Katharina Breininger

Katharina Breininger
Friedrich-Alexander-University of Erlangen-Nürnberg | FAU · Department Artificial Intelligence in Biomedical Imaging

Professor

About

100
Publications
7,717
Reads
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512
Citations
Citations since 2016
99 Research Items
510 Citations
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2016201720182019202020212022020406080100120140
2016201720182019202020212022020406080100120140

Publications

Publications (100)
Article
Full-text available
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-ba...
Preprint
Tumor segmentation in histopathology images is often complicated by its composition of different histological subtypes and class imbalance. Oversampling subtypes with low prevalence features is not a satisfactory solution since it eventually leads to overfitting. We propose to create synthetic images with semantically-conditioned deep generative ne...
Preprint
Full-text available
Histopathology imaging is crucial for the diagnosis and treatment of skin diseases. For this reason, computer-assisted approaches have gained popularity and shown promising results in tasks such as segmentation and classification of skin disorders. However, collecting essential data and sufficiently high-quality annotations is a challenge. This wor...
Article
Full-text available
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 robu...
Chapter
This paper presents a new multimodal interventional radiology dataset, called PoCaP (Port Catheter Placement) Corpus. This corpus consists of speech and audio signals in German, X-ray images, and system commands collected from 31 PoCaP interventions by six surgeons with average duration of \(81.4 \pm 41.0\) min. The corpus aims to provide a resourc...
Preprint
Full-text available
Optical coherence tomography (OCT) is a micrometer-scale, volumetric imaging modality that has become a clinical standard in ophthalmology. OCT instruments image by raster-scanning a focused light spot across the retina, acquiring sequential cross-sectional images to generate volumetric data. Patient eye motion during the acquisition poses unique c...
Chapter
Optical coherence tomography (OCT) is a micrometer-scale, volumetric imaging modality that has become a clinical standard in ophthalmology. OCT instruments image by raster-scanning a focused light spot across the retina, acquiring sequential cross-sectional images to generate volumetric data. Patient eye motion during the acquisition poses unique c...
Article
Full-text available
Glottis segmentation is a crucial step to quantify endoscopic footage in laryngeal high-speed videoendoscopy. Recent advances in deep neural networks for glottis segmentation allow for a fully automatic workflow. However, exact knowledge of integral parts of these deep segmentation networks remains unknown, and understanding the inner workings is c...
Conference Paper
Automated Electrocardiogram (ECG) classification using deep neural networks requires large datasets annotated by medical professionals, which is time-consuming and expensive. This work examines ECG augmentation as a method for enriching existing datasets at low cost. First, we introduce three novel augmentations: Limb Electrode Move and Chest Elect...
Preprint
Full-text available
Automated Electrocardiogram (ECG) classification using deep neural networks requires large datasets annotated by medical professionals, which is time-consuming and expensive. This work examines ECG augmentation as a method for enriching existing datasets at low cost. First, we introduce three novel augmentations: Limb Electrode Move and Chest Elect...
Preprint
This paper presents a new multimodal interventional radiology dataset, called PoCaP (Port Catheter Placement) Corpus. This corpus consists of speech and audio signals in German, X-ray images, and system commands collected from 31 PoCaP interventions by six surgeons with average duration of 81.4 $\pm$ 41.0 minutes. The corpus aims to provide a resou...
Article
Full-text available
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...
Article
Background While MRI evaluation of joints has been primarily used to quantify inflammation at a cross-sectional and longitudinal level, less is known about the potential of MRI in distinguishing different patterns of inflammation in the various forms of arthritis. Objectives To evaluate (i) whether deep learning using neural networks can be traine...
Preprint
Full-text available
The density of mitotic figures within tumor tissue is known to be highly correlated with tumor proliferation and thus is an important marker in tumor grading. Recognition of mitotic figures by pathologists is known to be subject to a strong inter-rater bias, which limits the prognostic value. State-of-the-art deep learning methods can support the e...
Chapter
In the past decade, deep neural networks have gained much attention in medical imaging applications. Especially fully supervised methods have received a lot of interest as medical decision making relies on robust predictions. The ability to be more flexible and adaptive to individual anatomical differences gives them an advantage compared to unsupe...
Conference Paper
For many medical questions, X-ray imaging belongs to the gold standard for diagnosis, treatment planning, treatment guidance, and surgery assessment. To improve the reading performance, standardized image rotation is an important step. We propose a new algorithm to estimate the correct image rotation. For many body regions, one line can be defined...
Chapter
Neuromuscular diseases (NMDs) cause a significant burden for both healthcare systems and society. They can lead to severe progressive muscle weakness, muscle degeneration, contracture, deformity and progressive disability. The NMDs evaluated in this study often manifest in early childhood. As subtypes of disease, e.g. Duchenne muscular dystropy (DM...
Article
Objectives: To evaluate whether neural networks can distinguish between seropositive rheumatoid arthritis (RA), seronegative RA and psoriatic arthritis (PsA) based on inflammatory patterns from hand MRI and to test how psoriasis patients with subclinical inflammation fit into such patterns. Methods: ResNet neural networks were utilized to compar...
Preprint
Full-text available
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 trained annotators and to validate a deep lear...
Chapter
Assessing the mitotic count has a known high degree of intra- and inter-rater variability. Computer-aided systems have proven to decrease this variability and reduce labeling time. These systems, however, are generally highly dependent on their training domain and show poor applicability to unseen domains. In histopathology, these domain shifts can...
Preprint
Full-text available
With coronary artery disease (CAD) persisting to be one of the leading causes of death worldwide, interest in supporting physicians with algorithms to speed up and improve diagnosis is high. In clinical practice, the severeness of CAD is often assessed with a coronary CT angiography (CCTA) scan and manually graded with the CAD-Reporting and Data Sy...
Preprint
Full-text available
Neuromuscular diseases (NMDs) cause a significant burden for both healthcare systems and society. They can lead to severe progressive muscle weakness, muscle degeneration, contracture, deformity and progressive disability. The NMDs evaluated in this study often manifest in early childhood. As subtypes of disease, e.g. Duchenne Muscular Dystropy (DM...
Preprint
Full-text available
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 robu...
Preprint
Full-text available
Chronic wounds including diabetic and arterial/venous insufficiency injuries have become a major burden for healthcare systems worldwide. Demographic changes suggest that wound care will play an even bigger role in the coming decades. Predicting and monitoring response to therapy in wound care is currently largely based on visual inspection with li...
Preprint
Supervised deep learning has shown state-of-the-art performance for medical image segmentation across different applications, including histopathology and cancer research; however, the manual annotation of such data is extremely laborious. In this work, we explore the use of superpixel approaches to compute a pre-segmentation of HER2 stained images...
Article
Full-text available
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...
Preprint
Full-text available
Annotating data, especially in the medical domain, requires expert knowledge and a lot of effort. This limits the amount and/or usefulness of available medical data sets for experimentation. Therefore, developing strategies to increase the number of annotations while lowering the needed domain knowledge is of interest. A possible strategy is the us...
Preprint
Full-text available
Assessing the Mitotic Count has a known high degree of intra- and inter-rater variability. Computer-aided systems have proven to decrease this variability and reduce labelling time. These systems, however, are generally highly dependent on their training domain and show poor applicability to unseen domains. In histopathology, these domain shifts ca...
Preprint
Pulmonary hemorrhage (P-Hem) occurs among multiple species and can have various causes. Cytology of bronchoalveolarlavage 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 co...
Preprint
Full-text available
Meningioma is one of the most prevalent brain tumors in adults. To determine its malignancy, it is graded by a pathologist into three grades according to WHO standards. This grade plays a decisive role in treatment, and yet may be subject to inter-rater discordance. In this work, we present and compare three approaches towards fully automatic menin...
Preprint
Full-text available
The mitotic count (MC) is an important histological parameter for prognostication of malignant neoplasms. However, it has inter- and intra-observer discrepancies due to difficulties in selecting the region of interest (MC-ROI) and in identifying/classifying mitotic figures (MFs). Recent progress in the field of artificial intelligence has allowed t...
Article
Full-text available
Purpose With the recent development of deep learning technologies, various neural networks have been proposed for fundus retinal vessel segmentation. Among them, the U-Net is regarded as one of the most successful architectures. In this work, we start with simplification of the U-Net, and explore the performance of few-parameter networks on this ta...
Preprint
Full-text available
Automated detection of mitotic figures in histopathology images has seen vast improvements, thanks to modern deep learning-based pipelines. Application of these methods, however, is in practice limited by strong variability of images between labs. This results in a domain shift of the images, which causes a performance drop of the models. Hypothesi...
Research Proposal
Full-text available
This is the challenge proposal for the MIDOG 2021 challenge, part of MICCAI 2021. Digital pathology is a fast-growing field that has seen strong scientific advances in recent years. Especially theaccurate diagnosis and prognosis of tumors is a topic of particular interest, as documented by recent challenges on MICCAI, ICPR and elsewhere. In this co...
Article
Full-text available
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 Coll...
Chapter
Density of mitotic figures in histologic sections is a prognostically relevant characteristic for many tumours. Due to high interpathologist variability, deep learning-based algorithms are a promising solution to improve tumour prognostication. Pathologists are the gold standard for database development, however, labelling errors may hamper develop...
Chapter
Tumor cells with two nuclei (binucleated cells, BiNC) or more nuclei (multinucleated cells, MuNC) indicate an increased amount of cellular genetic material which is thought to facilitate oncogenesis, tumor progression and treatment resistance. In canine cutaneous mast cell tumors (ccMCT), binucleation and multinucleation are parameters used in cyto...
Chapter
Coronary CT angiography (CCTA) has established its role as a noninvasive modality for the diagnosis of coronary artery disease (CAD). The CAD-Reporting and Data System (CAD-RADS) has been developed to standardize communication and aid in decision making based on CCTA findings. The CAD-RADS score is determined by manual assessment of all coronary ve...
Chapter
Asthma is a chronic inflammatory disorder of the lower respiratory tract and naturally occurs in humans and animals including horses. The annotation of an asthma microscopy whole slide image (WSI) is an extremely labour-intensive task due to the hundreds of thousands of cells per WSI. To overcome the limitation of annotating WSI incompletely, we de...
Chapter
Endovascular aortic repair (EVAR) is an X-ray guided procedure for treating aortic aneurysms with the goal to prevent rupture. During this minimally invasive intervention, stent grafts are inserted into the vasculature to support the diseased vessel wall. By overlaying information from preoperative 3-D imaging onto the intraoperative images, radiat...
Preprint
Full-text available
Asthma is a chronic inflammatory disorder of the lower respiratory tract and naturally occurs in humans and animals including horses. The annotation of an asthma microscopy whole slide image (WSI) is an extremely labour-intensive task due to the hundreds of thousands of cells per WSI. To overcome the limitation of annotating WSI incompletely, we de...
Preprint
Full-text available
Tumor cells with two nuclei (binucleated cells, BiNC) or more nuclei (multinucleated cells, MuNC) indicate an increased amount of cellular genetic material which is thought to facilitate oncogenesis, tumor progression and treatment resistance. In canine cutaneous mast cell tumors (ccMCT), binucleation and multinucleation are parameters used in cyto...
Thesis
Full-text available
Fluoroscopy-guided endovascular aortic repair (EVAR) has become the predominant treatment strategy for elective repair of abdominal aortic aneurysms in many western countries. During the procedure, stent grafts are implanted into the vasculature to reduce the pressure on the vessel wall and prevent a potentially fatal aneurysm rupture. The fusion o...
Preprint
Full-text available
Density of mitotic figures in histologic sections is a prognostically relevant characteristic for many tumours. Due to high inter-pathologist variability, deep learning-based algorithms are a promising solution to improve tumour prognostication. Pathologists are the gold standard for database development, however, labelling errors may hamper develo...
Preprint
Full-text available
Coronary CT angiography (CCTA) has established its role as a non-invasive modality for the diagnosis of coronary artery disease (CAD). The CAD-Reporting and Data System (CAD-RADS) has been developed to standardize communication and aid in decision making based on CCTA findings. The CAD-RADS score is determined by manual assessment of all coronary v...
Chapter
Coronary CT angiography (CCTA) has established its role as a non-invasive modality for the diagnosis of coronary artery disease (CAD). The CAD-Reporting and Data System (CAD-RADS) has been developed to standardize communication and aid in decision making based on CCTA findings. The CAD-RADS score is determined by manual assessment of all coronary v...
Chapter
Fusing intraoperative X-ray with information from preoperative computed tomography for endovascular aortic repair has been shown to reduce radiation exposure, need for contrast agent, and procedure time. However, due to the instruments inserted during the intervention, the vasculature deforms and the fusion loses accuracy. In this paper, we propose...
Chapter
Image-based diagnosis of the human eye is crucial for the early detection of several diseases in ophthalmology. In this work, we investigate the possibility to use image retrieval to support the diagnosis of diabetic retinopathy. To this end, we evaluate different feature learning techniques. In particular, we evaluate the performance of cost funct...
Preprint
Full-text available
Analysing coronary artery plaque segments with respect to their functional significance and therefore their influence to patient management in a non-invasive setup is an important subject of current research. In this work we compare and improve three deep learning algorithms for this task: A 3D recurrent convolutional neural network (RCNN), a 2D mu...
Preprint
Full-text available
Assessing coronary artery plaque segments in coronary CT angiography scans is an important task to improve patient management and clinical outcomes, as it can help to decide whether invasive investigation and treatment are necessary. In this work, we present three machine learning approaches capable of performing this task. The first approach is ba...
Article
Full-text available
Hybrid X-ray and magnetic resonance (MR) imaging promises large potential in interventional medical imaging applications due to the broad variety of contrast of MRI combined with fast imaging of X-ray-based modalities. To fully utilize the potential of the vast amount of existing image enhancement techniques, the corresponding information from both...