Toxicologic Pathology Forum: A Roadmap for Building State-of-the-Art Digital Image Data Resources for Toxicologic Pathology in the Pharmaceutical Industry. (December 2022)

• Record Type: Journal Article
• Authors: Ge, Xing-Yue; Funk, Juergen; Albrecht, Tom; Birkhimer, Merima; Gilsdorf, Moritz; Hayes, Matthew; Hu, Fangyao; Maliver, Pierre; McCreary, Mark; Nguyen, Trung; Romero-Palomo, Fernando; Seger, Shanon; Fuji, Reina N.; Schumacher, Vanessa; Sullivan, Ruth
• Is Part Of: Toxicologic pathology. Volume 50:Number 8(2022)
• Page Start: 942
• Page End: 949
• Publication Date: 2022-12
• Subjects: digital pathology -- whole slide images -- slide scanning -- image data management -- FAIR data -- pharmaceutical industry; Pathology -- Periodicals; Toxicology -- Periodicals; Pathology; Toxicology; 615.9
• DOI: 10.1177/01926233221132747
• Languages: English
• ISSNs: 0192-6233

Abstract

Digitization of histologic slides brings with it the promise of enhanced toxicologic pathology practice through the increased application of computational methods. However, the development of these advanced methods requires access to substrate image data, that is, whole slide images (WSIs). Deep learning methods, in particular, rely on extensive training data to develop robust algorithms. As a result, pharmaceutical companies interested in leveraging computational methods in their digital pathology workflows must first invest in data infrastructure to enable data access for both data scientists and pathologists. The process of building robust image data resources is challenging and includes considerations of generation, curation, and storage of WSI files, and WSI access including via linked metadata. This opinion piece describes the collective experience of building resources for WSI data in the Roche group. We elaborate on the challenges encountered and solutions developed with the goal of providing examples of how to build a data resource for digital pathology analytics in the pharmaceutical industry.