{"id":18496591,"url":"https://github.com/mouseland/cellpose-napari","last_synced_at":"2025-04-05T07:02:50.565Z","repository":{"id":38328720,"uuid":"361503255","full_name":"MouseLand/cellpose-napari","owner":"MouseLand","description":"napari plugin for cellpose (see www.cellpose.org) - an anatomical segmentation tool","archived":false,"fork":false,"pushed_at":"2024-10-27T12:57:30.000Z","size":7229,"stargazers_count":52,"open_issues_count":12,"forks_count":25,"subscribers_count":6,"default_branch":"main","last_synced_at":"2025-03-29T06:07:01.108Z","etag":null,"topics":["napari","segmentation"],"latest_commit_sha":null,"homepage":"https://cellpose-napari.readthedocs.org","language":"Python","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":"bsd-3-clause","status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/MouseLand.png","metadata":{"files":{"readme":"README.md","changelog":null,"contributing":null,"funding":null,"license":"LICENSE","code_of_conduct":null,"threat_model":null,"audit":null,"citation":null,"codeowners":null,"security":null,"support":null,"governance":null,"roadmap":null,"authors":null,"dei":null,"publiccode":null,"codemeta":null}},"created_at":"2021-04-25T18:10:26.000Z","updated_at":"2025-02-18T11:54:52.000Z","dependencies_parsed_at":"2024-06-21T14:12:49.484Z","dependency_job_id":"b32eaad3-a48f-4190-b379-7afce1a502ac","html_url":"https://github.com/MouseLand/cellpose-napari","commit_stats":{"total_commits":60,"total_committers":8,"mean_commits":7.5,"dds":0.2833333333333333,"last_synced_commit":"41455e047583e67361965c37f341db89173ffe9a"},"previous_names":[],"tags_count":7,"template":false,"template_full_name":null,"repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/MouseLand%2Fcellpose-napari","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/MouseLand%2Fcellpose-napari/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/MouseLand%2Fcellpose-napari/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/MouseLand%2Fcellpose-napari/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/MouseLand","download_url":"https://codeload.github.com/MouseLand/cellpose-napari/tar.gz/refs/heads/main","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":247299831,"owners_count":20916190,"icon_url":"https://github.com/github.png","version":null,"created_at":"2022-05-30T11:31:42.601Z","updated_at":"2022-07-04T15:15:14.044Z","host_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub","repositories_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories","repository_names_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repository_names","owners_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners"}},"keywords":["napari","segmentation"],"created_at":"2024-11-06T13:30:03.587Z","updated_at":"2025-04-05T07:02:50.536Z","avatar_url":"https://github.com/MouseLand.png","language":"Python","funding_links":[],"categories":[],"sub_categories":[],"readme":"# cellpose-napari \u003cimg src=\"docs/_static/favicon.ico\" width=\"50\" title=\"cellpose\" alt=\"cellpose\" align=\"right\" vspace = \"50\"\u003e\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/) (\u003e=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","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fmouseland%2Fcellpose-napari","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fmouseland%2Fcellpose-napari","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fmouseland%2Fcellpose-napari/lists"}