Metadata-Version: 2.1
Name: napari-lazy-openslide
Version: 0.2.0
Summary: A plugin to lazily load multiscale whole-slide images with openslide and dask.
Home-page: https://github.com/manzt/napari-lazy-openslide
Author: Trevor Manz
Author-email: trevor.j.manz@gmail.com
License: BSD-3
Description: # napari-lazy-openslide
        
        [![License](https://img.shields.io/pypi/l/napari-lazy-openslide.svg?color=green)](https://github.com/manzt/napari-lazy-openslide/raw/master/LICENSE)
        [![PyPI](https://img.shields.io/pypi/v/napari-lazy-openslide.svg?color=green)](https://pypi.org/project/napari-lazy-openslide)
        [![Python Version](https://img.shields.io/pypi/pyversions/napari-lazy-openslide.svg?color=green)](https://python.org)
        [![tests](https://github.com/manzt/napari-lazy-openslide/workflows/tests/badge.svg)](https://github.com/manzt/napari-lazy-openslide/actions)
        
        An experimental plugin to lazily load multiscale whole-slide tiff images with openslide and dask.
        
        ----------------------------------
        
        This [napari] plugin was generated with [Cookiecutter] using with [@napari]'s [cookiecutter-napari-plugin] template.
        
        <!--
        Don't miss the full getting started guide to set up your new package:
        https://github.com/napari/cookiecutter-napari-plugin#getting-started
        
        and review the napari docs for plugin developers:
        https://napari.org/docs/plugins/index.html
        -->
        
        ## Installation
        
        **Step 1.)** Make sure you have OpenSlide installed. Download instructions [here](https://openslide.org/download/).
        
        > NOTE: Installation on macOS is easiest via Homebrew: `brew install openslide`. Up-to-date and multiplatform 
        > binaries for `openslide` are also avaiable via `conda`: `conda install -c sdvillal openslide-python`
        
        **Step 2.)** Install `napari-lazy-openslide` via [pip]:
        
            pip install napari-lazy-openslide
        
        ## Usage
        
        This plugin tries to be conservative with what files it will attempt to provide a reader.
        It will only attempt to read `.tif` and `.tiff` files that `openslide` will open and are 
        detected as multiscale (`openslide.OpenSlide.level_count > 1`). Under the hood, 
        `napari-lazy-openslide` wraps the `openslide` reader with a valid `zarr.Store` where each 
        each pyramidal level is exposed as a separate `zarr.Array` with shape `(y,x,4)`.
        
        The plugin is experimental and has only been tested with `CAMELYON16` and `CAMELYON17` datasets, 
        which can be downloaded [here](https://camelyon17.grand-challenge.org/Data/).
        
        ```bash
        $ napari tumor_004.tif
        ```
        
        ![Interactive deep zoom of whole-slide image](tumor_004.gif)
        
        ## Contributing
        
        Contributions are very welcome. Tests can be run with [tox], please ensure
        the coverage at least stays the same before you submit a pull request.
        
        ## License
        
        Distributed under the terms of the [BSD-3] license,
        "napari-lazy-openslide" is free and open source software
        
        ## Issues
        
        If you encounter any problems, please [file an issue] along with a detailed description.
        
        [napari]: https://github.com/napari/napari
        [Cookiecutter]: https://github.com/audreyr/cookiecutter
        [@napari]: https://github.com/napari
        [MIT]: http://opensource.org/licenses/MIT
        [BSD-3]: http://opensource.org/licenses/BSD-3-Clause
        [GNU GPL v3.0]: http://www.gnu.org/licenses/gpl-3.0.txt
        [GNU LGPL v3.0]: http://www.gnu.org/licenses/lgpl-3.0.txt
        [Apache Software License 2.0]: http://www.apache.org/licenses/LICENSE-2.0
        [Mozilla Public License 2.0]: https://www.mozilla.org/media/MPL/2.0/index.txt
        [cookiecutter-napari-plugin]: https://github.com/napari/cookiecutter-napari-plugin
        [file an issue]: https://github.com/manzt/napari-lazy-openslide/issues
        [napari]: https://github.com/napari/napari
        [tox]: https://tox.readthedocs.io/en/latest/
        [pip]: https://pypi.org/project/pip/
        [PyPI]: https://pypi.org/
        
Platform: UNKNOWN
Classifier: Development Status :: 4 - Beta
Classifier: Intended Audience :: Developers
Classifier: Topic :: Software Development :: Testing
Classifier: Programming Language :: Python
Classifier: Programming Language :: Python :: 3
Classifier: Programming Language :: Python :: 3.6
Classifier: Programming Language :: Python :: 3.7
Classifier: Programming Language :: Python :: 3.8
Classifier: Programming Language :: Python :: Implementation :: CPython
Classifier: Programming Language :: Python :: Implementation :: PyPy
Classifier: Operating System :: OS Independent
Classifier: License :: OSI Approved :: BSD License
Classifier: Framework :: napari
Requires-Python: >=3.6
Description-Content-Type: text/markdown
