waliens/sldc-openslide

A binding for using the OpenSlide image library with SLDC

SLDC-OpenSlide

SLDC is a Python library that aims at accelerating development of large images analysis workflows. SLDC-OpenSlide is a Python binding for using SLDC with the OpenSlide image library. In practice, it enables workflows to process large images stored locally on disk.

Install

1. Install SLDC: https://github.com/waliens/sldc
2. Install OpenSlide and openslide-python: https://github.com/openslide/openslide-python
3. Install SLDC-OpenSlide:
   1. Clone or download the repository
   2. Move to the root folder
   3. Install: python setup.py install
4. Test your install: python -c "import sldc_openslide"

Usage

SLDC-OpenSlide provides mostly two classes:

• OpenSlideTileBuilder: a builder that builds tiles using an OpenSlideImage as parent image. This is the tile builder that must be passed to the builder at the workflow construction.
• OpenSlideImage: adapts OpenSlide class to match SLDC Image interface. This is the Image object that must be passed to the process method of your workflow.

Note: Any instance of OpenSlideImage hold a file resource which must hence be released when the image is not needed anymore. You can either explicitely close the resource by calling image.close() or by using a context manager. In both case, the instance image cannot be used anymore after being closed, otherwise resulting in undefined behavior.