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cellpose-napari.json
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{
"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": "0.2.0",
"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[](https://cellpose-napari.readthedocs.io/en/latest/?badge=latest)\n[](https://github.com/mouseland/cellpose-napari/actions)\n[](https://codecov.io/gh/MouseLand/cellpose-napari)\n[](https://badge.fury.io/py/cellpose-napari)\n[](https://pypistats.org/packages/cellpose-napari)\n[](https://pypistats.org/packages/cellpose-napari)\n[](https://github.com/mouseland/cellpose-napari/raw/master/LICENSE)\n[](https://github.com/MouseLand/cellpose-napari/graphs/contributors)\n[](https://www.cellpose.org)\n[](https://github.com/MouseLand/cellpose-napari/)\n[](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": "[email protected]",
"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\"",
"tox; extra == \"testing\"",
"pytest; extra == \"testing\"",
"pytest-cov; extra == \"testing\"",
"pytest-qt; extra == \"testing\"",
"napari; extra == \"testing\"",
"pyqt5; extra == \"testing\""
],
"requires_python": ">=3.7",
"requires_external": null,
"project_url": null,
"provides_extra": [
"docs",
"testing"
],
"provides_dist": null,
"obsoletes_dist": null
},
"npe1_shim": false
}