@article{AubrevilleStathonikosBertrametal.2022, author = {Aubreville, Marc and Stathonikos, Nikolas and Bertram, Christof and Klopfleisch, Robert and Hoeve, Natalie ter and Ciompi, Francesco and Wilm, Frauke and Marzahl, Christian and Donovan, Taryn and Maier, Andreas and Breen, Jack and Ravikumar, Nishant and Chung, Youjin and Park, Jinah and Nateghi, Ramin and Pourakpour, Fattaneh and Fick, Rutger H. J. and Ben Hadj, Saima and Jahanifar, Mostafa and Shepard, Adam and Dexl, Jakob and Wittenberg, Thomas and Kondo, Satoshi and Lafarge, Maxime W. and Kolezer, Viktor H. and Liang, Jingtang and Wang, Yubo and Long, Xi and Liu, Jingxin and Razavi, Salar and Khademi, April and Yang, Sen and Wang, Xiyue and Erber, Ramona and Klang, Andrea and Lipnik, Karoline and Bolfa, Pompei and Dark, Michael and Wasinger, Gabriel and Veta, Mitko and Breininger, Katharina}, title = {Mitosis domain generalization in histopathology images — The MIDOG challenge}, volume = {2023}, pages = {102699}, journal = {Medical Image Analysis}, number = {84}, publisher = {Elsevier}, address = {Amsterdam}, issn = {1361-8415}, doi = {https://doi.org/10.1016/j.media.2022.102699}, year = {2022}, language = {en} } @inproceedings{TheelkeWilmMarzahletal.2021, author = {Theelke, Luisa and Wilm, Frauke and Marzahl, Christian and Bertram, Christof and Klopfleisch, Robert and Maier, Andreas and Aubreville, Marc and Breininger, Katharina}, title = {Iterative Cross-Scanner Registration for Whole Slide Images}, booktitle = {2021 IEEE/CVF International Conference on Computer Vision Workshops (ICCVW)}, publisher = {IEEE}, address = {Piscataway}, isbn = {978-1-6654-0191-3}, issn = {2473-9944}, doi = {https://doi.org/10.1109/ICCVW54120.2021.00071}, pages = {582 -- 590}, year = {2021}, language = {en} } @inproceedings{AubrevilleBertramStathonikosetal.2021, author = {Aubreville, Marc and Bertram, Christof and Stathonikos, Nikolas and ter Hoeve, Natalie and Ciompi, Francesco and Klopfleisch, Robert and Veta, Mitko and Donovan, Taryn and Marzahl, Christian and Wilm, Frauke and Breininger, Katharina and Maier, Andreas}, title = {Quantifying the Scanner-Induced Domain Gap in Mitosis Detection}, booktitle = {MIDL: Medical Imaging with Deep Learning 2021}, publisher = {MIDL Foundation}, address = {Nijmegen}, url = {https://2021.midl.io/papers/i6}, year = {2021}, language = {en} } @article{BertramMarzahlBarteletal.2022, author = {Bertram, Christof and Marzahl, Christian and Bartel, Alexander and Stayt, Jason and Bonsembiante, Federico and Beeler-Marfisi, Janet and Barton, Ann K. and Brocca, Ginevra and Gelain, Maria Elena and Gl{\"a}sel, Agnes C. and du Preez, Kelly and Weiler, Kristina and Weissenbacher-Lang, Christiane and Breininger, Katharina and Aubreville, Marc and Maier, Andreas and Klopfleisch, Robert and Hill, Jenny}, title = {Cytologic scoring of equine exercise-induced pulmonary hemorrhage: Performance of human experts and a deep learning-based algorithm}, volume = {60}, journal = {Veterinary Pathology}, number = {1}, publisher = {Sage}, address = {London}, issn = {1544-2217}, doi = {https://doi.org/10.1177/03009858221137582}, pages = {75 -- 85}, year = {2022}, abstract = {Exercise-induced pulmonary hemorrhage (EIPH) is a relevant respiratory disease in sport horses, which can be diagnosed by examination of bronchoalveolar lavage fluid (BALF) cells using the total hemosiderin score (THS). The aim of this study was to evaluate the diagnostic accuracy and reproducibility of annotators and to validate a deep learning-based algorithm for the THS. Digitized cytological specimens stained for iron were prepared from 52 equine BALF samples. Ten annotators produced a THS for each slide according to published methods. The reference methods for comparing annotator's and algorithmic performance included a ground truth dataset, the mean annotators' THSs, and chemical iron measurements. Results of the study showed that annotators had marked interobserver variability of the THS, which was mostly due to a systematic error between annotators in grading the intracytoplasmatic hemosiderin content of individual macrophages. Regarding overall measurement error between the annotators, 87.7\% of the variance could be reduced by using standardized grades based on the ground truth. The algorithm was highly consistent with the ground truth in assigning hemosiderin grades. Compared with the ground truth THS, annotators had an accuracy of diagnosing EIPH (THS of < or ≥ 75) of 75.7\%, whereas, the algorithm had an accuracy of 92.3\% with no relevant differences in correlation with chemical iron measurements. The results show that deep learning-based algorithms are useful for improving reproducibility and routine applicability of the THS. For THS by experts, a diagnostic uncertainty interval of 40 to 110 is proposed. THSs within this interval have insufficient reproducibility regarding the EIPH diagnosis.}, language = {en} } @article{MarzahlAubrevilleBertrametal.2021, author = {Marzahl, Christian and Aubreville, Marc and Bertram, Christof and Maier, Jennifer and Bergler, Christian and Kr{\"o}ger, Christine and Voigt, J{\"o}rn and Breininger, Katharina and Klopfleisch, Robert and Maier, Andreas}, title = {EXACT: a collaboration toolset for algorithm-aided annotation of images with annotation version control}, volume = {11}, pages = {4343}, journal = {Scientific Reports}, publisher = {Springer Nature}, address = {London}, issn = {2045-2322}, doi = {https://doi.org/10.1038/s41598-021-83827-4}, year = {2021}, abstract = {In many research areas, scientific progress is accelerated by multidisciplinary access to image data and their interdisciplinary annotation. However, keeping track of these annotations to ensure a high-quality multi-purpose data set is a challenging and labour intensive task. We developed the open-source online platform EXACT (EXpert Algorithm Collaboration Tool) that enables the collaborative interdisciplinary analysis of images from different domains online and offline. EXACT supports multi-gigapixel medical whole slide images as well as image series with thousands of images. The software utilises a flexible plugin system that can be adapted to diverse applications such as counting mitotic figures with a screening mode, finding false annotations on a novel validation view, or using the latest deep learning image analysis technologies. This is combined with a version control system which makes it possible to keep track of changes in the data sets and, for example, to link the results of deep learning experiments to specific data set versions. EXACT is freely available and has already been successfully applied to a broad range of annotation tasks, including highly diverse applications like deep learning supported cytology scoring, interdisciplinary multi-centre whole slide image tumour annotation, and highly specialised whale sound spectroscopy clustering.}, language = {en} } @article{MeutenMooreDonovanetal.2021, author = {Meuten, Donald J. and Moore, Frances M. and Donovan, Taryn and Bertram, Christof and Klopfleisch, Robert and Foster, Robert A. and Smedley, Rebecca C. and Dark, Michael and Milovancev, Milan and Stromberg, Paul and Williams, Bruce H. and Aubreville, Marc and Avallone, Giancarlo and Bolfa, Pompei and Cullen, John and Dennis, Michelle M. and Goldschmidt, Michael and Luong, Richard and Miller, Andrew D. and Miller, Margaret A. and Munday, John S. and Roccabianca, Paola and Salas, Elisa N. and Schulman, F. Yvonne and Laufer-Amorim, Renee and Asakawa, Midori G. and Craig, Linden and Dervisis, Nick and Esplin, D. Glen and George, Jeanne W. and Hauck, Marlene and Kagawa, Yumiko and Kiupel, Matti and Linder, Keith and Meichner, Kristina and Marconato, Laura and Oblak, Michelle L. and Santos, Renato L. and Simpson, R. Mark and Tvedten, Harold and Whitley, Derick}, title = {International Guidelines for Veterinary Tumor Pathology: A Call to Action}, volume = {58}, journal = {Veterinary Pathology}, number = {5}, publisher = {Sage}, address = {London}, issn = {1544-2217}, doi = {https://doi.org/10.1177/03009858211013712}, pages = {766 -- 794}, year = {2021}, language = {en} } @inproceedings{WilmBertramMarzahletal.2021, author = {Wilm, Frauke and Bertram, Christof and Marzahl, Christian and Bartel, Alexander and Donovan, Taryn and Assenmacher, Charles-Antoine and Becker, Kathrin and Bennett, Mark and Corner, Sarah M. and Cossic, Brieuc and Denk, Daniela and Dettwiler, Martina and Garcia Gonzalez, Beatriz and Gurtner, Corinne and Heier, Annabelle and Lehmbecker, Annika and Merz, Sophie and Plog, Stephanie and Schmidt, Anja and Sebastian, Franziska and Smedley, Rebecca C. and Tecilla, Marco and Thaiwong, Tuddow and Breininger, Katharina and Kiupel, Matti and Maier, Andreas and Klopfleisch, Robert and Aubreville, Marc}, title = {Influence of inter-annotator variability on automatic mitotic figure assessment}, booktitle = {Bildverarbeitung f{\"u}r die Medizin 2021}, publisher = {Springer}, address = {Wiesbaden}, isbn = {978-3-658-33198-6}, doi = {https://doi.org/10.1007/978-3-658-33198-6_56}, pages = {241 -- 246}, year = {2021}, language = {en} } @inproceedings{BertramDonovanTecillaetal.2021, author = {Bertram, Christof and Donovan, Taryn and Tecilla, Marco and Bartenschlager, Florian and Fragoso-Garcia, Marco and Wilm, Frauke and Marzahl, Christian and Breininger, Katharina and Maier, Andreas and Klopfleisch, Robert and Aubreville, Marc}, title = {Dataset on bi- and multi-nucleated tumor cells in canine cutaneous mast cell tumors}, booktitle = {Bildverarbeitung f{\"u}r die Medizin 2021: Proceedings, German Workshop on Medical Image Computing, Regensburg, March 7-9, 2021}, publisher = {Springer Vieweg}, address = {Wiesbaden}, isbn = {978-3-658-33197-9}, issn = {1431-472X}, doi = {https://doi.org/10.1007/978-3-658-33198-6_33}, pages = {134 -- 139}, year = {2021}, language = {en} } @inproceedings{MarzahlBertramWilmetal.2021, author = {Marzahl, Christian and Bertram, Christof and Wilm, Frauke and Voigt, J{\"o}rn and Barton, Ann K. and Klopfleisch, Robert and Breininger, Katharina and Maier, Andreas and Aubreville, Marc}, title = {Cell detection for asthma on partially annotated whole slide images}, booktitle = {Bildverarbeitung f{\"u}r die Medizin 2021: Proceedings, German Workshop on Medical Image Computing, Regensburg, March 7-9, 2021}, subtitle = {learning to be EXACT}, publisher = {Springer Vieweg}, address = {Wiesbaden}, isbn = {978-3-658-33197-9}, issn = {1431-472X}, doi = {https://doi.org/10.1007/978-3-658-33198-6_36}, pages = {147 -- 152}, year = {2021}, language = {en} } @article{AmmelingGanzRosbachetal.2026, author = {Ammeling, Jonas and Ganz, Jonathan and Rosbach, Emely and Lausser, Ludwig and Bertram, Christof and Breininger, Katharina and Aubreville, Marc}, title = {Benchmarking Foundation Models for Mitotic Figure Classification}, volume = {3}, pages = {2026:003}, journal = {Machine Learning for Biomedical Imaging}, number = {MELBA-BVM 2025 Special Issue}, publisher = {Melba editors}, address = {[s. l.]}, issn = {2766-905X}, doi = {https://doi.org/10.59275/j.melba.2026-a3eb}, pages = {38 -- 55}, year = {2026}, abstract = {The performance of deep learning models is known to scale with data quantity and diversity. In pathology, as in many other medical imaging domains, the availability of labeled images for a specific task is often limited. Self-supervised learning techniques have enabled the use of vast amounts of unlabeled data to train large-scale neural networks, i.e., foundation models, that can address the limited data problem by providing semantically rich feature vectors that can generalize well to new tasks with minimal training effort increasing model performance and robustness. In this work, we investigate the use of foundation models for mitotic figure classification. The mitotic count, which can be derived from this classification task, is an independent prognostic marker for specific tumors and part of certain tumor grading systems. In particular, we investigate the data scaling laws on multiple current foundation models and evaluate their robustness to unseen tumor domains. Next to the commonly used linear probing paradigm, we also adapt the models using low-rank adaptation (LoRA) of their attention mechanisms. We compare all models against end-to-end-trained baselines, both CNNs and Vision Transformers. Our results demonstrate that LoRA-adapted foundation models provide superior performance to those adapted with standard linear probing, reaching performance levels close to 100 \% data availability with only 10 \% of training data. Furthermore, LoRA-adaptation of the most recent foundation models almost closes the out-of-domain performance gap when evaluated on unseen tumor domains. However, full fine-tuning of traditional architectures still yields competitive performance.}, language = {en} } @inproceedings{GanzAmmelingRosbachetal.2025, author = {Ganz, Jonathan and Ammeling, Jonas and Rosbach, Emely and Lausser, Ludwig and Bertram, Christof and Breininger, Katharina and Aubreville, Marc}, title = {Is Self-supervision Enough?}, booktitle = {Bildverarbeitung f{\"u}r die Medizin 2025: Proceedings, German Conference on Medical Image Computing, Regensburg March 09-11, 2025}, subtitle = {Benchmarking Foundation Models Against End-to-end Training for Mitotic Figure Classification}, editor = {Palm, Christoph and Breininger, Katharina and Deserno, Thomas Martin and Handels, Heinz and Maier, Andreas and Maier-Hein, Klaus H. and Tolxdorff, Thomas}, publisher = {Springer Vieweg}, address = {Wiesbaden}, isbn = {978-3-658-47422-5}, doi = {https://doi.org/10.1007/978-3-658-47422-5_15}, pages = {63 -- 68}, year = {2025}, language = {en} }