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 - CHAP A1 - Marzahl, Christian A1 - Aubreville, Marc A1 - Bertram, Christof A1 - Gerlach, Stefan A1 - Maier, Jennifer A1 - Voigt, Jörn A1 - Hill, Jenny A1 - Klopfleisch, Robert A1 - Maier, Andreas ED - Tolxdorff, Thomas ED - Deserno, Thomas M. ED - Handels, Heinz ED - Maier, Andreas ED - Maier-Hein, Klaus H. ED - Palm, Christoph T1 - Is crowd-algorithm collaboration an advanced alternative to crowd-sourcing on cytology slides? T2 - Bildverarbeitung für die Medizin 2020, Algorithmen – Systeme – Anwendungen. Proceedings des Workshops vom 15. bis 17. März 2020 in Berlin UR - https://doi.org/10.1007/978-3-658-29267-6_5 Y1 - 2020 UR - https://doi.org/10.1007/978-3-658-29267-6_5 SN - 978-3-658-29266-9 SN - 978-3-658-29267-6 N1 - Access to this content is enabled by Nationallizenz Ebooks Medicine SP - 26 EP - 31 PB - Springer Vieweg CY - Wiesbaden ER - TY - JOUR A1 - Aubreville, Marc A1 - Knipfer, Christian A1 - Oetter, Nicolai A1 - Jaremenko, Christian A1 - Rodner, Erik A1 - Denzler, Joachim A1 - Bohr, Christopher A1 - Neumann, Helmut A1 - Stelzle, Florian A1 - Maier, Andreas T1 - Automatic classification of cancerous tissue in laserendomicroscopy images of the oral cavity using deep learning JF - Scientific Reports N2 - Oral Squamous Cell Carcinoma (OSCC) is a common type of cancer of the oral epithelium. Despite their high impact on mortality, sufficient screening methods for early diagnosis of OSCC often lack accuracy and thus OSCCs are mostly diagnosed at a late stage. Early detection and accurate outline estimation of OSCCs would lead to a better curative outcome and a reduction in recurrence rates after surgical treatment. Confocal Laser Endomicroscopy (CLE) records sub-surface micro-anatomical images for in vivo cell structure analysis. Recent CLE studies showed great prospects for a reliable, real-time ultrastructural imaging of OSCC in situ. We present and evaluate a novel automatic approach for OSCC diagnosis using deep learning technologies on CLE images. The method is compared against textural feature-based machine learning approaches that represent the current state of the art. For this work, CLE image sequences (7894 images) from patients diagnosed with OSCC were obtained from 4 specific locations in the oral cavity, including the OSCC lesion. The present approach is found to outperform the state of the art in CLE image recognition with an area under the curve (AUC) of 0.96 and a mean accuracy of 88.3% (sensitivity 86.6%, specificity 90%). UR - https://doi.org/10.1038/s41598-017-12320-8 Y1 - 2017 UR - https://doi.org/10.1038/s41598-017-12320-8 UR - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:573-12464 SN - 2045-2322 VL - 7 PB - Springer Nature CY - London ER - TY - JOUR A1 - Aubreville, Marc A1 - Stoeve, Maike A1 - Oetter, Nicolai A1 - Goncalves, Miguel A1 - Knipfer, Christian A1 - Neumann, Helmut A1 - Bohr, Christopher A1 - Stelzle, Florian A1 - Maier, Andreas T1 - Deep learning-based detection of motion artifacts in probe-based confocal laser endomicroscopy images JF - International journal of computer assisted radiology and surgery UR - https://doi.org/10.1007/s11548-018-1836-1 KW - Deep convolutional neural networks KW - Confocal laser endomicroscopy KW - Motion artifact detection Y1 - 2019 UR - https://doi.org/10.1007/s11548-018-1836-1 SN - 1861-6429 VL - 14 IS - 1 SP - 31 EP - 42 PB - Springer CY - Berlin ER - TY - CHAP A1 - Aubreville, Marc A1 - Goncalves, Miguel A1 - Knipfer, Christian A1 - Oetter, Nicolai A1 - Würfl, Tobias A1 - Neumann, Helmut A1 - Stelzle, Florian A1 - Bohr, Christopher A1 - Maier, Andreas ED - Wiebe, Sheldon ED - Gamboa, Hugo ED - Fred, Ana ED - Bermúdez i Badia, Sergi T1 - Patch-based Carcinoma Detection on Confocal Laser Endomicroscopy Images BT - A Cross-Site Robustness Assessment T2 - Proceedings of the 11th International Joint Conference on Biomedical Engineering Systems and Technologies N2 - Deep learning technologies such as convolutional neural networks (CNN) provide powerful methods for image recognition and have recently been employed in the field of automated carcinoma detection in confocal laser endomicroscopy (CLE) images. CLE is a (sub-)surface microscopic imaging technique that reaches magnifications of up to 1000x and is thus suitable for in vivo structural tissue analysis. In this work, we aim to evaluate the prospects of a priorly developed deep learning-based algorithm targeted at the identification of oral squamous cell carcinoma with regard to its generalization to further anatomic locations of squamous cell carcinomas in the area of head and neck. We applied the algorithm on images acquired from the vocal fold area of five patients with histologically verified squamous cell carcinoma and presumably healthy control images of the clinically normal contra-lateral vocal cord. We find that the network trained on the oral cavity data reaches an accurac y of 89.45% and an area-under-the-curve (AUC) value of 0.955, when applied on the vocal cords data. Compared to the state of the art, we achieve very similar results, yet with an algorithm that was trained on a completely disjunct data set. Concatenating both data sets yielded further improvements in cross-validation with an accuracy of 90.81% and AUC of 0.970. In this study, for the first time to our knowledge, a deep learning mechanism for the identification of oral carcinomas using CLE Images could be applied to other disciplines in the area of head and neck. This study shows the prospect of the algorithmic approach to generalize well on other malignant entities of the head and neck, regardless of the anatomical location and furthermore in an examiner-independent manner. UR - https://doi.org/10.5220/0006534700270034 KW - Automatic Carcinoma Detection KW - Confocal Laser Endomicroscopy KW - Deep Convolutional Networks KW - Squamous Cell Carcinoma Y1 - 2018 UR - https://doi.org/10.5220/0006534700270034 SN - 978-989-758-278-3 SP - 27 EP - 34 PB - SciTePress CY - Setúbal ER - TY - CHAP A1 - Marzahl, Christian A1 - Aubreville, Marc A1 - Voigt, Jörn A1 - Maier, Andreas T1 - Classification of leukemic b-lymphoblast cells from blood smear microscopic images with an attention-based deep learning method and advanced augmentation techniques T2 - ISBI 2019 C-NMC challenge: classification in cancer cell imaging UR - https://doi.org/10.1007/978-981-15-0798-4_2 Y1 - 2019 UR - https://doi.org/10.1007/978-981-15-0798-4_2 SN - 978-981-15-0797-7 SN - 978-981-15-0798-4 SN - 978-981-15-0800-4 SN - 2195-271X SN - 2195-2728 SP - 13 EP - 22 PB - Springer CY - Singapore ER - TY - JOUR A1 - Aubreville, Marc A1 - Bertram, Christof A1 - Donovan, Taryn A. A1 - Marzahl, Christian A1 - Maier, Andreas A1 - Klopfleisch, Robert T1 - A completely annotated whole slide image dataset of canine breast cancer to aid human breast cancer research JF - Scientific data N2 - Canine mammary carcinoma (CMC) has been used as a model to investigate the pathogenesis of human breast cancer and the same grading scheme is commonly used to assess tumor malignancy in both. One key component of this grading scheme is the density of mitotic figures (MF). Current publicly available datasets on human breast cancer only provide annotations for small subsets of whole slide images (WSIs). We present a novel dataset of 21 WSIs of CMC completely annotated for MF. For this, a pathologist screened all WSIs for potential MF and structures with a similar appearance. A second expert blindly assigned labels, and for non-matching labels, a third expert assigned the final labels. Additionally, we used machine learning to identify previously undetected MF. Finally, we performed representation learning and two-dimensional projection to further increase the consistency of the annotations. Our dataset consists of 13,907 MF and 36,379 hard negatives. We achieved a mean F1-score of 0.791 on the test set and of up to 0.696 on a human breast cancer dataset. UR - https://doi.org/10.1038/s41597-020-00756-z Y1 - 2020 UR - https://doi.org/10.1038/s41597-020-00756-z UR - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:573-11765 SN - 2052-4463 VL - 7 PB - Springer Nature CY - London ER - TY - JOUR A1 - Bertram, Christof A1 - Aubreville, Marc A1 - Marzahl, Christian A1 - Maier, Andreas A1 - Klopfleisch, Robert T1 - A large-scale dataset for mitotic figure assessment on whole slide images of canine cutaneous mast cell tumor JF - Scientific data N2 - 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. UR - https://doi.org/10.1038/s41597-019-0290-4 Y1 - 2019 UR - https://doi.org/10.1038/s41597-019-0290-4 UR - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:573-11838 SN - 2052-4463 VL - 6 PB - Nature CY - London ER - TY - JOUR A1 - Marzahl, Christian A1 - Aubreville, Marc A1 - Bertram, Christof A1 - Stayt, Jason A1 - Jasensky, Anne-Katherine A1 - Bartenschlager, Florian A1 - Fragoso-Garcia, Marco A1 - Barton, Ann K. A1 - Elsemann, Svenja A1 - Jabari, Samir A1 - Krauth, Jens A1 - Madhu, Prathmesh A1 - Voigt, Jörn A1 - Hill, Jenny A1 - Klopfleisch, Robert A1 - Maier, Andreas T1 - Deep Learning-based quantification of pulmonary hemosiderophages in cytology slides JF - Scientific reports N2 - Exercise-induced pulmonary hemorrhage (EIPH) is a common condition in sport horses with negative impact on performance. Cytology of bronchoalveolar lavage fluid by use of a scoring system is considered the most sensitive diagnostic method. Macrophages are classified depending on the degree of cytoplasmic hemosiderin content. The current gold standard is manual grading, which is however monotonous and time-consuming. We evaluated state-of-the-art deep learning-based methods for single cell macrophage classification and compared them against the performance of nine cytology experts and evaluated inter- and intra-observer variability. Additionally, we evaluated object detection methods on a novel data set of 17 completely annotated cytology whole slide images (WSI) containing 78,047 hemosiderophages. Our deep learning-based approach reached a concordance of 0.85, partially exceeding human expert concordance (0.68 to 0.86, mean of 0.73, SD of 0.04). Intra-observer variability was high (0.68 to 0.88) and inter-observer concordance was moderate (Fleiss’ kappa = 0.67). Our object detection approach has a mean average precision of 0.66 over the five classes from the whole slide gigapixel image and a computation time of below two minutes. To mitigate the high inter- and intra-rater variability, we propose our automated object detection pipeline, enabling accurate, reproducible and quick EIPH scoring in WSI. UR - https://doi.org/10.1038/s41598-020-65958-2 Y1 - 2020 UR - https://doi.org/10.1038/s41598-020-65958-2 UR - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:573-11783 SN - 2045-2322 VL - 10 PB - Springer Nature CY - London ER - TY - JOUR A1 - Wilm, Frauke A1 - Ihling, Christian A1 - Méhes, Gábor A1 - Terracciano, Luigi A1 - Puget, Chloé A1 - Klopfleisch, Robert A1 - Schüffler, Peter A1 - Aubreville, Marc A1 - Maier, Andreas A1 - Mrowiec, Thomas A1 - Breininger, Katharina T1 - Pan-tumor T-lymphocyte detection using deep neural networks: Recommendations for transfer learning in immunohistochemistry JF - Journal of Pathology Informatics N2 - The success of immuno-oncology treatments promises long-term cancer remission for an increasing number of patients. The response to checkpoint inhibitor drugs has shown a correlation with the presence of immune cells in the tumor and tumor microenvironment. An in-depth understanding of the spatial localization of immune cells is therefore critical for understanding the tumor’s immune landscape and predicting drug response. Computer-aided systems are well suited for efficiently quantifying immune cells in their spatial context. Conventional image analysis approaches are often based on color features and therefore require a high level of manual interaction. More robust image analysis methods based on deep learning are expected to decrease this reliance on human interaction and improve the reproducibility of immune cell scoring. However, these methods require sufficient training data and previous work has reported low robustness of these algorithms when they are tested on out-of-distribution data from different pathology labs or samples from different organs. In this work, we used a new image analysis pipeline to explicitly evaluate the robustness of marker-labeled lymphocyte quantification algorithms depending on the number of training samples before and after being transferred to a new tumor indication. For these experiments, we adapted the RetinaNet architecture for the task of T-lymphocyte detection and employed transfer learning to bridge the domain gap between tumor indications and reduce the annotation costs for unseen domains. On our test set, we achieved human-level performance for almost all tumor indications with an average precision of 0.74 in-domain and 0.72–0.74 cross-domain. From our results, we derive recommendations for model development regarding annotation extent, training sample selection, and label extraction for the development of robust algorithms for immune cell scoring. By extending the task of marker-labeled lymphocyte quantification to a multi-class detection task, the pre-requisite for subsequent analyses, e.g., distinguishing lymphocytes in the tumor stroma from tumor-infiltrating lymphocytes, is met. UR - https://doi.org/10.1016/j.jpi.2023.100301 KW - Tumor-infiltrating lymphocytes KW - Immuno-oncology KW - Immunohistochemistry KW - Deep learning KW - Transfer learning KW - Domain adaptation Y1 - 2023 UR - https://doi.org/10.1016/j.jpi.2023.100301 UR - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:573-40458 SN - 2153-3539 VL - 2023 IS - 14 PB - Elsevier CY - Amsterdam ER - TY - CHAP A1 - Marzahl, Christian A1 - Wilm, Frauke A1 - Tharun, Lars A1 - Perner, Sven A1 - Kröger, Christine A1 - Voigt, Jörn A1 - Klopfleisch, Robert A1 - Maier, Andreas A1 - Aubreville, Marc A1 - Breininger, Katharina T1 - Robust quad-tree based registration on whole slide images T2 - Proceedings of Machine Learning Research: Proceedings of COMPAY 2021 KW - Registration KW - Microscopy KW - Pathology Y1 - 2021 UR - https://proceedings.mlr.press/v156/marzahl21a.html IS - 156 SP - 181 EP - 190 PB - PMLR CY - [s. l.] ER - TY - JOUR A1 - Aubreville, Marc A1 - Bertram, Christof A1 - Marzahl, Christian A1 - Gurtner, Corinne A1 - Dettwiler, Martina A1 - Schmidt, Anja A1 - Bartenschlager, Florian A1 - Merz, Sophie A1 - Fragoso-Garcia, Marco A1 - Kershaw, Olivia A1 - Klopfleisch, Robert A1 - Maier, Andreas T1 - Deep learning algorithms out-perform veterinary pathologists in detecting the mitotically most active tumor region JF - Scientific reports N2 - Manual count of mitotic figures, which is determined in the tumor region with the highest mitotic activity, is a key parameter of most tumor grading schemes. It can be, however, strongly dependent on the area selection due to uneven mitotic figure distribution in the tumor section. We aimed to assess the question, how significantly the area selection could impact the mitotic count, which has a known high inter-rater disagreement. On a data set of 32 whole slide images of H&E-stained canine cutaneous mast cell tumor, fully annotated for mitotic figures, we asked eight veterinary pathologists (five board-certified, three in training) to select a field of interest for the mitotic count. To assess the potential difference on the mitotic count, we compared the mitotic count of the selected regions to the overall distribution on the slide. Additionally, we evaluated three deep learning-based methods for the assessment of highest mitotic density: In one approach, the model would directly try to predict the mitotic count for the presented image patches as a regression task. The second method aims at deriving a segmentation mask for mitotic figures, which is then used to obtain a mitotic density. Finally, we evaluated a two-stage object-detection pipeline based on state-of-the-art architectures to identify individual mitotic figures. We found that the predictions by all models were, on average, better than those of the experts. The two-stage object detector performed best and outperformed most of the human pathologists on the majority of tumor cases. The correlation between the predicted and the ground truth mitotic count was also best for this approach (0.963–0.979). Further, we found considerable differences in position selection between pathologists, which could partially explain the high variance that has been reported for the manual mitotic count. To achieve better inter-rater agreement, we propose to use a computer-based area selection for support of the pathologist in the manual mitotic count. UR - https://doi.org/10.1038/s41598-020-73246-2 Y1 - 2020 UR - https://doi.org/10.1038/s41598-020-73246-2 UR - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:573-11794 SN - 2045-2322 VL - 10 PB - Springer Nature CY - London ER - TY - CHAP A1 - Marzahl, Christian A1 - Bertram, Christof A1 - Aubreville, Marc A1 - Petrick, Anne A1 - Weiler, Kristina A1 - Gläsel, Agnes C. A1 - Fragoso-Garcia, Marco A1 - Merz, Sophie A1 - Bartenschlager, Florian A1 - Hoppe, Judith A1 - Langenhagen, Alina A1 - Jasensky, Anne-Katherine A1 - Voigt, Jörn A1 - Klopfleisch, Robert A1 - Maier, Andreas T1 - Are Fast Labeling Methods Reliable? A Case Study of Computer-Aided Expert Annotations on Microscopy Slides T2 - Medical Image Computing and Computer Assisted Intervention – MICCAI 2020 UR - https://doi.org/10.1007/978-3-030-59710-8_3 KW - Pathology KW - Microscopy KW - Computer-aided labelling KW - Expert-algorithm collaboration Y1 - 2020 UR - https://doi.org/10.1007/978-3-030-59710-8_3 SN - 978-3-030-59710-8 SN - 1611-3349 N1 - Der Nachweis einer Preprint-Version dieser Veröffentlichung ist ebenfalls in diesem Repositorium verzeichnet, s. https://opus4.kobv.de/opus4-haw/frontdoor/index/index/docId/1257 SP - 24 EP - 32 PB - Springer CY - Cham ER - TY - CHAP A1 - Bertram, Christof A1 - Veta, Mitko A1 - Marzahl, Christian A1 - Stathonikos, Nikolas A1 - Maier, Andreas A1 - Klopfleisch, Robert A1 - Aubreville, Marc T1 - Are Pathologist-Defined Labels Reproducible? Comparison of the TUPAC16 Mitotic Figure Dataset with an Alternative Set of Labels T2 - Interpretable and Annotation-Efficient Learning for Medical Image Computing UR - https://doi.org/10.1007/978-3-030-61166-8_22 KW - Breast cancer KW - Mitotic figures KW - Computer-aided annotation KW - Deep learning Y1 - 2020 UR - https://doi.org/10.1007/978-3-030-61166-8_22 SN - 978-3-030-61166-8 SN - 1611-3349 N1 - Der Nachweis einer Preprint-Version dieser Veröffentlichung ist ebenfalls in diesem Repositorium verzeichnet, s. https://opus4.kobv.de/opus4-haw/frontdoor/index/index/docId/1254 SP - 204 EP - 213 PB - Springer CY - Cham ER - TY - CHAP A1 - Stoeve, Maike A1 - Aubreville, Marc A1 - Oetter, Nicolai A1 - Knipfer, Christian A1 - Neumann, Helmut A1 - Stelzle, Florian A1 - Maier, Andreas ED - Maier, Andreas ED - Deserno, Thomas M. ED - Handels, Heinz ED - Maier-Hein, Klaus H. ED - Palm, Christoph ED - Tolxdorff, Thomas T1 - Motion Artifact Detection in Confocal Laser Endomicroscopy Images T2 - Bildverarbeitung für die Medizin 2018: Algorithmen - Systeme - Anwendungen UR - https://doi.org/10.1007/978-3-662-56537-7_85 Y1 - 2018 UR - https://doi.org/10.1007/978-3-662-56537-7_85 SN - 978-3-662-56537-7 N1 - Der Nachweis einer Preprint-Version dieser Veröffentlichung ist ebenfalls in diesem Repositorium verzeichnet, s. https://opus4.kobv.de/opus4-haw/frontdoor/index/index/docId/1258 SP - 328 EP - 333 PB - Springer Vieweg CY - Berlin ER - TY - INPR A1 - Marzahl, Christian A1 - Bertram, Christof A1 - Aubreville, Marc A1 - Petrick, Anne A1 - Weiler, Kristina A1 - Gläsel, Agnes C. A1 - Fragoso-Garcia, Marco A1 - Merz, Sophie A1 - Bartenschlager, Florian A1 - Hoppe, Judith A1 - Langenhagen, Alina A1 - Jasensky, Anne-Katherine A1 - Voigt, Jörn A1 - Klopfleisch, Robert A1 - Maier, Andreas T1 - Are Fast Labeling Methods Reliable? A Case Study of Computer-Aided Expert Annotations on Microscopy Slides UR - https://doi.org/10.48550/arXiv.2004.05838 Y1 - 2020 UR - https://doi.org/10.48550/arXiv.2004.05838 N1 - Die veröffentlichte Version dieses Preprints ist ebenfalls in diesem Repositorium verzeichnet, s. https://opus4.kobv.de/opus4-haw/frontdoor/index/index/docId/1917 PB - arXiv CY - Ithaca ER - TY - INPR A1 - Bertram, Christof A1 - Veta, Mitko A1 - Marzahl, Christian A1 - Stathonikos, Nikolas A1 - Maier, Andreas A1 - Klopfleisch, Robert A1 - Aubreville, Marc T1 - Are pathologist-defined labels reproducible? Comparison of the TUPAC16 mitotic figure dataset with an alternative set of labels UR - https://doi.org/10.48550/arXiv.2007.05351 Y1 - 2020 UR - https://doi.org/10.48550/arXiv.2007.05351 N1 - Die veröffentlichte Version dieses Preprints ist ebenfalls in diesem Repositorium verzeichnet, s. https://opus4.kobv.de/opus4-haw/frontdoor/index/index/docId/1919 PB - arXiv CY - Ithaca ER - TY - INPR A1 - Stoeve, Maike A1 - Aubreville, Marc A1 - Oetter, Nicolai A1 - Knipfer, Christian A1 - Neumann, Helmut A1 - Stelzle, Florian A1 - Maier, Andreas T1 - Motion Artifact Detection in Confocal Laser Endomicroscopy Images N2 - Confocal Laser Endomicroscopy (CLE), an optical imaging technique allowing non-invasive examination of the mucosa on a (sub)- cellular level, has proven to be a valuable diagnostic tool in gastroenterology and shows promising results in various anatomical regions including the oral cavity. Recently, the feasibility of automatic carcinoma detection for CLE images of sufficient quality was shown. However, in real world data sets a high amount of CLE images is corrupted by artifacts. Amongst the most prevalent artifact types are motion-induced image deteriorations. In the scope of this work, algorithmic approaches for the automatic detection of motion artifact-tainted image regions were developed. Hence, this work provides an important step towards clinical applicability of automatic carcinoma detection. Both, conventional machine learning and novel, deep learning-based approaches were assessed. The deep learning-based approach outperforms the conventional approaches, attaining an AUC of 0.90. UR - https://doi.org/10.48550/arXiv.1711.01117 Y1 - 2018 UR - https://doi.org/10.48550/arXiv.1711.01117 UR - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:573-12588 N1 - Die veröffentlichte Version dieses Preprints ist ebenfalls in diesem Repositorium verzeichnet, s. https://opus4.kobv.de/opus4-haw/frontdoor/index/index/docId/2203 PB - arXiv CY - Ithaca ER - TY - THES A1 - Maier, Christian T1 - Carving von fragmentierten Dateien mithilfe von Neuralen Netzwerken N2 - Carving von Dateien wird zur Dateiwiederherstellung oder in der IT-Forensik genutzt, um verlorene oder verstecke Dateien auf Datenträgern wiederherzustellen oder zu finden. Fragmentierte Dateien stellen dabei jedoch ein großes Problem dar, da herkömmliche Programme diese nicht zuverlässig von Datenträgern mit beliebiger Größe auslesen können. Bei fragmentierten Dateien sind die Daten einer einzelnen Datei nicht an einem Stück auf dem Datenträger gespeichert, sondern in mindestens zwei Teilen. Zusätzlich muss die Reihenfolge der Teile der Daten nicht dieselbe auf dem Datenträger sein. Dadurch stoßen viele Programme auf ein großes Problem. Sie können die zusammengehörende nicht identifizieren und sortieren, damit die Daten nutzbar sind. Die Hilfe von Neuralen Netzwerken könnte die Lösung zum Carven von fragmentierten Dateien sein, da sie bei komplizierten Problemen sich mit niedriger Fehlerquote bewiesen haben. Trotzdem könnte es sein, dass Neurale Netzwerke nicht mit der großen Anzahl an verschiedenen Dateitypen, die in der Praxis vorliegen, funktionieren, da die mögliche Anzahl an Byte-Kombination zu groß sein könnte, um Muster in den Daten zu erkennen. In meiner Bachelorarbeit untersuche ich deshalb, ob es möglich ist Carving von fragmentierten Dateien mithilfe von Neuralen Netzwerken zuverlässig zu nutzen. Zunächst werde ich hierfür die Grundlagen und die Theorie vom klassischen Datei Carving und von künstlichen Neuralen Netzwerken erläutern. Anschließend werden Techniken zum Carven von fragmentierten Dateien beschrieben, um zu zeigen, wo meinem Ermessen nach Neurale Netzwerke beim Carving von fragmentierten Dateien nützlich sein könnten. Abschließend erläutere ich meine verwendete Methodik und stelle die damit verbundenen Ergebnisse dar. Y1 - 2021 UR - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:573-22714 CY - Ingolstadt ER - TY - JOUR A1 - Wilm, Frauke A1 - Fragoso-Garcia, Marco A1 - Marzahl, Christian A1 - Qiu, Jingna A1 - Puget, Chloé A1 - Diehl, Laura A1 - Bertram, Christof A1 - Klopfleisch, Robert A1 - Maier, Andreas A1 - Breininger, Katharina A1 - Aubreville, Marc T1 - Pan-tumor CAnine cuTaneous Cancer Histology (CATCH) dataset JF - Scientific Data N2 - Due to morphological similarities, the differentiation of histologic sections of cutaneous tumors into individual subtypes can be challenging. Recently, deep learning-based approaches have proven their potential for supporting pathologists in this regard. However, many of these supervised algorithms require a large amount of annotated data for robust development. We present a publicly available dataset of 350 whole slide images of seven different canine cutaneous tumors complemented by 12,424 polygon annotations for 13 histologic classes, including seven cutaneous tumor subtypes. In inter-rater experiments, we show a high consistency of the provided labels, especially for tumor annotations. We further validate the dataset by training a deep neural network for the task of tissue segmentation and tumor subtype classification. We achieve a class-averaged Jaccard coefficient of 0.7047, and 0.9044 for tumor in particular. For classification, we achieve a slide-level accuracy of 0.9857. Since canine cutaneous tumors possess various histologic homologies to human tumors the added value of this dataset is not limited to veterinary pathology but extends to more general fields of application. UR - https://doi.org/10.1038/s41597-022-01692-w Y1 - 2022 UR - https://doi.org/10.1038/s41597-022-01692-w UR - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:573-28741 SN - 2052-4463 VL - 9 PB - Springer Nature CY - New York ER - TY - JOUR A1 - Bertram, Christof A1 - Aubreville, Marc A1 - Donovan, Taryn A. A1 - Bartel, Alexander A1 - Wilm, Frauke A1 - Marzahl, Christian 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 - Haverkamp, Ann-Kathrin A1 - Heier, Annabelle A1 - Lehmbecker, Annika A1 - Merz, Sophie A1 - Noland, Erica L. A1 - Plog, Stephanie A1 - Schmidt, Anja A1 - Sebastian, Franziska A1 - Sledge, Dodd G. A1 - Smedley, Rebecca C. A1 - Tecilla, Marco A1 - Thaiwong, Tuddow A1 - Fuchs-Baumgartinger, Andrea A1 - Meuten, Donald J. A1 - Breininger, Katharina A1 - Kiupel, Matti A1 - Maier, Andreas A1 - Klopfleisch, Robert T1 - Computer-assisted mitotic count using a deep learning–based algorithm improves interobserver reproducibility and accuracy JF - Veterinary Pathology N2 - The mitotic count (MC) is an important histological parameter for prognostication of malignant neoplasms. However, it has inter- and intraobserver discrepancies due to difficulties in selecting the region of interest (MC-ROI) and in identifying or classifying mitotic figures (MFs). Recent progress in the field of artificial intelligence has allowed the development of high-performance algorithms that may improve standardization of the MC. As algorithmic predictions are not flawless, computer-assisted review by pathologists may ensure reliability. In the present study, we compared partial (MC-ROI preselection) and full (additional visualization of MF candidates and display of algorithmic confidence values) computer-assisted MC analysis to the routine (unaided) MC analysis by 23 pathologists for whole-slide images of 50 canine cutaneous mast cell tumors (ccMCTs). Algorithmic predictions aimed to assist pathologists in detecting mitotic hotspot locations, reducing omission of MFs, and improving classification against imposters. The interobserver consistency for the MC significantly increased with computer assistance (interobserver correlation coefficient, ICC = 0.92) compared to the unaided approach (ICC = 0.70). Classification into prognostic stratifications had a higher accuracy with computer assistance. The algorithmically preselected hotspot MC-ROIs had a consistently higher MCs than the manually selected MC-ROIs. Compared to a ground truth (developed with immunohistochemistry for phosphohistone H3), pathologist performance in detecting individual MF was augmented when using computer assistance (F1-score of 0.68 increased to 0.79) with a reduction in false negatives by 38%. The results of this study demonstrate that computer assistance may lead to more reproducible and accurate MCs in ccMCTs. UR - https://doi.org/10.1177/03009858211067478 KW - canine cutaneous mast cell tumors KW - artificial intelligence KW - digital pathology KW - deep learning KW - mitotic figures KW - mitotic count KW - automated image analysis KW - computer assistance Y1 - 2021 UR - https://doi.org/10.1177/03009858211067478 UR - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:573-13141 SN - 1544-2217 VL - 59 IS - 2 SP - 211 EP - 226 PB - SAGE Publications Inc CY - London ER - TY - JOUR A1 - Marzahl, Christian A1 - Hill, Jenny A1 - Stayt, Jason A1 - Bienzle, Dorothee A1 - Welker, Lutz A1 - Wilm, Frauke A1 - Voigt, Jörn A1 - Aubreville, Marc A1 - Maier, Andreas A1 - Klopfleisch, Robert A1 - Breininger, Katharina A1 - Bertram, Christof T1 - Inter-species cell detection BT - datasets on pulmonary hemosiderophages in equine, human and feline specimens JF - Scientific Data N2 - Pulmonary hemorrhage (P-Hem) occurs among multiple species and can have various causes. Cytology of bronchoalveolar lavage fluid (BALF) using a 5-tier scoring system of alveolar macrophages based on their hemosiderin content is considered the most sensitive diagnostic method. We introduce a novel, fully annotated multi-species P-Hem dataset, which consists of 74 cytology whole slide images (WSIs) with equine, feline and human samples. To create this high-quality and high-quantity dataset, we developed an annotation pipeline combining human expertise with deep learning and data visualisation techniques. We applied a deep learning-based object detection approach trained on 17 expertly annotated equine WSIs, to the remaining 39 equine, 12 human and 7 feline WSIs. The resulting annotations were semi-automatically screened for errors on multiple types of specialised annotation maps and finally reviewed by a trained pathologist. Our dataset contains a total of 297,383 hemosiderophages classified into five grades. It is one of the largest publicly available WSIs datasets with respect to the number of annotations, the scanned area and the number of species covered. UR - https://doi.org/10.1038/s41597-022-01389-0 Y1 - 2022 UR - https://doi.org/10.1038/s41597-022-01389-0 UR - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:573-29319 SN - 2052-4463 VL - 9 PB - Springer Nature CY - London 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 BT - 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 - CHAP A1 - Wilm, Frauke A1 - Bertram, Christof A1 - Marzahl, Christian A1 - Bartel, Alexander A1 - Donovan, Taryn A. 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 A. 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 - CHAP A1 - Aubreville, Marc A1 - Goncalves, Miguel A1 - Knipfer, Christian A1 - Oetter, Nicolai A1 - Würfl, Tobias A1 - Neumann, Helmut A1 - Stelzle, Florian A1 - Bohr, Christopher A1 - Maier, Andreas T1 - Transferability of deep learning algorithms for malignancy detection in confocal laser endomicroscopy images from different anatomical locations of the upper gastrointestinal tract T2 - Biomedical Engineering Systems and Technologies UR - https://doi.org/10.1007/978-3-030-29196-9_4 KW - Confocal Laser Endomicroscopy KW - Transfer learning KW - Head and neck squamous cell carcinoma Y1 - 2019 UR - https://doi.org/10.1007/978-3-030-29196-9_4 SN - 978-3-030-29195-2 SN - 978-3-030-29196-9 SN - 1865-0929 N1 - Access to this content is enabled by Nationallizenz Ebooks Medicine SP - 67 EP - 85 PB - Springer CY - Cham 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 - Jabari, Samir A1 - Marzahl, Christian A1 - Klopfleisch, Robert A1 - Maier, Andreas ED - Tolxdorff, Thomas ED - Deserno, Thomas M. ED - Handels, Heinz ED - Maier, Andreas ED - Maier-Hein, Klaus H. ED - Palm, Christoph T1 - Inter-species, inter-tissue domain adaptation for mitotic figure assessment BT - learning new tricks from old dogs T2 - Bildverarbeitung für die Medizin 2020, Algorithmen – Systeme – Anwendungen. Proceedings des Workshops vom 15. bis 17. März 2020 in Berlin UR - https://doi.org/10.1007/978-3-658-29267-6_1 Y1 - 2020 UR - https://doi.org/10.1007/978-3-658-29267-6_1 SN - 978-3-658-29266-9 SN - 978-3-658-29267-6 N1 - Access to this content is enabled by Nationallizenz Ebooks Medicine SP - 1 EP - 7 PB - Springer Vieweg CY - Wiesbaden ER - TY - JOUR A1 - Fragoso-Garcia, Marco A1 - Wilm, Frauke A1 - Bertram, Christof A1 - Merz, Sophie A1 - Schmidt, Anja A1 - Donovan, Taryn A. A1 - Fuchs-Baumgartinger, Andrea A1 - Bartel, Alexander A1 - Marzahl, Christian A1 - Diehl, Laura A1 - Puget, Chloe A1 - Maier, Andreas A1 - Aubreville, Marc A1 - Breininger, Katharina A1 - Klopfleisch, Robert T1 - Automated diagnosis of 7 canine skin tumors using machine learning on H&E-stained whole slide images JF - Veterinary Pathology N2 - Microscopic evaluation of hematoxylin and eosin-stained slides is still the diagnostic gold standard for a variety of diseases, including neoplasms. Nevertheless, intra- and interrater variability are well documented among pathologists. So far, computer assistance via automated image analysis has shown potential to support pathologists in improving accuracy and reproducibility of quantitative tasks. In this proof of principle study, we describe a machine-learning-based algorithm for the automated diagnosis of 7 of the most common canine skin tumors: trichoblastoma, squamous cell carcinoma, peripheral nerve sheath tumor, melanoma, histiocytoma, mast cell tumor, and plasmacytoma. We selected, digitized, and annotated 350 hematoxylin and eosin-stained slides (50 per tumor type) to create a database divided into training, n = 245 whole-slide images (WSIs), validation ( n = 35 WSIs), and test sets ( n = 70 WSIs). Full annotations included the 7 tumor classes and 6 normal skin structures. The data set was used to train a convolutional neural network (CNN) for the automatic segmentation of tumor and nontumor classes. Subsequently, the detected tumor regions were classified patch-wise into 1 of the 7 tumor classes. A majority of patches-approach led to a tumor classification accuracy of the network on the slide-level of 95% (133/140 WSIs), with a patch-level precision of 85%. The same 140 WSIs were provided to 6 experienced pathologists for diagnosis, who achieved a similar slide-level accuracy of 98% (137/140 correct majority votes). Our results highlight the feasibility of artificial intelligence-based methods as a support tool in diagnostic oncologic pathology with future applications in other species and tumor types. UR - https://doi.org/10.1177/03009858231189205 KW - computer-aided diagnosis KW - computational pathology KW - digital pathology KW - dog KW - machine learning KW - skin KW - veterinary oncology Y1 - 2023 UR - https://doi.org/10.1177/03009858231189205 UR - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:573-38321 SN - 0300-9858 VL - 60 IS - 6 SP - 865 EP - 875 PB - SAGE CY - London ER - 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 A. 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 - 1361-8415 VL - 2023 IS - 84 PB - Elsevier CY - Amsterdam ER -