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

Nature Communications, vol. 15, pp. 10685

Abstract

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.

Authors 21

1. Alexander Seper

   Danube Private University

   Affiliation as printed

   Danube Private University, 3500, Krems an der Donau, Austria

2. Alexey Pryalukhin

   Danube Private University · Universitätsklinikum Wiener Neustadt

   Affiliation as printed

   Institute of Pathology, University Hospital Wiener Neustadt / Danube Private University, 2700, Wiener Neustadt, Austria

3. Fabian Dominik Mairinger

   Essen University Hospital · Stiftung Universitätsmedizin Essen

   Affiliation as printed

   Institute of Pathology, University Hospital Essen, Essen, Germany

4. Claudia Wickenhauser

   University Hospital in Halle · Martin Luther University Halle-Wittenberg

   Affiliation as printed

   Institute of Pathology, University Hospital Halle, Martin Luther University Halle-Wittenberg, Halle (Salle), Germany

5. Marcus Bauer

   University Hospital in Halle · Martin Luther University Halle-Wittenberg

   Affiliation as printed

   Institute of Pathology, University Hospital Halle, Martin Luther University Halle-Wittenberg, Halle (Salle), Germany

6. Lennert Glamann

   University Hospital in Halle · Martin Luther University Halle-Wittenberg

   Affiliation as printed

   Institute of Pathology, University Hospital Halle, Martin Luther University Halle-Wittenberg, Halle (Salle), Germany

7. Hendrik Bläker

   University Hospital Leipzig

   Affiliation as printed

   Institute of Pathology, University Hospital Leipzig, Leipzig, Germany

8. Thomas Lingscheidt

   University Hospital Leipzig

   Affiliation as printed

   Institute of Pathology, University Hospital Leipzig, Leipzig, Germany

9. Wolfgang Hulla

   Danube Private University · Universitätsklinikum Wiener Neustadt

   Affiliation as printed

   Institute of Pathology, University Hospital Wiener Neustadt / Danube Private University, 2700, Wiener Neustadt, Austria

10. Danny David Jonigk Aachen Institute of Pathology

    Universitätsklinikum Aachen · German Center for Lung Research

    Affiliation as printed

    German Center for Lung Research (DZL), Biomedical Research in Endstage and Obstructive Lung Disease Hannover (BREATH), Hannover, Germany

    Institute of Pathology, University Hospital Aachen, Aachen, Germany

11. Simon Schallenberg

    Charité - Universitätsmedizin Berlin

    Affiliation as printed

    Institute of Pathology, University Hospital Charite, Berlin, Germany

12. Andrey Bychkov

    Kameda Medical Center · Nagasaki University Hospital

    Affiliation as printed

    Department of Pathology Informatics, University Hospital Nagasaki, Nagasaki, Japan

    Kameda Medical Center, Tamogawa, Japan

13. Junya Fukuoka

    Kameda Medical Center · Nagasaki University Hospital

    Affiliation as printed

    Department of Pathology Informatics, University Hospital Nagasaki, Nagasaki, Japan

    Kameda Medical Center, Tamogawa, Japan

14. MARTIN A. BRAUN
    Affiliation as printed

    MVZ Pathology and Cytology Rhein-Sieg, Troisdorf, Germany

15. Birgid Schömig‐Markiefka

    University Hospital Cologne

    Affiliation as printed

    Institute of Pathology, University Hospital Cologne, 50937, Cologne, Germany

16. Sebastian Klein

    University Hospital Cologne

    Affiliation as printed

    Institute of Pathology, University Hospital Cologne, 50937, Cologne, Germany

17. Andreas Thiel
    Affiliation as printed

    MVZ Pathology Bethesda, Duisburg, Germany

18. Katarzyna Bożek

    University of Cologne · Cologne Excellence Cluster on Cellular Stress Responses in Aging Associated Diseases · University Hospital Cologne

    Affiliation as printed

    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

    Institute for Biomedical Informatics, Faculty of Medicine and University Hospital Cologne, University of Cologne, Cologne, Germany

19. George Jabboure Netto

    University of Pennsylvania

    Affiliation as printed

    Department of Pathology and Laboratory Medicine, Perelman School of Medicine at the University of Pennsylvania, Pennsylvania, USA

20. Reinhard Büttner

    University Hospital Cologne

    Affiliation as printed

    Institute of Pathology, University Hospital Cologne, 50937, Cologne, Germany

21. Yuri Tolkach corresponding

    University Hospital Cologne

    Affiliation as printed

    Institute of Pathology, University Hospital Cologne, 50937, Cologne, Germany. yuri.tolkach@gmail.com

    Institute of Pathology, University Hospital Cologne, 50937, Cologne, Germany