Package: cellpose-napari
cellpose-naparia napari plugin for anatomical segmentation of general cellular imagesThisnapariplugin was generated withCookiecutterusing with@napari'scookiecutter-napari-plugintemplate.The plugin code was written by Carsen Stringer, and the cellpose code was written by Carsen Stringer and Marius Pachitariu. To learn about Cellpose, read thepaperor watch thistalk.For support with the plugin, please open anissue. For support with cellpose, please open anissueon the cellpose repo.If you use this plugin please cite thepaper:
::@article{stringer2021cellpose,
  title={Cellpose: a generalist algorithm for cellular segmentation},
  author={Stringer, Carsen and Wang, Tim and Michaelos, Michalis and Pachitariu, Marius},
  journal={Nature Methods},
  volume={18},
  number={1},
  pages={100--106},
  year={2021},
  publisher={Nature Publishing Group}
  }InstallationInstall anAnacondadistribution of Python -- ChoosePython 3and your operating system. Note you might need to use an anaconda prompt if you did not add anaconda to the path.Installnapariwith pip:pip install napari[all]. Then installcellpose-naparivia [pip]:pip install cellpose-napariOr install the plugin inside napari in the plugin window.If install fails in your base environment, create a new environment:Download theenvironment.ymlfile 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.Open an anaconda prompt / command prompt withcondaforpython 3in the pathChange directories to where theenvironment.ymlis and runconda env create -f environment.ymlTo activate this new environment, runconda activate cellpose-napariYou should see(cellpose-napari)on the left side of the terminal line.If you haveissueswith cellpose installation, see thecellpose docsfor more details, and then if the suggestions fail, open an issue.Upgrading softwareYou can upgrade the plugin withpip install cellpose-napari --upgradeand you can upgrade cellpose withpip install cellpose --upgradeGPU version (CUDA) on Windows or LinuxIf you plan on running many images, you may want to install a GPU version oftorch(if it isn't already installed).Before installing the GPU version, remove the CPU version:pip uninstall torchFollow the instructionshereto 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 thetorchvisionandtorchaudiocommands are removed because cellpose doesn't require them):conda install pytorch cudatoolkit=10.2 -c pytorchWhen upgrading GPU Cellpose in the future, you will want to ignore dependencies (to ensure that the pip version of torch does not install):pip install --no-deps cellpose --upgradeInstallation of github versionFollow steps from above to install the dependencies. In the github repository, runpip install -e .and the github version will be installed. If you want to go back to the pip version of cellpose-napari, then saypip install cellpose-napari.Running the softwareOpen napari with the cellpose-napari dock widget opennapari -w cellpose-napariThere is sample data in the File menu, or get started with your own images!Detailed usagedocumentation.ContributingContributions are very welcome. Tests are run with pytest.LicenseDistributed under the terms of theBSD-3license,
"cellpose-napari" is free and open source software.Dependenciescellpose-napari relies on the following excellent packages (which are automatically installed with conda/pip if missing):naparimagicguicellpose relies on the following excellent packages (which are automatically installed with conda/pip if missing):torchnumpy(>=1.16.0)numbascipynatsorttifffileopencv