arXiv subjects

Andreas Maier

Publications and source records attributed to Andreas Maier.

At least 361 records · Page 20Linked to original sources

arXiv2021

Synthetic Glacier SAR Image Generation from Arbitrary Masks Using Pix2Pix Algorithm

Supervised machine learning requires a large amount of labeled data to achieve proper test results. However, generating accurately labeled segmentation maps on remote sensing imagery, including images from synthetic aperture radar (SAR), is tedious and highly subjective. In this work, we propose to alleviate the issue of limited training data by generating synthetic SAR images with the pix2pix algorithm. This algorithm uses conditional Generative Adversarial Networks (cGANs) to generate an artificial image while preserving the structure of the input. In our case, the input is a segmentation mask, from which a corresponding synthetic SAR image is generated. We present different models, perform a comparative study and demonstrate that this approach synthesizes convincing glaciers in SAR images with promising qualitative and quantitative results.

cs.LG↗

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.

eess.IV↗

arXiv2021

Coronary Plaque Analysis for CT Angiography Clinical Research

The analysis of plaque deposits in the coronary vasculature is an important topic in current clinical research. From a technical side mostly new algorithms for different sub tasks - e.g. centerline extraction or vessel/plaque segmentation - are proposed. However, to enable clinical research with the help of these algorithms, a software solution, which enables manual correction, comprehensive visual feedback and tissue analysis capabilities, is needed. Therefore, we want to present such an integrated software solution. It is able to perform robust automatic centerline extraction and inner and outer vessel wall segmentation, while providing easy to use manual correction tools. Also, it allows for annotation of lesions along the centerlines, which can be further analyzed regarding their tissue composition. Furthermore, it enables research in upcoming technologies and research directions: it does support dual energy CT scans with dedicated plaque analysis and the quantification of the fatty tissue surrounding the vasculature, also in automated set-ups.

cs.CV↗

arXiv2021

Glacier Calving Front Segmentation Using Attention U-Net

An essential climate variable to determine the tidewater glacier status is the location of the calving front position and the separation of seasonal variability from long-term trends. Previous studies have proposed deep learning-based methods to semi-automatically delineate the calving fronts of tidewater glaciers. They used U-Net to segment the ice and non-ice regions and extracted the calving fronts in a post-processing step. In this work, we show a method to segment the glacier calving fronts from SAR images in an end-to-end fashion using Attention U-Net. The main objective is to investigate the attention mechanism in this application. Adding attention modules to the state-of-the-art U-Net network lets us analyze the learning process by extracting its attention maps. We use these maps as a tool to search for proper hyperparameters and loss functions in order to generate higher qualitative results. Our proposed attention U-Net performs comparably to the standard U-Net while providing additional insight into those regions on which the network learned to focus more. In the best case, the attention U-Net achieves a 1.5% better Dice score compared to the canonical U-Net with a glacier front line prediction certainty of up to 237.12 meters.

cs.LG↗

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.

cs.CV↗

arXiv2020

2-D Respiration Navigation Framework for 3-D Continuous Cardiac Magnetic Resonance Imaging

Continuous protocols for cardiac magnetic resonance imaging enable sampling of the cardiac anatomy simultaneously resolved into cardiac phases. To avoid respiration artifacts, associated motion during the scan has to be compensated for during reconstruction. In this paper, we propose a sampling adaption to acquire 2-D respiration information during a continuous scan. Further, we develop a pipeline to extract the different respiration states from the acquired signals, which are used to reconstruct data from one respiration phase. Our results show the benefit of the proposed workflow on the image quality compared to no respiration compensation, as well as a previous 1-D respiration navigation approach.

cs.CV↗

arXiv2020

Spatio-temporal Multi-task Learning for Cardiac MRI Left Ventricle Quantification

Quantitative assessment of cardiac left ventricle (LV) morphology is essential to assess cardiac function and improve the diagnosis of different cardiovascular diseases. In current clinical practice, LV quantification depends on the measurement of myocardial shape indices, which is usually achieved by manual contouring of the endo- and epicardial. However, this process subjected to inter and intra-observer variability, and it is a time-consuming and tedious task. In this paper, we propose a spatio-temporal multi-task learning approach to obtain a complete set of measurements quantifying cardiac LV morphology, regional-wall thickness (RWT), and additionally detecting the cardiac phase cycle (systole and diastole) for a given 3D Cine-magnetic resonance (MR) image sequence. We first segment cardiac LVs using an encoder-decoder network and then introduce a multitask framework to regress 11 LV indices and classify the cardiac phase, as parallel tasks during model optimization. The proposed deep learning model is based on the 3D spatio-temporal convolutions, which extract spatial and temporal features from MR images. We demonstrate the efficacy of the proposed method using cine-MR sequences of 145 subjects and comparing the performance with other state-of-the-art quantification methods. The proposed method obtained high prediction accuracy, with an average mean absolute error (MAE) of 129 $mm^2$, 1.23 $mm$, 1.76 $mm$, Pearson correlation coefficient (PCC) of 96.4%, 87.2%, and 97.5% for LV and myocardium (Myo) cavity regions, 6 RWTs, 3 LV dimensions, and an error rate of 9.0\% for phase classification. The experimental results highlight the robustness of the proposed method, despite varying degrees of cardiac morphology, image appearance, and low contrast in the cardiac MR sequences.

eess.IV↗

arXiv2020

Robustness Investigation on Deep Learning CT Reconstruction for Real-Time Dose Optimization

In computed tomography (CT), automatic exposure control (AEC) is frequently used to reduce radiation dose exposure to patients. For organ-specific AEC, a preliminary CT reconstruction is necessary to estimate organ shapes for dose optimization, where only a few projections are allowed for real-time reconstruction. In this work, we investigate the performance of automated transform by manifold approximation (AUTOMAP) in such applications. For proof of concept, we investigate its performance on the MNIST dataset first, where the dataset containing all the 10 digits are randomly split into a training set and a test set. We train the AUTOMAP model for image reconstruction from 2 projections or 4 projections directly. The test results demonstrate that AUTOMAP is able to reconstruct most digits well with a false rate of 1.6% and 6.8% respectively. In our subsequent experiment, the MNIST dataset is split in a way that the training set contains 9 digits only while the test set contains the excluded digit only, for instance "2". In the test results, the digit "2"s are falsely predicted as "3" or "5" when using 2 projections for reconstruction, reaching a false rate of 94.4%. For the application in medical images, AUTOMAP is also trained on patients' CT images. The test images reach an average root-mean-square error of 290 HU. Although the coarse body outlines are well reconstructed, some organs are misshaped.

eess.IV↗

arXiv2020

A completely annotated whole slide image dataset of canine breast cancer to aid human breast cancer research

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.

cs.CV↗

arXiv2020

Deep Learning-based Pipeline for Module Power Prediction from EL Measurements

Automated inspection plays an important role in monitoring large-scale photovoltaic power plants. Commonly, electroluminescense measurements are used to identify various types of defects on solar modules but have not been used to determine the power of a module. However, knowledge of the power at maximum power point is important as well, since drops in the power of a single module can affect the performance of an entire string. By now, this is commonly determined by measurements that require to discontact or even dismount the module, rendering a regular inspection of individual modules infeasible. In this work, we bridge the gap between electroluminescense measurements and the power determination of a module. We compile a large dataset of 719 electroluminescense measurementsof modules at various stages of degradation, especially cell cracks and fractures, and the corresponding power at maximum power point. Here,we focus on inactive regions and cracks as the predominant type of defect. We set up a baseline regression model to predict the power from electroluminescense measurements with a mean absolute error of 9.0+/-3.7$W_P$ (4.0+/-8.4%). Then, we show that deep-learning can be used to train a model that performs significantly better (7.3+/-2.7$W_P$ or 3.2+/-6.5%) and propose a variant of class activation maps to obtain the per cell power loss, as predicted by the model. With this work, we aim to open a new research topic. Therefore, we publicly release the dataset, the code and trained models to empower other researchers to compare against our results. Finally, we present a thorough evaluation of certain boundary conditions like the dataset size and an automated preprocessing pipeline for on-site measurements showing multiple modules at once.

cs.CV↗

arXiv2020

Synthetic Image Rendering Solves Annotation Problem in Deep Learning Nanoparticle Segmentation

Nanoparticles occur in various environments as a consequence of man-made processes, which raises concerns about their impact on the environment and human health. To allow for proper risk assessment, a precise and statistically relevant analysis of particle characteristics (such as e.g. size, shape and composition) is required that would greatly benefit from automated image analysis procedures. While deep learning shows impressive results in object detection tasks, its applicability is limited by the amount of representative, experimentally collected and manually annotated training data. Here, we present an elegant, flexible and versatile method to bypass this costly and tedious data acquisition process. We show that using a rendering software allows to generate realistic, synthetic training data to train a state-of-the art deep neural network. Using this approach, we derive a segmentation accuracy that is comparable to man-made annotations for toxicologically relevant metal-oxide nanoparticle ensembles which we chose as examples. Our study paves the way towards the use of deep learning for automated, high-throughput particle detection in a variety of imaging techniques such as microscopies and spectroscopies, for a wide variety of studies and applications, including the detection of plastic micro- and nanoparticles.

cs.LG↗

arXiv2020

Maximum a posteriori signal recovery for optical coherence tomography angiography image generation and denoising

Optical coherence tomography angiography (OCTA) is a novel and clinically promising imaging modality to image retinal and sub-retinal vasculature. Based on repeated optical coherence tomography (OCT) scans, intensity changes are observed over time and used to compute OCTA image data. OCTA data are prone to noise and artifacts caused by variations in flow speed and patient movement. We propose a novel iterative maximum a posteriori signal recovery algorithm in order to generate OCTA volumes with reduced noise and increased image quality. This algorithm is based on previous work on probabilistic OCTA signal models and maximum likelihood estimates. Reconstruction results using total variation minimization and wavelet shrinkage for regularization were compared against an OCTA ground truth volume, merged from six co-registered single OCTA volumes. The results show a significant improvement in peak signal-to-noise ratio and structural similarity. The presented algorithm brings together OCTA image generation and Bayesian statistics and can be developed into new OCTA image generation and denoising algorithms.

eess.IV↗

arXiv2020

Reconstruction of Voxels with Position- and Angle-Dependent Weightings

The reconstruction problem of voxels with individual weightings can be modeled a position- and angle- dependent function in the forward-projection. This changes the system matrix and prohibits to use standard filtered backprojection. In this work we first formulate this reconstruction problem in terms of a system matrix and weighting part. We compute the pseudoinverse and show that the solution is rank-deficient and hence very ill posed. This is a fundamental limitation for reconstruction. We then derive an iterative solution and experimentally show its uperiority to any closed-form solution.

cs.CV↗

arXiv2020

Deep learning algorithms out-perform veterinary pathologists in detecting the mitotically most active tumor region

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 to 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.

cs.CV↗

arXiv2020

ICFHR 2020 Competition on Image Retrieval for Historical Handwritten Fragments

This competition succeeds upon a line of competitions for writer and style analysis of historical document images. In particular, we investigate the performance of large-scale retrieval of historical document fragments in terms of style and writer identification. The analysis of historic fragments is a difficult challenge commonly solved by trained humanists. In comparison to previous competitions, we make the results more meaningful by addressing the issue of sample granularity and moving from writer to page fragment retrieval. The two approaches, style and author identification, provide information on what kind of information each method makes better use of and indirectly contribute to the interpretability of the participating method. Therefore, we created a large dataset consisting of more than 120 000 fragments. Although the most teams submitted methods based on convolutional neural networks, the winning entry achieves an mAP below 40%.

cs.CV↗

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.

eess.IV↗

arXiv2020

Graph convolutional regression of cardiac depolarization from sparse endocardial maps

Electroanatomic mapping as routinely acquired in ablation therapy of ventricular tachycardia is the gold standard method to identify the arrhythmogenic substrate. To reduce the acquisition time and still provide maps with high spatial resolution, we propose a novel deep learning method based on graph convolutional neural networks to estimate the depolarization time in the myocardium, given sparse catheter data on the left ventricular endocardium, ECG, and magnetic resonance images. The training set consists of data produced by a computational model of cardiac electrophysiology on a large cohort of synthetically generated geometries of ischemic hearts. The predicted depolarization pattern has good agreement with activation times computed by the cardiac electrophysiology model in a validation set of five swine heart geometries with complex scar and border zone morphologies. The mean absolute error hereby measures 8 ms on the entire myocardium when providing 50\% of the endocardial ground truth in over 500 computed depolarization patterns. Furthermore, when considering a complete animal data set with high density electroanatomic mapping data as reference, the neural network can accurately reproduce the endocardial depolarization pattern, even when a small percentage of measurements are provided as input features (mean absolute error of 7 ms with 50\% of input samples). The results show that the proposed method, trained on synthetically generated data, may generalize to real data.

physics.med-ph↗