FAIR CRCC - image conversion Version 1
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Snakemake workflow: FAIR CRCC - image conversion
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.
What's the CRC Cohort?
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.
Usage
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).
Version History
Version 1 (earliest) Created 31st Jan 2022 at 11:03 by Luca Pireddu
Open
master3a465d0
Creators and SubmitterViews: 1872 Downloads: 103
Created: 31st Jan 2022 at 11:03
Last updated: 6th Sep 2022 at 08:52
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Teams: IBISBA Workflows, CRC Cohort
Organizations: Unspecified, CRS4
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Web page: Not specified
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.
Space: Independent Teams
Public web page: Not specified
