• Version:

    • 0.2.0
  • Release date:

    • 30 January 2021
  • First released:

    • 14 July 2020
  • Development status:

    • 4 - Beta
  • License:

    • BSD-3-Clause

Github Activity

  • Stars: 17
  • Forks: 4
  • Issues + PRs: 1
  • Python versions supported:

    • >=3.6
  • Operating system:

    • OS Independent
  • Requirements:

    • napari-plugin-engine (>=0.1.4)
    • numpy (>=0.1.19)
    • zarr (>=0.2.4)
    • dask[array] (>=2.20.0)
    • openslide-python (==1.1.2)

napari-lazy-openslide

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

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.

  • Version:

    • 0.2.0
  • Release date:

    • 30 January 2021
  • First released:

    • 14 July 2020
  • Development status:

    • 4 - Beta
  • License:

    • BSD-3-Clause

Github Activity

  • Stars: 17
  • Forks: 4
  • Issues + PRs: 1
  • Python versions supported:

    • >=3.6
  • Operating system:

    • OS Independent
  • Requirements:

    • napari-plugin-engine (>=0.1.4)
    • numpy (>=0.1.19)
    • zarr (>=0.2.4)
    • dask[array] (>=2.20.0)
    • openslide-python (==1.1.2)

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