TY - JOUR A1 - Aubreville, Marc A1 - Stathonikos, Nikolas A1 - Bertram, Christof A1 - Klopfleisch, Robert A1 - Hoeve, Natalie ter A1 - Ciompi, Francesco A1 - Wilm, Frauke A1 - Marzahl, Christian A1 - Donovan, Taryn A1 - Maier, Andreas A1 - Breen, Jack A1 - Ravikumar, Nishant A1 - Chung, Youjin A1 - Park, Jinah A1 - Nateghi, Ramin A1 - Pourakpour, Fattaneh A1 - Fick, Rutger H. J. A1 - Ben Hadj, Saima A1 - Jahanifar, Mostafa A1 - Shepard, Adam A1 - Dexl, Jakob A1 - Wittenberg, Thomas A1 - Kondo, Satoshi A1 - Lafarge, Maxime W. A1 - Kolezer, Viktor H. A1 - Liang, Jingtang A1 - Wang, Yubo A1 - Long, Xi A1 - Liu, Jingxin A1 - Razavi, Salar A1 - Khademi, April A1 - Yang, Sen A1 - Wang, Xiyue A1 - Erber, Ramona A1 - Klang, Andrea A1 - Lipnik, Karoline A1 - Bolfa, Pompei A1 - Dark, Michael A1 - Wasinger, Gabriel A1 - Veta, Mitko A1 - Breininger, Katharina T1 - Mitosis domain generalization in histopathology images — The MIDOG challenge JF - Medical Image Analysis UR - https://doi.org/10.1016/j.media.2022.102699 KW - Domain generalization KW - Histopathology KW - Challenge KW - Deep Learning KW - Mitosis Y1 - 2022 UR - https://doi.org/10.1016/j.media.2022.102699 SN - 1361-8423 SN - 1361-8415 VL - 2023 IS - 84 PB - Elsevier CY - Amsterdam ER - TY - CHAP A1 - Theelke, Luisa A1 - Wilm, Frauke A1 - Marzahl, Christian A1 - Bertram, Christof A1 - Klopfleisch, Robert A1 - Maier, Andreas A1 - Aubreville, Marc A1 - Breininger, Katharina T1 - Iterative Cross-Scanner Registration for Whole Slide Images T2 - 2021 IEEE/CVF International Conference on Computer Vision Workshops (ICCVW) UR - https://doi.org/10.1109/ICCVW54120.2021.00071 KW - Pathology KW - Computer vision KW - Image resolution KW - Microscopy KW - Conferences KW - Estimation KW - Registers Y1 - 2021 UR - https://doi.org/10.1109/ICCVW54120.2021.00071 SN - 978-1-6654-0191-3 SN - 2473-9944 N1 - Eine frei zugängliche Version ist veröffentlicht unter: https://openaccess.thecvf.com/content/ICCV2021W/CDPath/html/Theelke_Iterative_Cross-Scanner_Registration_for_Whole_Slide_Images_ICCVW_2021_paper.html SP - 582 EP - 590 PB - IEEE CY - Piscataway ER - TY - CHAP A1 - Aubreville, Marc A1 - Bertram, Christof A1 - Stathonikos, Nikolas A1 - ter Hoeve, Natalie A1 - Ciompi, Francesco A1 - Klopfleisch, Robert A1 - Veta, Mitko A1 - Donovan, Taryn A1 - Marzahl, Christian A1 - Wilm, Frauke A1 - Breininger, Katharina A1 - Maier, Andreas T1 - Quantifying the Scanner-Induced Domain Gap in Mitosis Detection T2 - MIDL: Medical Imaging with Deep Learning 2021 Y1 - 2021 UR - https://2021.midl.io/papers/i6 PB - MIDL Foundation CY - Nijmegen ER - TY - JOUR A1 - Bertram, Christof A1 - Marzahl, Christian A1 - Bartel, Alexander A1 - Stayt, Jason A1 - Bonsembiante, Federico A1 - Beeler-Marfisi, Janet A1 - Barton, Ann K. A1 - Brocca, Ginevra A1 - Gelain, Maria Elena A1 - Gläsel, Agnes C. A1 - du Preez, Kelly A1 - Weiler, Kristina A1 - Weissenbacher-Lang, Christiane A1 - Breininger, Katharina A1 - Aubreville, Marc A1 - Maier, Andreas A1 - Klopfleisch, Robert A1 - Hill, Jenny T1 - Cytologic scoring of equine exercise-induced pulmonary hemorrhage: Performance of human experts and a deep learning-based algorithm JF - Veterinary Pathology N2 - 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. UR - https://doi.org/10.1177/03009858221137582 KW - artificial intelligence KW - automated image analysis KW - bronchoalveolar lavage fluid KW - computational pathology KW - digital pathology KW - equine KW - pulmonary hemorrhage KW - respiratory disease KW - total hemosiderin score Y1 - 2022 UR - https://doi.org/10.1177/03009858221137582 UR - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:573-35196 SN - 1544-2217 VL - 60 IS - 1 SP - 75 EP - 85 PB - Sage CY - London ER - TY - JOUR A1 - Marzahl, Christian A1 - Aubreville, Marc A1 - Bertram, Christof A1 - Maier, Jennifer A1 - Bergler, Christian A1 - Kröger, Christine A1 - Voigt, Jörn A1 - Breininger, Katharina A1 - Klopfleisch, Robert A1 - Maier, Andreas T1 - EXACT: a collaboration toolset for algorithm-aided annotation of images with annotation version control JF - Scientific Reports N2 - 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. UR - https://doi.org/10.1038/s41598-021-83827-4 Y1 - 2021 UR - https://doi.org/10.1038/s41598-021-83827-4 UR - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:573-10943 SN - 2045-2322 VL - 11 PB - Springer Nature CY - London ER - TY - JOUR A1 - Meuten, Donald J. A1 - Moore, Frances M. A1 - Donovan, Taryn A1 - Bertram, Christof A1 - Klopfleisch, Robert A1 - Foster, Robert A. A1 - Smedley, Rebecca C. A1 - Dark, Michael A1 - Milovancev, Milan A1 - Stromberg, Paul A1 - Williams, Bruce H. A1 - Aubreville, Marc A1 - Avallone, Giancarlo A1 - Bolfa, Pompei A1 - Cullen, John A1 - Dennis, Michelle M. A1 - Goldschmidt, Michael A1 - Luong, Richard A1 - Miller, Andrew D. A1 - Miller, Margaret A. A1 - Munday, John S. A1 - Roccabianca, Paola A1 - Salas, Elisa N. A1 - Schulman, F. Yvonne A1 - Laufer-Amorim, Renee A1 - Asakawa, Midori G. A1 - Craig, Linden A1 - Dervisis, Nick A1 - Esplin, D. Glen A1 - George, Jeanne W. A1 - Hauck, Marlene A1 - Kagawa, Yumiko A1 - Kiupel, Matti A1 - Linder, Keith A1 - Meichner, Kristina A1 - Marconato, Laura A1 - Oblak, Michelle L. A1 - Santos, Renato L. A1 - Simpson, R. Mark A1 - Tvedten, Harold A1 - Whitley, Derick T1 - International Guidelines for Veterinary Tumor Pathology: A Call to Action JF - Veterinary Pathology UR - https://doi.org/10.1177/03009858211013712 KW - standardization KW - oncology KW - guidelines KW - protocols KW - validation Y1 - 2021 UR - https://doi.org/10.1177/03009858211013712 SN - 1544-2217 VL - 58 IS - 5 SP - 766 EP - 794 PB - Sage CY - London ER - TY - CHAP A1 - Wilm, Frauke A1 - Bertram, Christof A1 - Marzahl, Christian A1 - Bartel, Alexander A1 - Donovan, Taryn A1 - Assenmacher, Charles-Antoine A1 - Becker, Kathrin A1 - Bennett, Mark A1 - Corner, Sarah M. A1 - Cossic, Brieuc A1 - Denk, Daniela A1 - Dettwiler, Martina A1 - Garcia Gonzalez, Beatriz A1 - Gurtner, Corinne A1 - Heier, Annabelle A1 - Lehmbecker, Annika A1 - Merz, Sophie A1 - Plog, Stephanie A1 - Schmidt, Anja A1 - Sebastian, Franziska A1 - Smedley, Rebecca C. A1 - Tecilla, Marco A1 - Thaiwong, Tuddow A1 - Breininger, Katharina A1 - Kiupel, Matti A1 - Maier, Andreas A1 - Klopfleisch, Robert A1 - Aubreville, Marc T1 - Influence of inter-annotator variability on automatic mitotic figure assessment T2 - Bildverarbeitung für die Medizin 2021 UR - https://doi.org/10.1007/978-3-658-33198-6_56 Y1 - 2021 UR - https://doi.org/10.1007/978-3-658-33198-6_56 SN - 978-3-658-33198-6 SP - 241 EP - 246 PB - Springer CY - Wiesbaden ER - TY - CHAP A1 - Bertram, Christof A1 - Donovan, Taryn A1 - Tecilla, Marco A1 - Bartenschlager, Florian A1 - Fragoso-Garcia, Marco A1 - Wilm, Frauke A1 - Marzahl, Christian A1 - Breininger, Katharina A1 - Maier, Andreas A1 - Klopfleisch, Robert A1 - Aubreville, Marc T1 - Dataset on bi- and multi-nucleated tumor cells in canine cutaneous mast cell tumors T2 - Bildverarbeitung für die Medizin 2021: Proceedings, German Workshop on Medical Image Computing, Regensburg, March 7–9, 2021 UR - https://doi.org/10.1007/978-3-658-33198-6_33 Y1 - 2021 UR - https://doi.org/10.1007/978-3-658-33198-6_33 SN - 978-3-658-33197-9 SN - 978-3-658-33198-6 SN - 1431-472X SP - 134 EP - 139 PB - Springer Vieweg CY - Wiesbaden ER - TY - CHAP A1 - Marzahl, Christian A1 - Bertram, Christof A1 - Wilm, Frauke A1 - Voigt, Jörn A1 - Barton, Ann K. A1 - Klopfleisch, Robert A1 - Breininger, Katharina A1 - Maier, Andreas A1 - Aubreville, Marc T1 - Cell detection for asthma on partially annotated whole slide images BT - learning to be EXACT T2 - Bildverarbeitung für die Medizin 2021: Proceedings, German Workshop on Medical Image Computing, Regensburg, March 7–9, 2021 UR - https://doi.org/10.1007/978-3-658-33198-6_36 Y1 - 2021 UR - https://doi.org/10.1007/978-3-658-33198-6_36 SN - 978-3-658-33197-9 SN - 978-3-658-33198-6 SN - 1431-472X SP - 147 EP - 152 PB - Springer Vieweg CY - Wiesbaden ER - TY - JOUR A1 - Ammeling, Jonas A1 - Ganz, Jonathan A1 - Rosbach, Emely A1 - Lausser, Ludwig A1 - Bertram, Christof A1 - Breininger, Katharina A1 - Aubreville, Marc T1 - Benchmarking Foundation Models for Mitotic Figure Classification JF - Machine Learning for Biomedical Imaging N2 - 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. UR - https://doi.org/10.59275/j.melba.2026-a3eb Y1 - 2026 UR - https://doi.org/10.59275/j.melba.2026-a3eb UR - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:573-66220 SN - 2766-905X VL - 3 IS - MELBA–BVM 2025 Special Issue SP - 38 EP - 55 PB - Melba editors CY - [s. l.] ER - TY - CHAP A1 - Ganz, Jonathan A1 - Ammeling, Jonas A1 - Rosbach, Emely A1 - Lausser, Ludwig A1 - Bertram, Christof A1 - Breininger, Katharina A1 - Aubreville, Marc ED - Palm, Christoph ED - Breininger, Katharina ED - Deserno, Thomas Martin ED - Handels, Heinz ED - Maier, Andreas ED - Maier-Hein, Klaus H. ED - Tolxdorff, Thomas T1 - Is Self-supervision Enough? BT - Benchmarking Foundation Models Against End-to-end Training for Mitotic Figure Classification T2 - Bildverarbeitung für die Medizin 2025: Proceedings, German Conference on Medical Image Computing, Regensburg March 09–11, 2025 UR - https://doi.org/10.1007/978-3-658-47422-5_15 Y1 - 2025 UR - https://doi.org/10.1007/978-3-658-47422-5_15 SN - 978-3-658-47422-5 SP - 63 EP - 68 PB - Springer Vieweg CY - Wiesbaden ER -