napari-lazy-openslide

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.

Installation

Step 1.) Make sure you have OpenSlide installed. Download instructions here.

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.

$ napari tumor_004.tif

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.