GrandQC: A comprehensive solution to quality control problem in digital pathology.

Autor: Weng Z; Institute of Pathology, University Hospital Cologne, 50937, Cologne, Germany., Seper A; Danube Private University, 3500, Krems an der Donau, Austria., Pryalukhin A; Institute of Pathology, University Hospital Wiener Neustadt / Danube Private University, 2700, Wiener Neustadt, Austria., Mairinger F; Institute of Pathology, University Hospital Essen, Essen, Germany., Wickenhauser C; Institute of Pathology, University Hospital Halle, Martin Luther University Halle-Wittenberg, Halle (Salle), Germany., Bauer M; Institute of Pathology, University Hospital Halle, Martin Luther University Halle-Wittenberg, Halle (Salle), Germany., Glamann L; Institute of Pathology, University Hospital Halle, Martin Luther University Halle-Wittenberg, Halle (Salle), Germany., Bläker H; Institute of Pathology, University Hospital Leipzig, Leipzig, Germany., Lingscheidt T; Institute of Pathology, University Hospital Leipzig, Leipzig, Germany., Hulla W; Institute of Pathology, University Hospital Wiener Neustadt / Danube Private University, 2700, Wiener Neustadt, Austria., Jonigk D; Institute of Pathology, University Hospital Aachen, Aachen, Germany.; German Center for Lung Research (DZL), Biomedical Research in Endstage and Obstructive Lung Disease Hannover (BREATH), Hannover, Germany., Schallenberg S; Institute of Pathology, University Hospital Charite, Berlin, Germany., Bychkov A; Department of Pathology Informatics, University Hospital Nagasaki, Nagasaki, Japan.; Kameda Medical Center, Tamogawa, Japan., Fukuoka J; Department of Pathology Informatics, University Hospital Nagasaki, Nagasaki, Japan.; Kameda Medical Center, Tamogawa, Japan., Braun M; MVZ Pathology and Cytology Rhein-Sieg, Troisdorf, Germany., Schömig-Markiefka B; Institute of Pathology, University Hospital Cologne, 50937, Cologne, Germany., Klein S; Institute of Pathology, University Hospital Cologne, 50937, Cologne, Germany., Thiel A; MVZ Pathology Bethesda, Duisburg, Germany., Bozek K; Institute for Biomedical Informatics, Faculty of Medicine and University Hospital Cologne, University of Cologne, Cologne, Germany.; Center for Molecular Medicine Cologne (CMMC), Faculty of Medicine and University Hospital Cologne, University of Cologne, Cologne, Germany.; Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne, Cologne, Germany., Netto GJ; Department of Pathology and Laboratory Medicine, Perelman School of Medicine at the University of Pennsylvania, Pennsylvania, USA., Quaas A; Institute of Pathology, University Hospital Cologne, 50937, Cologne, Germany., Büttner R; Institute of Pathology, University Hospital Cologne, 50937, Cologne, Germany., Tolkach Y; Institute of Pathology, University Hospital Cologne, 50937, Cologne, Germany. yuri.tolkach@gmail.com.
Jazyk: angličtina
Zdroj: Nature communications [Nat Commun] 2024 Dec 16; Vol. 15 (1), pp. 10685. Date of Electronic Publication: 2024 Dec 16.
DOI: 10.1038/s41467-024-54769-y
Abstrakt: Histological slides contain numerous artifacts that can significantly deteriorate the performance of image analysis algorithms. Here we develop the GrandQC tool for tissue and multi-class artifact segmentation. GrandQC allows for high-precision tissue segmentation (Dice score 0.957) and segmentation of tissue without artifacts (Dice score 0.919-0.938 dependent on magnification). Slides from 19 international pathology departments digitized with the most common scanning systems and from The Cancer Genome Atlas dataset were used to establish a QC benchmark, analyzing inter-institutional, intra-institutional, temporal, and inter-scanner slide quality variations. GrandQC improves the performance of downstream image analysis algorithms. We open-source the GrandQC tool, our large manually annotated test dataset, and all QC masks for the entire TCGA cohort to address the problem of QC in digital/computational pathology. GrandQC can be used as a tool to monitor sample preparation and scanning quality in pathology departments and help to track and eliminate major artifact sources.
Competing Interests: Competing interests: The authors declare no relevant competing interests.
(© 2024. The Author(s).)
Databáze: MEDLINE
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