arXiv subjects

Katharina Breininger

Publications and source records attributed to Katharina Breininger.

72 records · Page 4Linked to original sources

arXiv2021

Inter-Species Cell Detection: Datasets on pulmonary hemosiderophages in equine, human and feline specimens

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 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 pathologists. Our dataset contains a total of 297,383 hemosiderophages classified into five grades. It is one of the largest publicly availableWSIs datasets with respect to the number of annotations, the scanned area and the number of species covered.

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arXiv2021

Automatic and explainable grading of meningiomas from histopathology images

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 meningioma grading from histology whole slide images. All approaches are following a two-stage paradigm, where we first identify a region of interest based on the detection of mitotic figures in the slide using a state-of-the-art object detection deep learning network. This region of highest mitotic rate is considered characteristic for biological tumor behavior. In the second stage, we calculate a score corresponding to tumor malignancy based on information contained in this region using three different settings. In a first approach, image patches are sampled from this region and regression is based on morphological features encoded by a ResNet-based network. We compare this to learning a logistic regression from the determined mitotic count, an approach which is easily traceable and explainable. Lastly, we combine both approaches in a single network. We trained the pipeline on 951 slides from 341 patients and evaluated them on a separate set of 141 slides from 43 patients. All approaches yield a high correlation to the WHO grade. The logistic regression and the combined approach had the best results in our experiments, yielding correct predictions in 32 and 33 of all cases, respectively, with the image-based approach only predicting 25 cases correctly. Spearman's correlation was 0.716, 0.792 and 0.790 respectively. It may seem counterintuitive at first that morphological features provided by image patches do not improve model performance. Yet, this mirrors the criteria of the grading scheme, where mitotic count is the only unequivocal parameter.

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arXiv2021

EXACT: A collaboration toolset for algorithm-aided annotation of images with annotation version control

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.

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arXiv2021

Quantifying the Scanner-Induced Domain Gap in Mitosis Detection

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. Hypothesizing that the scanner device plays a decisive role in this effect, we evaluated the susceptibility of a standard mitosis detection approach to the domain shift introduced by using a different whole slide scanner. Our work is based on the MICCAI-MIDOG challenge 2021 data set, which includes 200 tumor cases of human breast cancer and four scanners. Our work indicates that the domain shift induced not by biochemical variability but purely by the choice of acquisition device is underestimated so far. Models trained on images of the same scanner yielded an average F1 score of 0.683, while models trained on a single other scanner only yielded an average F1 score of 0.325. Training on another multi-domain mitosis dataset led to mean F1 scores of 0.52. We found this not to be reflected by domain-shifts measured as proxy A distance-derived metric.

cs.CV↗

arXiv2021

Learning to be EXACT, Cell Detection for Asthma on Partially Annotated Whole Slide Images

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 developed a training pipeline which can train a deep learning-based object detection model with partially annotated WSIs and compensate class imbalances on the fly. With this approach we can freely sample from annotated WSIs areas and are not restricted to fully annotated extracted sub-images of the WSI as with classical approaches. We evaluated our pipeline in a cross-validation setup with a fixed training set using a dataset of six equine WSIs of which four are partially annotated and used for training, and two fully annotated WSI are used for validation and testing. Our WSI-based training approach outperformed classical sub-image-based training methods by up to 15\% $mAP$ and yielded human-like performance when compared to the annotations of ten trained pathologists.

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arXiv2021

How Many Annotators Do We Need? -- A Study on the Influence of Inter-Observer Variability on the Reliability of Automatic Mitotic Figure Assessment

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 development of accurate algorithms. In the present work we evaluated the benefit of multi-expert consensus (n = 3, 5, 7, 9, 11) on algorithmic performance. While training with individual databases resulted in highly variable F$_1$ scores, performance was notably increased and more consistent when using the consensus of three annotators. Adding more annotators only resulted in minor improvements. We conclude that databases by few pathologists and high label accuracy may be the best compromise between high algorithmic performance and time investment.

cs.CV↗

arXiv2021

Dataset on Bi- and Multi-Nucleated Tumor Cells in Canine Cutaneous Mast Cell Tumors

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 cytologic and histologic grading schemes (respectively) which correlate with poor patient outcome. For this study, we created the first open source data-set with 19,983 annotations of BiNC and 1,416 annotations of MuNC in 32 histological whole slide images of ccMCT. Labels were created by a pathologist and an algorithmic-aided labeling approach with expert review of each generated candidate. A state-of-the-art deep learning-based model yielded an $F_1$ score of 0.675 for BiNC and 0.623 for MuNC on 11 test whole slide images. In regions of interest ($2.37 mm^2$) extracted from these test images, 6 pathologists had an object detection performance between 0.270 - 0.526 for BiNC and 0.316 - 0.622 for MuNC, while our model archived an $F_1$ score of 0.667 for BiNC and 0.685 for MuNC. This open dataset can facilitate development of automated image analysis for this task and may thereby help to promote standardization of this facet of histologic tumor prognostication.

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arXiv2020

Automatic CAD-RADS Scoring Using Deep Learning

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 vessels and the grading of lesions within the coronary artery tree. We propose a bottom-up approach for fully-automated prediction of this score using deep-learning operating on a segment-wise representation of the coronary arteries. The method relies solely on a prior fully-automated centerline extraction and segment labeling and predicts the segment-wise stenosis degree and the overall calcification grade as auxiliary tasks in a multi-task learning setup. We evaluate our approach on a data collection consisting of 2,867 patients. On the task of identifying patients with a CAD-RADS score indicating the need for further invasive investigation our approach reaches an area under curve (AUC) of 0.923 and an AUC of 0.914 for determining whether the patient suffers from CAD. This level of performance enables our approach to be used in a fully-automated screening setup or to assist diagnostic CCTA reading, especially due to its neural architecture design -- which allows comprehensive predictions.

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arXiv2019

Deep Learning Algorithms for Coronary Artery Plaque Characterisation from CCTA Scans

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 multi-view ensemble approach based on texture analysis, and a newly proposed 2.5D approach. Current state of the art methods utilising fluid dynamics based fractional flow reserve (FFR) simulation reach an AUC of up to 0.93 for the task of predicting an abnormal invasive FFR value. For the comparable task of predicting revascularisation decision, we are able to improve the performance in terms of AUC of both existing approaches with the proposed modifications, specifically from 0.80 to 0.90 for the 3D-RCNN, and from 0.85 to 0.90 for the multi-view texture-based ensemble. The newly proposed 2.5D approach achieves comparable results with an AUC of 0.90.

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arXiv2019

Coronary Artery Plaque Characterization from CCTA Scans using Deep Learning and Radiomics

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 based on radiomics, where a plaque segmentation is used to calculate various shape-, intensity- and texture-based features under different image transformations. A second approach is based on deep learning and relies on centerline extraction as sole prerequisite. In the third approach, we fuse the deep learning approach with radiomic features. On our data the methods reached similar scores as simulated fractional flow reserve (FFR) measurements, which - in contrast to our methods - requires an exact segmentation of the whole coronary tree and often time-consuming manual interaction. In literature, the performance of simulated FFR reaches an AUC between 0.79-0.93 predicting an abnormal invasive FFR that demands revascularization. The radiomics approach achieves an AUC of 0.86, the deep learning approach 0.84 and the combined method 0.88 for predicting the revascularization decision directly. While all three proposed methods can be determined within seconds, the FFR simulation typically takes several minutes. Provided representative training data in sufficient quantities, we believe that the presented methods can be used to create systems for fully automatic non-invasive risk assessment for a variety of adverse cardiac events.

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arXiv2019

Projection-to-Projection Translation for Hybrid X-ray and Magnetic Resonance Imaging

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 modalities must be present in the same domain. For image-guided interventional procedures, X-ray fluoroscopy has proven to be the modality of choice. Synthesizing one modality from another in this case is an ill-posed problem due to ambiguous signal and overlapping structures in projective geometry. To take on these challenges, we present a learning-based solution to MR to X-ray projection-to-projection translation. We propose an image generator network that focuses on high representation capacity in higher resolution layers to allow for accurate synthesis of fine details in the projection images. Additionally, a weighting scheme in the loss computation that favors high-frequency structures is proposed to focus on the important details and contours in projection imaging. The proposed extensions prove valuable in generating X-ray projection images with natural appearance. Our approach achieves a deviation from the ground truth of only $6$% and structural similarity measure of $0.913\,\pm\,0.005$. In particular the high frequency weighting assists in generating projection images with sharp appearance and reduces erroneously synthesized fine details.

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arXiv2019

What Do We Really Need? Degenerating U-Net on Retinal Vessel Segmentation

Retinal vessel segmentation is an essential step for fundus image analysis. With the recent advances of deep learning technologies, many convolutional neural networks have been applied in this field, including the successful U-Net. In this work, we firstly modify the U-Net with functional blocks aiming to pursue higher performance. The absence of the expected performance boost then lead us to dig into the opposite direction of shrinking the U-Net and exploring the extreme conditions such that its segmentation performance is maintained. Experiment series to simplify the network structure, reduce the network size and restrict the training conditions are designed. Results show that for retinal vessel segmentation on DRIVE database, U-Net does not degenerate until surprisingly acute conditions: one level, one filter in convolutional layers, and one training sample. This experimental discovery is both counter-intuitive and worthwhile. Not only are the extremes of the U-Net explored on a well-studied application, but also one intriguing warning is raised for the research methodology which seeks for marginal performance enhancement regardless of the resource cost.

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arXiv2019

A Divide-and-Conquer Approach towards Understanding Deep Networks

Deep neural networks have achieved tremendous success in various fields including medical image segmentation. However, they have long been criticized for being a black-box, in that interpretation, understanding and correcting architectures is difficult as there is no general theory for deep neural network design. Previously, precision learning was proposed to fuse deep architectures and traditional approaches. Deep networks constructed in this way benefit from the original known operator, have fewer parameters, and improved interpretability. However, they do not yield state-of-the-art performance in all applications. In this paper, we propose to analyze deep networks using known operators, by adopting a divide-and-conquer strategy to replace network components, whilst retaining its performance. The task of retinal vessel segmentation is investigated for this purpose. We start with a high-performance U-Net and show by step-by-step conversion that we are able to divide the network into modules of known operators. The results indicate that a combination of a trainable guided filter and a trainable version of the Frangi filter yields a performance at the level of U-Net (AUC 0.974 vs. 0.972) with a tremendous reduction in parameters (111,536 vs. 9,575). In addition, the trained layers can be mapped back into their original algorithmic interpretation and analyzed using standard tools of signal processing.

cs.LG↗

arXiv2019

Projection image-to-image translation in hybrid X-ray/MR imaging

The potential benefit of hybrid X-ray and MR imaging in the interventional environment is large due to the combination of fast imaging with high contrast variety. However, a vast amount of existing image enhancement methods requires the image information of both modalities to be present in the same domain. To unlock this potential, we present a solution to image-to-image translation from MR projections to corresponding X-ray projection images. The approach is based on a state-of-the-art image generator network that is modified to fit the specific application. Furthermore, we propose the inclusion of a gradient map in the loss function to allow the network to emphasize high-frequency details in image generation. Our approach is capable of creating X-ray projection images with natural appearance. Additionally, our extensions show clear improvement compared to the baseline method.

cs.CV↗

arXiv2018

Decoupling Respiratory and Angular Variation in Rotational X-ray Scans Using a Prior Bilinear Model

Data-driven respiratory signal extraction from rotational X-ray scans is a challenge as angular effects overlap with respiration-induced change in the scene. In this paper, we use the linearity of the X-ray transform to propose a bilinear model based on a prior 4D scan to separate angular and respiratory variation. The bilinear estimation process is supported by a B-spline interpolation using prior knowledge about the trajectory angle. Consequently, extraction of respiratory features simplifies to a linear problem. Though the need for a prior 4D CT seems steep, our proposed use-case of driving a respiratory motion model in radiation therapy usually meets this requirement. We evaluate on DRRs of 5 patient 4D CTs in a leave-one-phase-out manner and achieve a mean estimation error of 3.01 % in the gray values for unseen viewing angles. We further demonstrate suitability of the extracted weights to drive a motion model for treatments with a continuously rotating gantry.

cs.CV↗

arXiv2018

Precision Learning: Reconstruction Filter Kernel Discretization

In this paper, we present substantial evidence that a deep neural network will intrinsically learn the appropriate way to discretize the ideal continuous reconstruction filter. Currently, the Ram-Lak filter or heuristic filters which impose different noise assumptions are used for filtered back-projection. All of these, however, inhibit a fully data-driven reconstruction deep learning approach. In addition, the heuristic filters are not chosen in an optimal sense. To tackle this issue, we propose a formulation to directly learn the reconstruction filter. The filter is initialized with the ideal Ramp filter as a strong pre-training and learned in frequency domain. We compare the learned filter with the Ram-Lak and the Ramp filter on a numerical phantom as well as on a real CT dataset. The results show that the network properly discretizes the continuous Ramp filter and converges towards the Ram-Lak solution. In our view these observations are interesting to gain a better understanding of deep learning techniques and traditional analytic techniques such as Wiener filtering and discretization theory. Furthermore, this will allow fully trainable data-driven reconstruction deep learning approaches.

cs.CV↗

arXiv2018

Learning from a Handful Volumes: MRI Resolution Enhancement with Volumetric Super-Resolution Forests

Magnetic resonance imaging (MRI) enables 3-D imaging of anatomical structures. However, the acquisition of MR volumes with high spatial resolution leads to long scan times. To this end, we propose volumetric super-resolution forests (VSRF) to enhance MRI resolution retrospectively. Our method learns a locally linear mapping between low-resolution and high-resolution volumetric image patches by employing random forest regression. We customize features suitable for volumetric MRI to train the random forest and propose a median tree ensemble for robust regression. VSRF outperforms state-of-the-art example-based super-resolution in term of image quality and efficiency for model training and inference in different MRI datasets. It is also superior to unsupervised methods with just a handful or even a single volume to assemble training data.

cs.CV↗

arXiv2017

Frangi-Net: A Neural Network Approach to Vessel Segmentation

In this paper, we reformulate the conventional 2-D Frangi vesselness measure into a pre-weighted neural network ("Frangi-Net"), and illustrate that the Frangi-Net is equivalent to the original Frangi filter. Furthermore, we show that, as a neural network, Frangi-Net is trainable. We evaluate the proposed method on a set of 45 high resolution fundus images. After fine-tuning, we observe both qualitative and quantitative improvements in the segmentation quality compared to the original Frangi measure, with an increase up to $17\%$ in F1 score.

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