Universität zu Köln

Weng, Zhilong ORCID: 0009-0002-0321-9406, Seper, Alexander, Pryalukhin, Alexey, Mairinger, Fabian, Wickenhauser, Claudia, Bauer, Marcus, Glamann, Lennert ORCID: 0009-0006-2462-0951, Bläker, Hendrik, Lingscheidt, Thomas, Hulla, Wolfgang, Jonigk, Danny ORCID: 0000-0002-5251-2281, Schallenberg, Simon, Bychkov, Andrey ORCID: 0000-0002-4203-5696, Fukuoka, Junya, Braun, Martin, Schömig-Markiefka, Birgid ORCID: 0000-0003-1893-8796, Klein, Sebastian ORCID: 0000-0002-2188-9377, Thiel, Andreas, Bozek, Katarzyna ORCID: 0000-0002-0917-6876, Netto, George J., Quaas, Alexander ORCID: 0000-0002-3537-6011, Büttner, Reinhard ORCID: 0000-0001-8806-4786 and Tolkach, Yuri ORCID: 0000-0001-5239-2841 (2024). GrandQC: A comprehensive solution to quality control problem in digital pathology. Nature Communications, 15 (1). pp. 1-12. Springer Nature. ISSN 2041-1723

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Abstract

[Artikel-Nr.: 10685] 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.

Item Type:	Article
Creators:	Creators Email ORCID ORCID Put Code Weng, Zhilong UNSPECIFIED https://orcid.org/0009-0002-0321-9406 UNSPECIFIED Seper, Alexander UNSPECIFIED UNSPECIFIED UNSPECIFIED Pryalukhin, Alexey UNSPECIFIED UNSPECIFIED UNSPECIFIED Mairinger, Fabian UNSPECIFIED UNSPECIFIED UNSPECIFIED Wickenhauser, Claudia UNSPECIFIED UNSPECIFIED UNSPECIFIED Bauer, Marcus UNSPECIFIED UNSPECIFIED UNSPECIFIED Glamann, Lennert UNSPECIFIED https://orcid.org/0009-0006-2462-0951 UNSPECIFIED Bläker, Hendrik UNSPECIFIED UNSPECIFIED UNSPECIFIED Lingscheidt, Thomas UNSPECIFIED UNSPECIFIED UNSPECIFIED Hulla, Wolfgang UNSPECIFIED UNSPECIFIED UNSPECIFIED Jonigk, Danny UNSPECIFIED https://orcid.org/0000-0002-5251-2281 UNSPECIFIED Schallenberg, Simon UNSPECIFIED UNSPECIFIED UNSPECIFIED Bychkov, Andrey UNSPECIFIED https://orcid.org/0000-0002-4203-5696 UNSPECIFIED Fukuoka, Junya UNSPECIFIED UNSPECIFIED UNSPECIFIED Braun, Martin UNSPECIFIED UNSPECIFIED UNSPECIFIED Schömig-Markiefka, Birgid UNSPECIFIED https://orcid.org/0000-0003-1893-8796 UNSPECIFIED Klein, Sebastian UNSPECIFIED https://orcid.org/0000-0002-2188-9377 UNSPECIFIED Thiel, Andreas UNSPECIFIED UNSPECIFIED UNSPECIFIED Bozek, Katarzyna UNSPECIFIED https://orcid.org/0000-0002-0917-6876 UNSPECIFIED Netto, George J. UNSPECIFIED UNSPECIFIED UNSPECIFIED Quaas, Alexander UNSPECIFIED https://orcid.org/0000-0002-3537-6011 UNSPECIFIED Büttner, Reinhard UNSPECIFIED https://orcid.org/0000-0001-8806-4786 UNSPECIFIED Tolkach, Yuri UNSPECIFIED https://orcid.org/0000-0001-5239-2841 UNSPECIFIED
URN:	urn:nbn:de:hbz:38-816122
Identification Number:	10.1038/s41467-024-54769-y
Journal or Publication Title:	Nature Communications
Volume:	15
Number:	1
Page Range:	pp. 1-12
Number of Pages:	12
Date:	16 December 2024
Publisher:	Springer Nature
ISSN:	2041-1723
Language:	English
Faculty:	Central Institutions / Interdisciplinary Research Centers Faculty of Medicine
Divisions:	CECAD - Cluster of Excellence Cellular Stress Responses in Aging-Associated Diseases Faculty of Medicine > Medizinische Statistik und Bioinformatik > Institut für Medizinische Statistik und Bioinformatik � IMSB Faculty of Medicine > Pathologie und Neuropathologie > Institut für Pathologie Zentrum für Molekulare Medizin
Subjects:	Medical sciences Medicine
['eprint_fieldname_oa_funders' not defined]:	Publikationsfonds UzK
Refereed:	Yes
URI:	http://kups.ub.uni-koeln.de/id/eprint/81612