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A plugin to lazily load multiscale whole-slide images with openslide and dask.

Project description

napari-lazy-openslide

License PyPI Python Version tests

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

Interactive deep zoom of whole-slide image

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.

Project details


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Files for napari-lazy-openslide, version 0.2.0
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Filename, size napari_lazy_openslide-0.2.0-py3-none-any.whl (8.0 kB) File type Wheel Python version py3 Upload date Hashes View
Filename, size napari-lazy-openslide-0.2.0.tar.gz (9.4 MB) File type Source Python version None Upload date Hashes View

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