Metadata-Version: 2.1
Name: cellpose-napari
Version: 0.1.1
Summary: a generalist algorithm for anatomical segmentation
Home-page: https://github.com/carsen-stringer/cellpose-napari
Author: Carsen Stringer
Author-email: stringerc@janelia.hhmi.org
License: BSD-3
Description: # cellpose-napari <img src="docs/_static/favicon.ico" width="50" title="cellpose" alt="cellpose" align="right" vspace = "50">
        
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        a napari plugin for anatomical segmentation of general cellular images
        
        ----------------------------------
        
        This [napari] plugin was generated with [Cookiecutter] using with [@napari]'s [cookiecutter-napari-plugin] template.
        
        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 the [paper](https://t.co/kBMXmPp3Yn?amp=1) or watch this [talk](https://t.co/JChCsTD0SK?amp=1). 
        
        For 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. 
        
        ![cellpose-napari_plugin](docs/_static/napari_main_demo_fast_small.gif?raw=true "cellpose-napari")
        
        ## Installation
        
        Install 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. 
        
        You can install `cellpose-napari` via [pip]:
        
            pip install cellpose-napari
        
        If install fails in your base environment, create a new environment:
        1. 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.
        2. Open an anaconda prompt / command prompt with `conda` for **python 3** in the path
        3. Change directories to where the `environment.yml` is and run `conda env create -f environment.yml`
        4. To activate this new environment, run `conda activate cellpose-napari`
        5. You should see `(cellpose-napari)` on the left side of the terminal line. 
        
        If 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.
        
        ### Upgrading software
        
        You can upgrade the plugin with
        ~~~
        pip install cellpose-napari --upgrade
        ~~~
        
        and you can upgrade cellpose with
        ~~~
        pip install cellpose --upgrade
        ~~~
        
        ### GPU version (CUDA) on Windows or Linux
        
        If you plan on running many images, you may want to install a GPU version of *torch* (if it isn't already installed).
        
        Before installing the GPU version, remove the CPU version:
        ~~~
        pip uninstall torch
        ~~~
        
        Follow 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):
        
        ~~~
        conda install pytorch cudatoolkit=10.2 -c pytorch
        ~~~~
        
        When 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 --upgrade
        ~~~
        
        ### Installation of github version
        
        Follow 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`.
        
        
        ## Running the software
        
        
        Open napari with the cellpose-napari dock widget open
        ```
        napari -w cellpose-napari
        ```
        
        There is sample data in the File menu, or get started with your own images!
        
        ### Detailed usage [documentation](https://cellpose-napari.readthedocs.io/).
        
        ## Contributing
        
        Contributions are very welcome. Tests are run with pytest.
        
        ## License
        
        Distributed under the terms of the [BSD-3] license,
        "cellpose-napari" is free and open source software.
        
        ## Dependencies
        cellpose-napari relies on the following excellent packages (which are automatically installed with conda/pip if missing):
        - [napari](https://napari.org)
        - [magicgui](https://napari.org/magicgui/)
        
        cellpose relies on the following excellent packages (which are automatically installed with conda/pip if missing):
        - [torch](https://pytorch.org/)
        - [numpy](http://www.numpy.org/) (>=1.16.0)
        - [numba](http://numba.pydata.org/numba-doc/latest/user/5minguide.html)
        - [scipy](https://www.scipy.org/)
        - [natsort](https://natsort.readthedocs.io/en/master/)
        - [tifffile](https://pypi.org/project/tifffile/)
        - [opencv](https://opencv.org/)
        
        
        [napari]: https://github.com/napari/napari
        [Cookiecutter]: https://github.com/audreyr/cookiecutter
        [@napari]: https://github.com/napari
        [BSD-3]: http://opensource.org/licenses/BSD-3-Clause
        [cookiecutter-napari-plugin]: https://github.com/napari/cookiecutter-napari-plugin
        
Platform: UNKNOWN
Classifier: Programming Language :: Python
Classifier: Programming Language :: Python :: 3
Classifier: Programming Language :: Python :: 3.7
Classifier: Programming Language :: Python :: 3.8
Classifier: Programming Language :: Python :: 3.9
Classifier: Operating System :: OS Independent
Classifier: License :: OSI Approved :: BSD License
Requires-Python: >=3.6
Description-Content-Type: text/markdown
Provides-Extra: docs
