A plugin to lazily load multiscale whole-slide images with openslide and dask.
An experimental plugin to lazily load multiscale whole-slide tiff images with openslide and dask.
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
openslideare also avaiable via
conda install -c sdvillal openslide-python
Step 2.) Install
napari-lazy-openslide via pip:
pip install napari-lazy-openslide
This plugin tries to be conservative with what files it will attempt to provide a reader.
It will only attempt to read
.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
The plugin is experimental and has only been tested with
which can be downloaded here.
$ napari tumor_004.tif
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.
Distributed under the terms of the BSD-3 license, "napari-lazy-openslide" is free and open source software
If you encounter any problems, please file an issue along with a detailed description.
- 30 January 2021
- 14 July 2020
- 4 - Beta
- Stars: 17
- Forks: 4
- Issues + PRs: 1
Python versions supported:
- OS Independent
- napari-plugin-engine (>=0.1.4)
- numpy (>=0.1.19)
- zarr (>=0.2.4)
- dask[array] (>=2.20.0)
- openslide-python (==1.1.2)