Central Repository for Digital Pathology

CORDIS provides links to public deliverables and publications of HORIZON projects.

Links to deliverables and publications from FP7 projects, as well as links to some specific result types such as dataset and software, are dynamically retrieved from OpenAIRE .

Deliverables

Report on initial requirements

Establishment of initial requirements on infrastructure as understood by academic and industrial partners, with a starting point in existing services for genomics (ELIXIR AAI, REMS, Federated EGA [code, documentation], Beacon) and for biobank discoverability (BBMRI Directory).

Report on private execution model implementation in operational environment
Report on unified open digital slide and annotation format specification
Report on status of operational services implementation

Report on status of operational services implementation (M30): Report on status of implementation of REMS, federated data access, Beacon, export to BBMRI Directory in the operational BIGPICTURE infrastructure

Overview of the legal frameworks of all countries involved in BIGPICTURE
Report on landscape of guidelines, standards and regulatory requirements relevant for digital pathology, non-clinical
Report on hardware scaling

Report on progress of BIGPICTURE hardware capacity scaling

Project website

A public project website will be delivered

Report on integration and validation of QC algorithms and associated source code in the BIGPICTURE infrastructure
Report on pilot operations

Report on results from T2.5 Pilot operation in WP2 Phase III Refinements

Report on landscape of guidelines, standards and regulatory requirements relevant for digital pathology, clinical
Report on status of pilot services implementation

Report on status of implementation of REMS, federated data access, Beacon, export to BBMRI Directory in the pilot BIGPICTURE infrastructure

Report on private execution model implementation in pilot environment

Report on private execution model implantation in pilot environment

Report on Hands-on workshops

Hands-on workshops for both non-clinical and clinical pathologists where they can review slide packs of potentially challenging cases/interpretive scenarios, learn about the evidence base underpinning digital pathology safety, and discuss challenges and benefits of digital pathology in their area of expertise

Report on the pilot system establishment

Report on establishment a pilot of state-of-the-art systems development platform to support collaborative development of digital pathology adaptations to forks of existing services, including version control, issue tracking, continuous integration and deployment

Report on node network organisation model

sustainable node network organisation model responsible for mediating and collecting datasets from beneficiaries and third - parties and to contribute them to the BIGPICTURE data repository

Report on employment of quality control automation

Report on results from 3.10 (qc tool)

Report on user requirements specification for Cytomine

End-users (e.g. clinical pathologists, toxicological pathologists, academic researchers) will establish precise requirements for end-user tools (incl. user interfaces, manual annotation tools, and workflows) and AI tools (including programming interfaces, inputs/outputs).

Report on defined and first collected datasets

Report on results from 3.2, 3.6 and 3.7

WSI format to DICOM conversion tools

Whole-slide image format to DICOM conversion tools

BIGPICTURE Community online

Community as part of the BIGPICTURE website is online

Publications

Report on landscape of guidelines, standards and regulatory requirements relevant for digital pathology, clinical (D5.05)

Author(s): Schröder, Ulrike; Deutsches Institut für Normung; Radboud University Medical Center; Gdańsk Medical University; Lygature
Published in: Issue 26, 2025
Publisher: Zenodo
DOI: 10.5281/zenodo.14931624

From slides (through tiles) to pixels: an explainability framework for weakly supervised models in pre-clinical pathology

Author(s): Marco Bertolini, Van-Khoa Le, Jake Pencharz, Andreas Poehlmann, Djork-Arne Clevert, Santiago Villalba, Floriane Montanari
Published in: 2023
Publisher: Arxiv
DOI: 10.48550/arxiv.2302.01653

A Spatially-Aware Multiple Instance Learning Framework for Digital Pathology

Author(s): KeshvariKhojasteh, Hassan; Veta, Mitko; Pluim, Josien; Hess, Sibylle; Mitrea, Mihail
Published in: Issue 16, 2025
Publisher: Zenodo

Bigpicture Flexible Metadata File Exchange Format (MetaFleX)

Author(s): Maximillan Koeller, Erik Gabrielsson, Erio Barale-Thomas, Fauve Versaevel, Bigpicture Metadata Integration Taskforce
Published in: 2024
Publisher: github

Report on status of pilot services implementation (D2.04)

Author(s): Hedlund, Joel; Linköping University; CSC, IT Center for Science Ltd.; Uppsala University; Janssen (Belgium); BAYER AKTIENGESELLSCHAFT
Published in: Issue 12, 2025
Publisher: zenodo
DOI: 10.5281/zenodo.14731706

Multi-head Attention-based Deep Multiple Instance Learning

Author(s): Hassan Keshvarikhojasteh, Josien Pluim, Mitko Veta
Published in: medRxiv, 2024, ISSN 3067-2007
Publisher: medRxiv
DOI: 10.48550/arxiv.2404.05362

Bigpicture Project Website (D1.05)

Author(s): van der Laak, Jeroen; Radboud University Medical Center; Lygature; Janssen (Belgium)
Published in: Issue 6, 2025
Publisher: zenodo
DOI: 10.5281/zenodo.14719012

Report on the pilot system establishment (D2.02)

Author(s): Hedlund, Joel; Linköping University; CSC, IT Center for Science Ltd.; Uppsala University; University of Liège; Janssen (Belgium); BAYER AKTIENGESELLSCHAFT
Published in: Issue 11, 2025
Publisher: zenodo
DOI: 10.5281/zenodo.14731542

WSI format to DICOM conversion tools (D4.04)

Author(s): Gabrielsson, Erik; Sectra (Sweden)
Published in: Issue 9, 2025
Publisher: zenodo
DOI: 10.5281/zenodo.14922779

Report on initial requirements (D2.01)

Author(s): Hedlund, Joel; Linköping University; CSC, IT Center for Science Ltd.; Uppsala University; Janssen (Switzerland); Lygature
Published in: Issue 36, 2025
Publisher: Zenodo
DOI: 10.5281/zenodo.14719442

Bigpicture SlideTap: Pathology data extraction and curation

Author(s): SECTRA
Published in: 2024
Publisher: github

Domain Generalization in Computational Pathology: Survey and Guidelines

Author(s): MOSTAFA JAHANIFAR, MANAHIL RAZA, KESI XU, TRINH THI LE VUONG, ROBERT JEWSBURY, ADAM SHEPHARD, NEDA ZAMANITAJEDDIN, JIN TAE KWAK, SHAN E AHMED RAZA, FAYYAZ MINHAS, NASIR RAJPOOT
Published in: 2023
Publisher: arxiv
DOI: 10.48550/arxiv.2310.19656

Report on private execution model implementation in operational environment (D2.07)

Author(s): Hedlund, Joel; Linköping University; CSC, IT Center for Science Ltd.; Uppsala University; Janssen (Belgium); BAYER AKTIENGESELLSCHAFT
Published in: Issue 23, 2025
Publisher: zenodo
DOI: 10.5281/zenodo.14732769

Self-supervised large-scale kidney abnormality detection in drug safety assessment studies

Author(s): Ivan Slootweg, Natalia P. García-De-La-Puente, Geert Litjens, Salma Dammak
Published in: 2025, ISSN 3067-2007
Publisher: medRxiv
DOI: 10.48550/arxiv.2509.00131

Report on node network organisation model (D3.01)

Author(s): Kain, Renate; Medical University of Vienna; Leeds Teaching Hospitals NHS Trust; University Medical Center Utrecht; Region Östergötland; Hospital District of Helsinki and Uusimaa; Philipps-Universität Marburg; Lygature; Deciphex; Janssen (Belgium); Boehringer Ingelheim (Germany)
Published in: Issue 2, 2025
Publisher: Zenodo
DOI: 10.5281/zenodo.14732896

Report on defined and first collected datasets (D3.03)

Author(s): Bodén, Anna; Region Östergötland; Medical University of Vienna; University Medical Center Utrecht; SECTRA AB
Published in: Issue 33, 2025
Publisher: Zenodo
DOI: 10.5281/zenodo.14733017

Benchmarking Domain Generalization Algorithms in Computational Pathology

Author(s): Neda Zamanitajeddin, Mostafa Jahanifar, Kesi Xu, Fouzia Siraj, Nasir Rajpoot
Published in: 2024
Publisher: arXiv
DOI: 10.48550/arxiv.2409.17063

"""No negatives needed"": weakly-supervised regression for interpretable tumor detection in whole-slide histopathology images"

Author(s): D'Amato, Marina; van der Laak, Jeroen; Ciompi, Francesco
Published in: Issue 39, 2025, ISSN 2331-8422
Publisher: ArXiv
DOI: 10.48550/arxiv.2502.21109

Tumor-infiltrating lymphocytes in breast cancer through artificial intelligence: biomarker analysis from the results of the TIGER challenge

Author(s): Mart van Rijthoven, Witali Aswolinskiy, Leslie Tessier, Maschenka Balkenhol, Joep M. A. Bogaerts, Damien Drubay, Laura Comerma Blesa, Dieter Peeters, Elisabeth Specht Stovgaard, Anne-Vibeke Lænkholm, Harry Haynes, Ligia Craciun, Denis Larsimont, Mohamed T. Amgad, Lee AD Cooper, Cyril de Kock, Valerie Dechering, Johannes Lotz, Nick Weiss, Mieke van Bockstal, Christine Galant, Esther Lips, Hugo M.
Published in: 2025, ISSN 3067-2007
Publisher: medRxiv
DOI: 10.1101/2025.02.28.25323078

Report on employment of quality control automation (D3.04)

Author(s): Brettle, David; Leeds Teaching Hospitals NHS Trust; Region Östergötland; Deciphex
Published in: Issue 21, 2025
Publisher: Zenodo
DOI: 10.5281/zenodo.14733042

Report on user requirements specification for Cytomine (D4.01)

Author(s): Marée, Raphaël; University of Liège; Radboud University Medical Center; Region Östergötland; Medical University of Vienna; Hospital District of Helsinki and Uusimaa; Cytomine; Novartis (Switzerland); Janssen (Belgium)
Published in: Issue 24, 2025
Publisher: zenodo
DOI: 10.5281/zenodo.14922657

DeeperHistReg: Robust Whole Slide Images Registration Framework

Author(s): Marek Wodzinski, Niccolò Marini, Manfredo Atzori, Henning Müller
Published in: 2024, ISSN 3067-2007
Publisher: medRxiv
DOI: 10.48550/arxiv.2404.14434

Report on status of operational services implementation (D2.08)

Author(s): Hedlund, Joel; Linköping University; CSC, IT Center for Science Ltd.; Janssen (Belgium); BAYER AKTIENGESELLSCHAFT; Uppsala University
Published in: Issue 3, 2025
Publisher: zenodo
DOI: 10.5281/zenodo.14732801

Overview of the legal frameworks of all countries involved in Bigpicture (D5.01)

Author(s): Kogut - Czarkowska, Magdalena; Timelex; Linköping University; Biobanking and Biomolecular Resources Research Infrastructure Consortium; Region Östergötland; EUROPEAN INSTITUTE FOR INNOVATION THROUGH HEALTH DATA; Philipps-Universität Marburg; Lygature
Published in: Issue 12, 2025
Publisher: zenodo
DOI: 10.5281/zenodo.14923234

Lightstream: Pytorch library to train CNN's with large input images

Author(s): Stephan Dooper, Geert Litjens, Hans Pinckaers
Published in: 2024
Publisher: github

Report on hardware scaling (D2.06)

Author(s): Hedlund, Joel; Linköping University; CSC, IT Center for Science Ltd.; Uppsala University; Janssen (Belgium); BAYER AKTIENGESELLSCHAFT
Published in: Issue 5, 2025
Publisher: zenodo
DOI: 10.5281/zenodo.14732739

Report on unified open digital slide and annotation format specification (D4.03)

Author(s): Gabrielsson, Erik; Sectra (Sweden); Deciphex; Medical University of Vienna; University of Liège; Cytomine
Published in: Issue 26, 2025
Publisher: zenodo
DOI: 10.5281/zenodo.14922729

Report on landscape of guidelines, standards and regulatory requirements relevant for digital pathology, non-clinical (D5.02)

Author(s): PALAZZI, Xavier; Pfizer (United Kingdom); Boehringer Ingelheim (Germany)
Published in: Issue 11, 2025
Publisher: zenodo
DOI: 10.5281/zenodo.14923401

An Automated Pipeline for Tumour-Infiltrating Lymphocyte Scoring in Breast Cancer (arxiv.org) 

Author(s): Adam J Shephard, Mostafa Jahanifar, Ruoyu Wang, Muhammad Dawood, Simon Graham, Kastytis Sidlauskas, Syed Ali Khurram, Nasir M Rajpoot, Shan E Ahmed Raza
Published in: 2023
Publisher: arxiv
DOI: 10.48550/arxiv.2311.06185

Report on integration and validation of QC algorithms and associated source code in the Bigpicture infrastructure (D4.07)

Author(s): Litjens, Geert; Radboud University Medical Center; Novartis (Switzerland); HES-SO University of Applied Sciences and Arts Western Switzerland
Published in: Issue 20, 2025
Publisher: zenodo
DOI: 10.5281/zenodo.14922929

SCRIBBLE-BASED FAST WEAK-SUPERVISION AND INTERACTIVE CORRECTIONS FOR SEGMENTING WHOLE SLIDE IMAGES

Author(s): Antoine Habis, Vannary Meas-Yedid, Elsa D. Angelini, Jean-Christophe Olivo-Marin
Published in: 2024
Publisher: Arxiv
DOI: 10.48550/arxiv.2402.08333

Report on pilot operations (D2.05)

Author(s): Hedlund, Joel; Linköping University; CSC, IT Center for Science Ltd.; Uppsala University; Janssen (Belgium); BAYER AKTIENGESELLSCHAFT
Published in: Issue 9, 2025
Publisher: zenodo
DOI: 10.5281/zenodo.14731919

Report on private execution model implementation in pilot environment (D2.03)

Lymphovascular Invasion Detection in Breast Cancer Using Deep Learning

Author(s): Hassan Keshvarikhojasteh, Nikolas Stathonikos, Paul Pham, Paul J. van Diest, Celien Vreuls, Christof A. Bertram, Josien P.W. Pluim, Mitko Veta
Published in: medRxiv, 2025, ISSN 3067-2007
Publisher: medRxiv
DOI: 10.1101/2025.06.07.25329195

Bigpicture Community online (D6.01)

Author(s): Radboud University Medical Center; Novartis (Switzerland); Roche Pharma AG (Germany); ttopstart
Published in: 2025
Publisher: Zenodo
DOI: 10.5281/zenodo.14931670

On the robustness of regressing tumor percentage as an explainable detector in histopathology whole-slide images

Author(s): Marina D’Amato Maschenka Balkenhol Mart van Rijthoven Jeroen van der Laak Francesco Ciompi
Published in: Medical Imaging with Deep Learning 2023, 2023
Publisher: NA

Deep Multitask Learning for Automated Tissue Segmentation and Cell Detection

Author(s): Mohamed Mounib Benimam,Astri Frafjord, Alexandre Corthay, Thibault Lagache, Jean-Christophe Olivo-Marin, Vannary Meas-Yedid
Published in: eusipco 2025, 2025, ISBN 978-9-46-459362-4
Publisher: European Association for Signal Processing

End-to-end learning for detecting MYC translocations

Author(s): Stephan Dooper, Geert Litjens
Published in: MIDL 2022 Short Papers, Issue Yearly, 2022, Page(s) -
Publisher: -

Robust Multiresolution and Multistain Background Segmentation in Whole Slide Images

Author(s): Artur Jurgas, Marek Wodzinski, Manfredo Atzori, and Henning Mueller
Published in: Issue PCBEE 2023 , 2023, Page(s) pp 29–40 , ISBN 978-3-031-38429-5
Publisher: Springer, Cham
DOI: 10.1007/978-3-031-38430-1_3

Streaming Convolutional Attention Models

Author(s): Stephan Dooper Geert Litjens Hans Pinckaers
Published in: MEDICAL IMAGING MEETS NEURIPS An official NeurIPS Workshop - 14 December 2021, Issue Yearly, 2021, Page(s) -
Publisher: -

Smart Learning of Click and Refine for Nuclei Segmentation on Histology Images

Author(s): Antoine Habis, Vannary Meas-Yedid, Daniel Felipe Gonzalez Obando, Jean-Christophe Olivo-Marin, Elsa D. Angelini
Published in: 2022 IEEE International Conference on Image Processing (ICIP), 2024, Page(s) 2281-2285
Publisher: IEEE
DOI: 10.1109/icip46576.2022.9897496

Artifact Augmentation for Learning-based Quality Control of Whole Slide Images

Author(s): Artur Jurgas, Marek Wodzinski, Weronika Celniak, Manfredo Atzori, Henning Mueller
Published in: -, Issue 1-4, 2023, Page(s) IEEE
Publisher: IEEE
DOI: 10.1109/embc40787.2023.10340997

Benchmarking Hierarchical Image Pyramid Transformer for the Classification of Colon Biopsies and Polyps Histopathology Images

Author(s): Nohemi S. Leon Contreras, Clément Grisi, Witali Aswolinskiy, Simona Vatrano, Filippo Fraggetta, Iris Nagtegaal, Marina D’Amato, Francesco Ciompi
Published in: 2024 IEEE International Symposium on Biomedical Imaging (ISBI), 2024, Page(s) 1-4
Publisher: IEEE
DOI: 10.1109/isbi56570.2024.10635841

Use of quality checks and processes across digital histopathology: an initial survey from the Bigpicture consortium

Author(s): Hayley Pye, David S Brettle, Caitríona Lyons, Fauve Versaevel, Erio Barale-Thomas, Kurt Zatloukal, Darren Treanor
Published in: Journal of Clinical Pathology, Issue 78, 2025, Page(s) 691-696, ISSN 0021-9746
Publisher: BMJ Publishing Group
DOI: 10.1136/jcp-2024-210010

Deep learning in histopathology: the path to the clinic

Author(s): Jeroen van der Laak, Geert Litjens & Francesco Ciompi
Published in: Nature Medicine, Issue 27 (2021), 2021, Page(s) pages775–784, ISSN 1078-8956
Publisher: Nature Publishing Group
DOI: 10.1038/s41591-021-01343-4

Detection and subtyping of basal cell carcinoma in whole-slide histopathology using weakly-supervised learning

Author(s): Daan J. Geijs, Stephan Dooper, Witali Aswolinskiy, Lisa M. Hillen, Avital L. Amir, Geert Litjens
Published in: Medical Image Analysis, Issue 93, 2025, Page(s) 103063, ISSN 1361-8415
Publisher: Elsevier BV
DOI: 10.1016/j.media.2023.103063

Improving Quality Control of Whole Slide Images by Explicit Artifact Augmentation

Author(s): Artur Jurgas, Marek Wodzinski, Marina D'Amato, Jeroen van der Laak, Manfredo Atzori, Henning Müller
Published in: Scientific Reports, Issue 14, 2024, ISSN 2045-2322
Publisher: Nature Publishing Group
DOI: 10.21203/rs.3.rs-3982522/v1

Trust, Trustworthiness, and the Future of Medical AI: Outcomes of an Interdisciplinary Expert Workshop

Author(s): Melanie Goisauf, Mónica Cano Abadía, Kaya Akyüz, Maciej Bobowicz, Alena Buyx, Ilaria Colussi, Marie-Christine Fritzsche, Karim Lekadir, Pekka Marttinen, Michaela Th Mayrhofer, Janos Meszaros
Published in: Journal of Medical Internet Research, Issue 27, 2025, Page(s) e71236, ISSN 1438-8871
Publisher: Journal of medical Internet Research
DOI: 10.2196/71236

Digital Pathology and Artificial Intelligence Applied to Nonclinical Toxicology Pathology—The Current State, Challenges, and Future Directions

Author(s): Gabriele Pohlmeyer-Esch, Charles Halsey, Julie Boisclair, Sripad Ram, Sarah Kirschner-Kitz, Brian Knight, Pierre Moulin, Anna-Lena Frisk
Published in: Toxicologic Pathology, Issue 53, 2025, Page(s) 516-535, ISSN 0192-6233
Publisher: SAGE Publications
DOI: 10.1177/01926233251340622

Statistical analysis of spatial patterns in tumor microenvironment images

Author(s): Mohamed M. Benimam, Vannary Meas-Yedid, Suvadip Mukherjee, Astri Frafjord, Alexandre Corthay, Thibault Lagache, Jean-Christophe Olivo-Marin
Published in: Nature Communications, Issue 16, 2025, ISSN 2041-1723
Publisher: Nature Publishing Group
DOI: 10.1038/s41467-025-57943-y

RegWSI: Whole slide image registration using combined deep feature- and intensity-based methods: Winner of the ACROBAT 2023 challenge

Author(s): Marek Wodzinski, Niccolò Marini, Manfredo Atzori, Henning Müller
Published in: Computer Methods and Programs in Biomedicine, Issue 250, 2024, Page(s) 108187, ISSN 0169-2607
Publisher: Elsevier BV
DOI: 10.1016/j.cmpb.2024.108187

DISBELIEVE: Distance Between Client Models Is Very Essential for Effective Local Model Poisoning Attacks

Author(s): Indu Joshi, Priyank Upadhya, Gaurav Kumar Nayak, Peter Schüffler, Nassir Navab
Published in: Lecture Notes in Computer Science, Medical Image Computing and Computer Assisted Intervention – MICCAI 2023 Workshops, 2024, Page(s) 297-310
Publisher: Springer Nature Switzerland
DOI: 10.1007/978-3-031-47401-9_29

Synergies Among Health Data Projects with Cancer Use Cases Based on Health Standards

Author(s): Amelie Gyrard, Philip Gribbon, Rada Hussein, Somayeh Abedian, Luis Marti Bonmati, Gibi Luisa Cabornero, George Manias, Gabriel Danciu, Stefano Dalmiani, Serge Autexier, Rick van Nuland, Mario Jendrossek, Ioannis Avramidis, Eva Garcia Alvarez
Published in: Studies in Health Technology and Informatics, Digital Health and Informatics Innovations for Sustainable Health Care Systems, Issue Volume 316, 2024, Page(s) 1292 - 1296
Publisher: IOS Press
DOI: 10.3233/shti240649

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