Publications
Publications, conference proceedings, abstracts
Journal publications
Xiaoyi Ji, Richard Salmon, Nita Mulliqi, Umair Khan, Yinxi Wang, Anders Blilie, Henrik Olsson, Bodil Ginnerup Pedersen, Karina Dalsgaard Sørensen, Benedicte Parm Ulhøi, Svein R. Kjosavik, Emilius A.M. Janssen, Mattias Rantalainen, Lars Egevad, Pekka Ruusuvuori, Martin Eklund, Kimmo Kartasalo,
Physical Color Calibration of Digital Pathology Scanners for Robust Artificial Intelligence Assisted Cancer Diagnosis, Modern Pathology, 2025, 100715, ISSN 0893-3952,
https://doi.org/10.1016/j.modpat.2025.100715.
Montezuma D, Oliveira SP, Tolkach Y, et al. Annotation Practices in Computational Pathology: A European Society of Digital and Integrative Pathology (ESDIP) Survey Study. Lab Invest. Published online November 29, 2024. doi:10.1016/j.labinv.2024.102203
Andrés Mosquera-Zamudio, Marcela Gomez-Suarez, John Sprockel, Julian Camilo Riaño-Moreno, Emiel A.M. Janssen, Liron Pantanowitz, Rafael Parra-Medina, Globalization of a telepathology network with artificial intelligence applications in Colombia: The GLORIA program study protocol, Journal of Pathology Informatics, 2024, 100394.
Lashen AG, Toss M, Miligy I, Rewcastle E, Kiraz U, Janssen EAM, Green AR, Quinn C, Ellis I, Rakha EA., Nottingham prognostic x (NPx): a risk stratification tool in ER-positive HER2-negative breast cancer: a validation study, Histopathology. 2024 Jun 13. doi: 10.1111/his.15234.
Mosquera-Zamudio, A., Launet, L., Colomer, A., Wiedemeyer, K., López-Takegami, J.C., Palma, L.F., Undersrud, E., Janssen, E., Brenn, T., Naranjo, V. and Monteagudo, C., Histological interpretation of spitzoid tumours: an extensive machine learning-based concordance analysis for improving decision making, Histopathology, 85: 155-170 (2024)
Rewcastle E, Skaland I, Gudlaugsson E, Fykse SK, Baak JPA, Janssen EAM., The Ki67 dilemma: investigating prognostic cut-offs and reproducibility for automated Ki67 scoring in breast cancer, Breast Cancer Res Treat. 2024 May 26. doi: 10.1007/s10549-024-07352-4.
Claudio Fernandez-Martín, Julio Silva-Rodriguez, Umay Kiraz, Sandra Morales, Emiel A.M. Janssen, Valery Naranjo, Uninformed Teacher-Student for hard-samples distillation in weakly supervised mitosis localization, Computerized Medical Imaging and Graphics, Volume 112, 2024, 102328.
Kvikstad V, Lillesand M, Gudlaugsson E, Mangrud OM, Rewcastle E, Skaland I, Baak JPA, Janssen EAM, Proliferation and immunohistochemistry for p53, CD25 and CK20 in predicting prognosis of non-muscle invasive papillary urothelial carcinomas, PLoS One. 2024 Jan 26;19(1):e0297141.
Jahangir CA, Page DB, Broeckx G, et al., Image-based multiplex immune profiling of cancer tissues: translational implications. A report of the International Immuno-oncology Biomarker Working Group on Breast Cancer. The Journal of pathology. 2024 Jan 17.
Timothy B. Fisher, Geetanjali Saini, T. S. Rekha, Jayashree Krishnamurthy, Shristi Bhattarai, Grace Callagy, Mark Webber, Emiel A. M. Janssen, Jun Kong & Ritu Aneja, Digital image analysis and machine learning-assisted prediction of neoadjuvant chemotherapy response in triple-negative breast cancer, Breast Cancer Res 26, 12 (2024).
O'Keeffe M, Oterhals Å, Weishaupt H, Leh S, Ulvik A, Ueland PM, Halstensen A, Marti HP, Gudbrandsen OA. A diet containing cod backbone proteins attenuated the development of mesangial sclerosis and tubular dysfunction in male obese BTBR ob/ob mice. Eur J Nutr. 2023 Dec;62(8):3227-3240
Bhattarai S, Saini G, Li H, Duanmu H, Seth G, Fisher TB, Janssen EAM, Kiraz U, Kong J, Aneja R., Predicting neoadjuvant treatment response in triple-negative breast cancer using machine learning, Accepted Diagnostics, December 2023
Kaur J, Chandrashekar DS, Varga Z, Sobottka B, Janssen E, Gandhi K, Kowalski J, Kiraz U, Varambally S, Aneja R., Whole-Exome Sequencing Reveals High Mutational Concordance between Primary and Matched Recurrent Triple-Negative Breast Cancers, Genes (Basel). 2023 Aug 25;14(9):1690.
N Kanwal, EAM Janssen, K Engan, Balancing privacy and progress in artificial intelligence: Anonymization in histopathology for biomedical research and education.- arXiv preprint arXiv:2307.09426, 2023
Thagaard J, Broeckx G, Page DB, et al., Pitfalls in machine learning-based assessment of tumor-infiltrating lymphocytes in breast cancer: a report of The International Immuno-Oncology Biomarker Working Group, J Pathol 2023; DOI:10.1002/path.6155.
Page D, Broeckx G, Jahangir C et al., Spatial analyses of immune cell infiltration in cancer: current methods and future directions: a report of The International Immuno-Oncology Biomarker Working Group, J Pathol 2023; DOI:10.1002/path.6165.
Emma Rewcastle, Einar Gudlaugsson, Melinda Lillesand, Ivar Skaland, Jan P.A. Baak, Emiel A.M. Janssen, Automated prognostic assessment of endometrial hyperplasia for progression risk evaluation using artificial intelligence, Modern Pathology, Volume 36, Issue 5, May 2023, 100116.
Andreassen, Christopher; Fuster Navarro, Saul; Hardardottir, Helga; Janssen, Emiel; Engan, Kjersti (2023), Deep Learning for Predicting Metastasis on Melanoma Wsis, IEEE International Symposium on Biomedical Imaging. ISSN 1945-7928.
Mosquera-Zamudio A, Launet L, Tabatabaei Z, Parra-Medina R, Colomer A, Oliver Moll J, Monteagudo C, Janssen E, Naranjo V., Deep Learning for Skin Melanocytic Tumors in Whole-Slide Images: A Systematic Review, Cancers. 2023; 15(1):42.
Conference proceedings
A Dual Convolutional Neural Network Pipeline for Melanoma Diagnostics and Prognostics.
Northern Lights Deep Learning Conference, 20-26,2024,PMLR.
Intelligent Tracing and Process Improvement of Pathology Workflows using Character Recognition
Detection and Localization of Melanoma Skin Cancer in Histopathological Whole Slide Images
31th European Signal Processing Conference EUSIPCO 2023, Helsinki, Finland
Link
Process Data Science for Workflow Optimization in Digital Pathology: A status report
The International Health Data Workshop HEDA 2022
Theses
Jennifer Janani Antonythasan (2024)
Image Registration for Automated Alignment and Ordering of Non-neoplastic Kidney Biopsy Sections
Master's thesis, University of Bergen
Supervisor: Hrafn Weishaupt; Co-supervisor: Sabine Leh
Emma Rewcastle (2024)
From Research to Clinical Diagnostics: Developing and Validating Biomarkers and Artificial Intelligence for Pathology
PhD thesis, University of Stavanger
Supervisor: Emiel Janssen; Co-supervisors: Einar Gudlaugsson, Ivar Skaland, Sabine Leh
Jon Tveit (2023)
Machine learning, unsupervised learning and stain normalization in digital nephropathology
Master's thesis, University of Stavanger
Supervisors: Hrafn Weishaupt, Sabine Leh, Kjersti Engan
Markus Hatlem (2023)
Digitizing pathology lab workflows using image processing and OCR
Master's thesis, University of Bergen
Supervisors: Fazle Rabbi; Co-supervisors: Patrick Stünkel, Friedemann Leh
Marie Bø-Sande, Edvin Benjaminsen (2023)
Diagnosis, Localization, and Prognosis of Melanoma in WSIs with a Complete Pipeline by Digital Pathology
Master's thesis, University of Stavanger
Supervisor: Kjersti Engan
Janne Kristin Hauglid (2022)
A web-based dashboard to facilitate progress management of pathology workflows
Master's thesis, University of Bergen
Supervisors: Yngve Lamo, Svein-Ivar Lillehaug
Roger Amundsen (2022)
Melanoma Diagnosis and Localization from Whole Slide Images using Convolutional Neural Networks
Master's thesis, University of Stavanger
Supervisor: Kjersti Engan; Co-supervisors: Emiel Janssen, Helga Hardardottir, Neel Kanwal
Christopher Andreassen (2022)
Melanoma prognosis prediction usin image processing and machine learning
Master's thesis, University of Stavanger
Supervisor: Kjersti Engan; Co-supervisors: Emiel Janssen, Helga Hardardottir, Saul Fuster Navarro
Hovedoppgaver (Cand.med.-degree programme)
Radwan Ashur Bashir Etwebi og LB (2024)
Calculation of Proliferation Index Ki-67 in Gastroenteropancreatic Neuroendocrine Tumours with Open- Source Software Qupath
University of Bergen
Supervisor: Hrafn Weishaupt; Co-supervisor: Sabine Leh
Lars-Eirik Høgsaas (2023)
Finding the right fit: A comparison of arteriosclerosis scoring systems in non-neoplastic kidney biopsies
University of Bergen
Supervisors: Hrafn Weishaupt, Sabine Leh
Finding the right fit - a comparison of arteriosclerosis scoring systems in non-neoplastic kidney biopsies.pdf
Bjarte Herikstad Tveit (2022)
Detection of malignant melanoma cells in sentinel lymph nodes by automatic image analysis
University of Bergen
Supervisor: Sabine Leh; Co-supervisor: Hrafn Weishaupt
Abstracts
Prognostic evaluation of endometrial hyperplasia using an AI-based image analysis tool on whole slide images
18th European Congress on Digital Pathology, Berlin.
Kidney Biopsy Codes: a multi-hierarchical terminology for non-neoplastic kidney biopsies
18th European Congress on Digital Pathology, Berlin.
Evaluation of automatic tumor cell detection in Ki-67 stained neuroendocrine tumors of the gastrointestinal tract.
16th European Congress on Digital Pathology, Porto.
