name":"Cells (3D+2Ch)"},{"command":"cellpose-napari.data.rgb_2D","key":"rgb_2D","display_name":"Cells 2D"}],"themes":null,"menus":{},"submenus":null,"keybindings":null,"configuration":[]},"package_metadata":{"metadata_version":"2.1","name":"cellpose-napari","version":"0.1.5","dynamic":null,"platform":null,"supported_platform":null,"summary":"a generalist algorithm for anatomical segmentation","description":"# cellpose-napari <img src=\"docs/_static/favicon.ico\" width=\"50\" title=\"cellpose\" alt=\"cellpose\" align=\"right\" vspace = \"50\">\n\n[![Documentation Status](https://readthedocs.org/projects/cellpose-napari/badge/?version=latest)](https://cellpose-napari.readthedocs.io/en/latest/?badge=latest)\n[![tests](https://github.com/mouseland/cellpose-napari/workflows/tests/badge.svg)](https://github.com/mouseland/cellpose-napari/actions)\n[![codecov](https://codecov.io/gh/Mouseland/cellpose-napari/branch/main/graph/badge.svg)](https://codecov.io/gh/MouseLand/cellpose-napari)\n[![PyPI version](https://badge.fury.io/py/cellpose-napari.svg)](https://badge.fury.io/py/cellpose-napari)\n[![PyPI - Downloads](https://img.shields.io/pypi/dm/cellpose-napari)](https://pypistats.org/packages/cellpose-napari)\n[![Python version](https://img.shields.io/pypi/pyversions/cellpose-napari)](https://pypistats.org/packages/cellpose-napari)\n[![License](https://img.shields.io/pypi/l/cellpose-napari.svg?color=green)](https://github.com/mouseland/cellpose-napari/raw/master/LICENSE)\n[![Contributors](https://img.shields.io/github/contributors-anon/MouseLand/cellpose-napari)](https://github.com/MouseLand/cellpose-napari/graphs/contributors)\n[![website](https://img.shields.io/website?url=https%3A%2F%2Fwww.cellpose.org)](https://www.cellpose.org)\n[![GitHub stars](https://img.shields.io/github/stars/MouseLand/cellpose-napari?style=social)](https://github.com/MouseLand/cellpose-napari/)\n[![GitHub forks](https://img.shields.io/github/forks/MouseLand/cellpose-napari?style=social)](https://github.com/MouseLand/cellpose-napari/)\n\na napari plugin for anatomical segmentation of general cellular images\n\n----------------------------------\n\nThis [napari] plugin was generated with [Cookiecutter] using with [@napari]'s [cookiecutter-napari-plugin] template.\n\nThe plugin code was written by Carsen Stringer, and the cellpose code was written by Carsen Stringer and Marius Pachitariu. To learn about Cellpose, read the [**paper**](https://t.co/kBMXmPp3Yn?amp=1) or watch this [**talk**](https://t.co/JChCsTD0SK?amp=1). \n\nFor support with the plugin, please open an [issue](https://github.com/MouseLand/cellpose-napari/issues). For support with cellpose, please open an [issue](https://github.com/MouseLand/cellpose/issues) on the cellpose repo. \n\n\nIf you use this plugin please cite the [paper](https://www.nature.com/articles/s41592-020-01018-x):\n::\n    \n      @article{stringer2021cellpose,\n      title={Cellpose: a generalist algorithm for cellular segmentation},\n      author={Stringer, Carsen and Wang, Tim and Michaelos, Michalis and Pachitariu, Marius},\n      journal={Nature Methods},\n      volume={18},\n      number={1},\n      pages={100--106},\n      year={2021},\n      publisher={Nature Publishing Group}\n      }\n\n\n![cellpose-napari_plugin](https://cellpose-napari.readthedocs.io/en/latest/_images/napari_main_demo_fast_small.gif?raw=true \"cellpose-napari\")\n\n## Installation\n\nInstall an [Anaconda](https://www.anaconda.com/download/) distribution of Python -- Choose **Python 3** and your operating system. Note you might need to use an anaconda prompt if you did not add anaconda to the path.\n\nInstall `napari` with pip: `pip install napari[all]`. Then install `cellpose-napari` via [pip]:\n\n    pip install cellpose-napari\n    \n Or install the plugin inside napari in the plugin window.\n\nIf install fails in your base environment, create a new environment:\n1. Download the [`environment.yml`](https://github.com/MouseLand/cellpose-napari/blob/master/environment.yml?raw=true) file from the repository. You can do this by cloning the repository, or copy-pasting the text from the file into a text document on your local computer.\n2. Open an anaconda prompt / command prompt with `conda` for **python 3** in the path\n3. Change directories to where the `environment.yml` is and run `conda env create -f environment.yml`\n4. To activate this new environment, run `conda activate cellpose-napari`\n5. You should see `(cellpose-napari)` on the left side of the terminal line. \n\nIf you have **issues** with cellpose installation, see the [cellpose docs](https://cellpose.readthedocs.io/en/latest/installation.html) for more details, and then if the suggestions fail, open an issue.\n\n### Upgrading software\n\nYou can upgrade the plugin with\n~~~\npip install cellpose-napari --upgrade\n~~~\n\nand you can upgrade cellpose with\n~~~\npip install cellpose --upgrade\n~~~\n\n### GPU version (CUDA) on Windows or Linux\n\nIf you plan on running many images, you may want to install a GPU version of *torch* (if it isn't already installed).\n\nBefore installing the GPU version, remove the CPU version:\n~~~\npip uninstall torch\n~~~\n\nFollow the instructions [here](https://pytorch.org/get-started/locally/) to determine what version to install. The Anaconda install is recommended along with CUDA version 10.2. For instance this command will install the 10.2 version on Linux and Windows (note the `torchvision` and `torchaudio` commands are removed because cellpose doesn't require them):\n\n~~~\nconda install pytorch cudatoolkit=10.2 -c pytorch\n~~~~\n\nWhen upgrading GPU Cellpose in the future, you will want to ignore dependencies (to ensure that the pip version of torch does not install):\n~~~\npip install --no-deps cellpose --upgrade\n~~~\n\n### Installation of github version\n\nFollow steps from above to install the dependencies. In the github repository, run `pip install -e .` and the github version will be installed. If you want to go back to the pip version of cellpose-napari, then say `pip install cellpose-napari`.\n\n\n## Running the software\n\n\nOpen napari with the cellpose-napari dock widget open\n```\nnapari -w cellpose-napari\n```\n\nThere is sample data in the File menu, or get started with your own images!\n\n### Detailed usage [documentation](https://cellpose-napari.readthedocs.io/).\n\n## Contributing\n\nContributions are very welcome. Tests are run with pytest.\n\n## License\n\nDistributed under the terms of the [BSD-3] license,\n\"cellpose-napari\" is free and open source software.\n\n## Dependencies\ncellpose-napari relies on the following excellent packages (which are automatically installed with conda/pip if missing):\n- [napari](https://napari.org)\n- [magicgui](https://napari.org/magicgui/)\n\ncellpose relies on the following excellent packages (which are automatically installed with conda/pip if missing):\n- [torch](https://pytorch.org/)\n- [numpy](http://www.numpy.org/) (>=1.16.0)\n- [numba](http://numba.pydata.org/numba-doc/latest/user/5minguide.html)\n- [scipy](https://www.scipy.org/)\n- [natsort](https://natsort.readthedocs.io/en/master/)\n- [tifffile](https://pypi.org/project/tifffile/)\n- [opencv](https://opencv.org/)\n\n\n[napari]: https://github.com/napari/napari\n[Cookiecutter]: https://github.com/audreyr/cookiecutter\n[@napari]: https://github.com/napari\n[BSD-3]: http://opensource.org/licenses/BSD-3-Clause\n[cookiecutter-napari-plugin]: https://github.com/napari/cookiecutter-napari-plugin\n","description_content_type":"text/markdown","keywords":null,"home_page":"https://github.com/Mouseland/cellpose-napari","download_url":null,"author":"Carsen Stringer","author_email":"stringerc@janelia.hhmi.org","maintainer":null,"maintainer_email":null,"license":"BSD-3","classifier":["Programming Language :: Python","Programming Language :: Python :: 3","Programming Language :: Python :: 3.7","Programming Language :: Python :: 3.8","Programming Language :: Python :: 3.9","Operating System :: OS Independent","License :: OSI Approved :: BSD License","Framework :: napari"],"requires_dist":["napari","napari-plugin-engine (>=0.1.4)","cellpose (>0.6.3)","imagecodecs","sphinx (>=3.0) ; extra == 'docs'","sphinxcontrib-apidoc ; extra == 'docs'","sphinx-rtd-theme ; extra == 'docs'","sphinx-prompt ; extra == 'docs'","sphinx-autodoc-typehints ; extra == 'docs'","pytest ; extra == 'tests_require'","pytest-qt ; extra == 'tests_require'"],"requires_python":">=3.7","requires_external":null,"project_url":null,"provides_extra":["docs","tests_require"],"provides_dist":null,"obsoletes_dist":null},"npe1_shim":false}