A Snakemake workflow for converting whole-slide images (WSI) from the CRC Cohort from vendor-specific image formats to open image formats (at the moment, OME-TIFF). The workflow also encrypts the new image files with Crypt4GH.
The CRC Cohort is a collection of clinical data and digital high-resolution digital pathology images pertaining to tumor cases. The collection has been assembled from a number of participating biobanks and other partners through the ADOPT BBMRI-ERIC project.
Researchers interested in using the data for science can apply for access.
The usage of this workflow is described in the Snakemake Workflow Catalog.
If you use this workflow in a paper, don't forget to give credits to the authors by citing the URL of this repository and its DOI (see above).