Tools for dividing pathology whole slide images into tiles and save them as individual files.
WSItiler tries to optimize the pre-processing of Pathology Whole Slide Images (WSI), which tend to be very large files of tiled images of different magnifications. We do this by identifying regions of interest in a downscaled copy of the WSI and only processing the tiles that correspond to said areas (the foreground) in a parallelized manner using multiprocessing.
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Install OpenSlide. WSItiler uses OpenSlide to interact with WSI files. It is a C library that must be installed separately before installing WSItiler. Here are some examples for some major operating systems:
- Debian (Linux):
apt-get install python3-openslide
- Windows: Download Windows binaries here, and copy the binary files (i.e. the contents of
openslide-win64-20171122\bin\) to the same directory where your Python interpreter of choice is (python.exe) located. This may be in your virtual/conda environment of choice.
- Debian (Linux):
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Use the package manager pip to install WSItiler like below. Rerun this command to check for and install updates.
pip install git+https://github.com/hwanglab/wsitiler
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You can
import wsitilerinto your own script to set up a custom pipeline withwsitiler.wsiManageror use the supplied color normalization methods underwsitiler.normalizer. -
You can run WSItiler from the command line as an executable script by running the following command within the appropriate Python environment:
python -m wsitiler.tiler <options>
For more information about how to run WSItiler as an independent command, use:
python -m wsitiler.tiler -h
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You can collect a summary of your processed WSI using the
describe_dataset.pyscript:python -m wsitiler.describe_dataset -i <list of input directories> -o <file output directory> -c <number of cores>
Pull requests are welcome. Ideally, please open an issue first to discuss what you would like to change. Please follow these steps:
- Create an issue detailing the required/desired changes.
- If reporting a bug, please include the run settings that caused the error and the error output in the description.
- Create a new branch from
mainand implement your changes there. - Commit your changes referencing your issue number.
- Once you make sure your changes do not break the main use, submit a pull request and notify @jeanrclemenceau
@jeanrclemenceau will review any changes and merge them to the main.