openslide-python 1.0.0

Python interface to OpenSlide

OpenSlide Python is a Python interface to the OpenSlide library.

OpenSlide is a C library that provides a simple interface for reading whole-slide images, also known as virtual slides, which are high-resolution images used in digital pathology. These images can occupy tens of gigabytes when uncompressed, and so cannot be easily read using standard tools or libraries, which are designed for images that can be comfortably uncompressed into RAM. Whole-slide images are typically multi-resolution; OpenSlide allows reading a small amount of image data at the resolution closest to a desired zoom level.

OpenSlide can read virtual slides in several formats:

• Aperio (.svs, .tif)

• Hamamatsu (.ndpi, .vms, .vmu)

• Leica (.scn)

• MIRAX (.mrxs)

• Sakura (.svslide)

• Trestle (.tif)

• Ventana (.bif)

• Generic tiled TIFF (.tif)

Requirements

• Python 2 >= 2.6 or Python 3 >= 3.3

• OpenSlide >= 3.4.0

• Python Imaging Library or Pillow

Installation

1. Install OpenSlide.

2. pip install openslide-python

Using PIL

setup.py assumes that you want to use the Pillow fork of PIL. If you already have classic PIL installed, you can use it instead. Install OpenSlide Python with:

pip install --no-deps openslide-python

or, if you are installing by hand:

python setup.py install --single-version-externally-managed --record /dev/null

More Information

• API documentation

• Website

• GitHub

• Sample data

License

OpenSlide Python is released under the terms of the GNU Lesser General Public License, version 2.1.