@article{BertramAubrevilleMarzahletal.2019, author = {Bertram, Christof and Aubreville, Marc and Marzahl, Christian and Maier, Andreas and Klopfleisch, Robert}, title = {A large-scale dataset for mitotic figure assessment on whole slide images of canine cutaneous mast cell tumor}, volume = {6}, pages = {274}, journal = {Scientific data}, publisher = {Springer}, address = {London}, issn = {2052-4463}, doi = {https://doi.org/10.1038/s41597-019-0290-4}, year = {2019}, abstract = {We introduce a novel, large-scale dataset for microscopy cell annotations. The dataset includes 32 whole slide images (WSI) of canine cutaneous mast cell tumors, selected to include both low grade cases as well as high grade cases. The slides have been completely annotated for mitotic figures and we provide secondary annotations for neoplastic mast cells, inflammatory granulocytes, and mitotic figure look-alikes. Additionally to a blinded two-expert manual annotation with consensus, we provide an algorithm-aided dataset, where potentially missed mitotic figures were detected by a deep neural network and subsequently assessed by two human experts. We included 262,481 annotations in total, out of which 44,880 represent mitotic figures. For algorithmic validation, we used a customized RetinaNet approach, followed by a cell classification network. We find F1-Scores of 0.786 and 0.820 for the manually labelled and the algorithm-aided dataset, respectively. The dataset provides, for the first time, WSIs completely annotated for mitotic figures and thus enables assessment of mitosis detection algorithms on complete WSIs as well as region of interest detection algorithms.}, language = {en} } @inproceedings{BertramWeissDonovanetal.2025, author = {Bertram, Christof and Weiss, Viktoria and Donovan, Taryn and Banerjee, Sweta and Conrad, Thomas and Ammeling, Jonas and Klopfleisch, Robert and Kaltenecker, Christopher and Aubreville, Marc}, title = {Histologic Dataset of Normal and Atypical Mitotic Figures on Human Breast Cancer (AMi-Br)}, booktitle = {Bildverarbeitung f{\"u}r die Medizin 2025: Proceedings, German Conference on Medical Image Computing, Regensburg March 09-11, 2025}, 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_25}, pages = {113 -- 118}, year = {2025}, language = {en} } @unpublished{AubrevilleGanzAmmelingetal.2024, author = {Aubreville, Marc and Ganz, Jonathan and Ammeling, Jonas and Kaltenecker, Christopher and Bertram, Christof}, title = {Model-based Cleaning of the QUILT-1M Pathology Dataset for Text-Conditional Image Synthesis}, publisher = {arXiv}, address = {Ithaca}, doi = {https://doi.org/10.48550/arXiv.2404.07676}, year = {2024}, abstract = {The QUILT-1M dataset is the first openly available dataset containing images harvested from various online sources. While it provides a huge data variety, the image quality and composition is highly heterogeneous, impacting its utility for text-conditional image synthesis. We propose an automatic pipeline that provides predictions of the most common impurities within the images, e.g., visibility of narrators, desktop environment and pathology software, or text within the image. Additionally, we propose to use semantic alignment filtering of the image-text pairs. Our findings demonstrate that by rigorously filtering the dataset, there is a substantial enhancement of image fidelity in text-to-image tasks.}, language = {en} } @inproceedings{BanerjeeGoschHesteretal.2026, author = {Banerjee, Sweta and Gosch, Timo and Hester, Sara and Weiss, Viktoria and Conrad, Thomas and Donovan, Taryn and Porsche, Nils and Ammeling, Jonas and Stroblberger, Christoph and Klopfleisch, Robert and Kaltenecker, Christopher and Bertram, Christof and Breininger, Katharina and Aubreville, Marc}, title = {Enabling Fast and Mobile Histopathology Image Annotation through Swipeable Interfaces SWAN}, booktitle = {Bildverarbeitung f{\"u}r die Medizin 2026: Proceedings, German Conference on Medical Image Computing, L{\"u}beck, March 15-17, 2026}, editor = {Handels, Heinz and Breininger, Katharina and Deserno, Thomas Martin and Maier, Andreas and Maier-Hein, Klaus H. and Palm, Christoph and Tolxdorff, Thomas}, publisher = {Springer Vieweg}, address = {Wiesbaden}, isbn = {978-3-658-51100-5}, doi = {https://doi.org/10.1007/978-3-658-51100-5_42}, pages = {203 -- 209}, year = {2026}, language = {en} } @inproceedings{BanerjeeBertramAmmelingetal.2025, author = {Banerjee, Sweta and Bertram, Christof and Ammeling, Jonas and Weiss, Viktoria and Conrad, Thomas and Klopfleisch, Robert and Kaltenecker, Christopher and Breininger, Katharina and Aubreville, Marc}, title = {Comprehensive Dataset of Coarse Tumor Annotations for The Cancer Genome Atlas Breast Invasive Carcinoma}, booktitle = {Bildverarbeitung f{\"u}r die Medizin 2025: Proceedings, German Conference on Medical Image Computing, Regensburg March 09-11, 2025}, 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_56}, pages = {260 -- 265}, year = {2025}, language = {en} } @unpublished{MarzahlBertramAubrevilleetal.2020, author = {Marzahl, Christian and Bertram, Christof and Aubreville, Marc and Petrick, Anne and Weiler, Kristina and Gl{\"a}sel, Agnes C. and Fragoso-Garcia, Marco and Merz, Sophie and Bartenschlager, Florian and Hoppe, Judith and Langenhagen, Alina and Jasensky, Anne-Katherine and Voigt, J{\"o}rn and Klopfleisch, Robert and Maier, Andreas}, title = {Are Fast Labeling Methods Reliable? A Case Study of Computer-Aided Expert Annotations on Microscopy Slides}, publisher = {arXiv}, address = {Ithaca}, doi = {https://doi.org/10.48550/arXiv.2004.05838}, year = {2020}, language = {en} } @unpublished{BertramVetaMarzahletal.2020, author = {Bertram, Christof and Veta, Mitko and Marzahl, Christian and Stathonikos, Nikolas and Maier, Andreas and Klopfleisch, Robert and Aubreville, Marc}, title = {Are pathologist-defined labels reproducible? Comparison of the TUPAC16 mitotic figure dataset with an alternative set of labels}, publisher = {arXiv}, address = {Ithaca}, doi = {https://doi.org/10.48550/arXiv.2007.05351}, year = {2020}, language = {en} }