arXiv subjects

Andreas Maier

Publications and source records attributed to Andreas Maier.

At least 433 records · Page 24Linked to original sources

arXiv2019

Learning New Tricks from Old Dogs -- Inter-Species, Inter-Tissue Domain Adaptation for Mitotic Figure Assessment

For histopathological tumor assessment, the count of mitotic figures per area is an important part of prognostication. Algorithmic approaches - such as for mitotic figure identification - have significantly improved in recent times, potentially allowing for computer-augmented or fully automatic screening systems in the future. This trend is further supported by whole slide scanning microscopes becoming available in many pathology labs and could soon become a standard imaging tool. For an application in broader fields of such algorithms, the availability of mitotic figure data sets of sufficient size for the respective tissue type and species is an important precondition, that is, however, rarely met. While algorithmic performance climbed steadily for e.g. human mammary carcinoma, thanks to several challenges held in the field, for most tumor types, data sets are not available. In this work, we assess domain transfer of mitotic figure recognition using domain adversarial training on four data sets, two from dogs and two from humans. We were able to show that domain adversarial training considerably improves accuracy when applying mitotic figure classification learned from the canine on the human data sets (up to +12.8% in accuracy) and is thus a helpful method to transfer knowledge from existing data sets to new tissue types and species.

cs.CV↗

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.

eess.IV↗

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.

eess.IV↗

arXiv2019

Superpixel-Based Background Recovery from Multiple Images

In this paper, we propose an intuitive method to recover background from multiple images. The implementation consists of three stages: model initialization, model update, and background output. We consider the pixels whose values change little in all input images as background seeds. Images are then segmented into superpixels with simple linear iterative clustering. When the number of pixels labelled as background in a superpixel is bigger than a predefined threshold, we label the superpixel as background to initialize the background candidate masks. Background candidate images are obtained from input raw images with the masks. Combining all candidate images, a background image is produced. The background candidate masks, candidate images, and the background image are then updated alternately until convergence. Finally, ghosting artifacts is removed with the k-nearest neighbour method. An experiment on an outdoor dataset demonstrates that the proposed algorithm can achieve promising results.

cs.CV↗

arXiv2019

Learning to Avoid Poor Images: Towards Task-aware C-arm Cone-beam CT Trajectories

Metal artifacts in computed tomography (CT) arise from a mismatch between physics of image formation and idealized assumptions during tomographic reconstruction. These artifacts are particularly strong around metal implants, inhibiting widespread adoption of 3D cone-beam CT (CBCT) despite clear opportunity for intra-operative verification of implant positioning, e.g. in spinal fusion surgery. On synthetic and real data, we demonstrate that much of the artifact can be avoided by acquiring better data for reconstruction in a task-aware and patient-specific manner, and describe the first step towards the envisioned task-aware CBCT protocol. The traditional short-scan CBCT trajectory is planar, with little room for scene-specific adjustment. We extend this trajectory by autonomously adjusting out-of-plane angulation. This enables C-arm source trajectories that are scene-specific in that they avoid acquiring "poor images", characterized by beam hardening, photon starvation, and noise. The recommendation of ideal out-of-plane angulation is performed on-the-fly using a deep convolutional neural network that regresses a detectability-rank derived from imaging physics.

eess.IV↗

arXiv2019

Magnetic Resonance Fingerprinting Reconstruction Using Recurrent Neural Networks

Magnetic Resonance Fingerprinting (MRF) is an imaging technique acquiring unique time signals for different tissues. Although the acquisition is highly accelerated, the reconstruction time remains a problem, as the state-of-the-art template matching compares every signal with a set of possible signals. To overcome this limitation, deep learning based approaches, e.g. Convolutional Neural Networks (CNNs) have been proposed. In this work, we investigate the applicability of Recurrent Neural Networks (RNNs) for this reconstruction problem, as the signals are correlated in time. Compared to previous methods based on CNNs, RNN models yield significantly improved results using in-vivo data.

eess.IV↗

arXiv2019

A Semi-Automated Usability Evaluation Framework for Interactive Image Segmentation Systems

For complex segmentation tasks, the achievable accuracy of fully automated systems is inherently limited. Specifically, when a precise segmentation result is desired for a small amount of given data sets, semi-automatic methods exhibit a clear benefit for the user. The optimization of human computer interaction (HCI) is an essential part of interactive image segmentation. Nevertheless, publications introducing novel interactive segmentation systems (ISS) often lack an objective comparison of HCI aspects. It is demonstrated, that even when the underlying segmentation algorithm is the same throughout interactive prototypes, their user experience may vary substantially. As a result, users prefer simple interfaces as well as a considerable degree of freedom to control each iterative step of the segmentation. In this article, an objective method for the comparison of ISS is proposed, based on extensive user studies. A summative qualitative content analysis is conducted via abstraction of visual and verbal feedback given by the participants. A direct assessment of the segmentation system is executed by the users via the system usability scale (SUS) and AttrakDiff-2 questionnaires. Furthermore, an approximation of the findings regarding usability aspects in those studies is introduced, conducted solely from the system-measurable user actions during their usage of interactive segmentation prototypes. The prediction of all questionnaire results has an average relative error of 8.9%, which is close to the expected precision of the questionnaire results themselves. This automated evaluation scheme may significantly reduce the resources necessary to investigate each variation of a prototype's user interface (UI) features and segmentation methodologies.

cs.HC↗

arXiv2019

Data Consistent Artifact Reduction for Limited Angle Tomography with Deep Learning Prior

Robustness of deep learning methods for limited angle tomography is challenged by two major factors: a) due to insufficient training data the network may not generalize well to unseen data; b) deep learning methods are sensitive to noise. Thus, generating reconstructed images directly from a neural network appears inadequate. We propose to constrain the reconstructed images to be consistent with the measured projection data, while the unmeasured information is complemented by learning based methods. For this purpose, a data consistent artifact reduction (DCAR) method is introduced: First, a prior image is generated from an initial limited angle reconstruction via deep learning as a substitute for missing information. Afterwards, a conventional iterative reconstruction algorithm is applied, integrating the data consistency in the measured angular range and the prior information in the missing angular range. This ensures data integrity in the measured area, while inaccuracies incorporated by the deep learning prior lie only in areas where no information is acquired. The proposed DCAR method achieves significant image quality improvement: for 120-degree cone-beam limited angle tomography more than 10% RMSE reduction in noise-free case and more than 24% RMSE reduction in noisy case compared with a state-of-the-art U-Net based method.

eess.IV↗

arXiv2019

Automated Multi-sequence Cardiac MRI Segmentation Using Supervised Domain Adaptation

Left ventricle segmentation and morphological assessment are essential for improving diagnosis and our understanding of cardiomyopathy, which in turn is imperative for reducing risk of myocardial infarctions in patients. Convolutional neural network (CNN) based methods for cardiac magnetic resonance (CMR) image segmentation rely on supervision with pixel-level annotations, and may not generalize well to images from a different domain. These methods are typically sensitive to variations in imaging protocols and data acquisition. Since annotating multi-sequence CMR images is tedious and subject to inter- and intra-observer variations, developing methods that can automatically adapt from one domain to the target domain is of great interest. In this paper, we propose an approach for domain adaptation in multi-sequence CMR segmentation task using transfer learning that combines multi-source image information. We first train an encoder-decoder CNN on T2-weighted and balanced-Steady State Free Precession (bSSFP) MR images with pixel-level annotation and fine-tune the same network with a limited number of Late Gadolinium Enhanced-MR (LGE-MR) subjects, to adapt the domain features. The domain-adapted network was trained with just four LGE-MR training samples and obtained an average Dice score of $\sim$85.0\% on the test set comprises of 40 LGE-MR subjects. The proposed method significantly outperformed a network without adaptation trained from scratch on the same set of LGE-MR training data.

eess.IV↗

arXiv2019

Deep Learning-Based Quantification of Pulmonary Hemosiderophages in Cytology Slides

Purpose: Exercise-induced pulmonary hemorrhage (EIPH) is a common syndrome 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. Methods: 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. Resultsf: Our deep learning-based approach reached a concordance of 0.85, partially exceeding human expert concordance (0.68 to 0.86, $μ$=0.73, $σ$ =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. Conclusion: 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.

eess.IV↗

arXiv2019

Top quark mass effects in $gg\to ZZ$ at two loops and off-shell Higgs interference

We consider top-quark mass effects in the Higgs-interference contribution to $Z$-boson pair production in gluon fusion. While this production mechanism is formally of next-to-next-to leading order, its contribution is numerically important above the top threshold $M_{ZZ}^2=4m_t^2$. This region is essential to constrain the width of the Higgs boson and good control over the top-quark mass dependence is crucial. We determine the form factors that are relevant for the interference contribution at two-loop order using a method based on a conformal mapping and Padé approximants constructed from the expansions of the amplitude for large top mass and around the top threshold.

hep-ph↗

arXiv2019

Multi-task Localization and Segmentation for X-ray Guided Planning in Knee Surgery

X-ray based measurement and guidance are commonly used tools in orthopaedic surgery to facilitate a minimally invasive workflow. Typically, a surgical planning is first performed using knowledge of bone morphology and anatomical landmarks. Information about bone location then serves as a prior for registration during overlay of the planning on intra-operative X-ray images. Performing these steps manually however is prone to intra-rater/inter-rater variability and increases task complexity for the surgeon. To remedy these issues, we propose an automatic framework for planning and subsequent overlay. We evaluate it on the example of femoral drill site planning for medial patellofemoral ligament reconstruction surgery. A deep multi-task stacked hourglass network is trained on 149 conventional lateral X-ray images to jointly localize two femoral landmarks, to predict a region of interest for the posterior femoral cortex tangent line, and to perform semantic segmentation of the femur, patella, tibia, and fibula with adaptive task complexity weighting. On 38 clinical test images the framework achieves a median localization error of 1.50 mm for the femoral drill site and mean IOU scores of 0.99, 0.97, 0.98, and 0.96 for the femur, patella, tibia, and fibula respectively. The demonstrated approach consistently performs surgical planning at expert-level precision without the need for manual correction.

eess.IV↗

arXiv2019

RinQ Fingerprinting: Recurrence-informed Quantile Networks for Magnetic Resonance Fingerprinting

Recently, Magnetic Resonance Fingerprinting (MRF) was proposed as a quantitative imaging technique for the simultaneous acquisition of tissue parameters such as relaxation times $T_1$ and $T_2$. Although the acquisition is highly accelerated, the state-of-the-art reconstruction suffers from long computation times: Template matching methods are used to find the most similar signal to the measured one by comparing it to pre-simulated signals of possible parameter combinations in a discretized dictionary. Deep learning approaches can overcome this limitation, by providing the direct mapping from the measured signal to the underlying parameters by one forward pass through a network. In this work, we propose a Recurrent Neural Network (RNN) architecture in combination with a novel quantile layer. RNNs are well suited for the processing of time-dependent signals and the quantile layer helps to overcome the noisy outliers by considering the spatial neighbors of the signal. We evaluate our approach using in-vivo data from multiple brain slices and several volunteers, running various experiments. We show that the RNN approach with small patches of complex-valued input signals in combination with a quantile layer outperforms other architectures, e.g. previously proposed CNNs for the MRF reconstruction reducing the error in $T_1$ and $T_2$ by more than 80%.

eess.IV↗

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

Analysis by Adversarial Synthesis -- A Novel Approach for Speech Vocoding

Classical parametric speech coding techniques provide a compact representation for speech signals. This affords a very low transmission rate but with a reduced perceptual quality of the reconstructed signals. Recently, autoregressive deep generative models such as WaveNet and SampleRNN have been used as speech vocoders to scale up the perceptual quality of the reconstructed signals without increasing the coding rate. However, such models suffer from a very slow signal generation mechanism due to their sample-by-sample modelling approach. In this work, we introduce a new methodology for neural speech vocoding based on generative adversarial networks (GANs). A fake speech signal is generated from a very compressed representation of the glottal excitation using conditional GANs as a deep generative model. This fake speech is then refined using the LPC parameters of the original speech signal to obtain a natural reconstruction. The reconstructed speech waveforms based on this approach show a higher perceptual quality than the classical vocoder counterparts according to subjective and objective evaluation scores for a dataset of 30 male and female speakers. Moreover, the usage of GANs enables to generate signals in one-shot compared to autoregressive generative models. This makes GANs promising for exploration to implement high-quality neural vocoders.

eess.AS↗

arXiv2019

Toward Bridging the Simulated-to-Real Gap: Benchmarking Super-Resolution on Real Data

Capturing ground truth data to benchmark super-resolution (SR) is challenging. Therefore, current quantitative studies are mainly evaluated on simulated data artificially sampled from ground truth images. We argue that such evaluations overestimate the actual performance of SR methods compared to their behavior on real images. Toward bridging this simulated-to-real gap, we introduce the Super-Resolution Erlangen (SupER) database, the first comprehensive laboratory SR database of all-real acquisitions with pixel-wise ground truth. It consists of more than 80k images of 14 scenes combining different facets: CMOS sensor noise, real sampling at four resolution levels, nine scene motion types, two photometric conditions, and lossy video coding at five levels. As such, the database exceeds existing benchmarks by an order of magnitude in quality and quantity. This paper also benchmarks 19 popular single-image and multi-frame algorithms on our data. The benchmark comprises a quantitative study by exploiting ground truth data and qualitative evaluations in a large-scale observer study. We also rigorously investigate agreements between both evaluations from a statistical perspective. One interesting result is that top-performing methods on simulated data may be surpassed by others on real data. Our insights can spur further algorithm development, and the publicy available dataset can foster future evaluations.

cs.CV↗

arXiv2019

A 2D dilated residual U-Net for multi-organ segmentation in thoracic CT

Automatic segmentation of organs-at-risk (OAR) in computed tomography (CT) is an essential part of planning effective treatment strategies to combat lung and esophageal cancer. Accurate segmentation of organs surrounding tumours helps account for the variation in position and morphology inherent across patients, thereby facilitating adaptive and computer-assisted radiotherapy. Although manual delineation of OARs is still highly prevalent, it is prone to errors due to complex variations in the shape and position of organs across patients, and low soft tissue contrast between neighbouring organs in CT images. Recently, deep convolutional neural networks (CNNs) have gained tremendous traction and achieved state-of-the-art results in medical image segmentation. In this paper, we propose a deep learning framework to segment OARs in thoracic CT images, specifically for the: heart, esophagus, trachea and aorta. Our approach employs dilated convolutions and aggregated residual connections in the bottleneck of a U-Net styled network, which incorporates global context and dense information. Our method achieved an overall Dice score of 91.57% on 20 unseen test samples from the ISBI 2019 SegTHOR challenge.

cs.CV↗

arXiv2019

Multi-task Learning for Chest X-ray Abnormality Classification on Noisy Labels

Chest X-ray (CXR) is the most common X-ray examination performed in daily clinical practice for the diagnosis of various heart and lung abnormalities. The large amount of data to be read and reported, with 100+ studies per day for a single radiologist, poses a challenge in maintaining consistently high interpretation accuracy. In this work, we propose a method for the classification of different abnormalities based on CXR scans of the human body. The system is based on a novel multi-task deep learning architecture that in addition to the abnormality classification, supports the segmentation of the lungs and heart and classification of regions where the abnormality is located. We demonstrate that by training these tasks concurrently, one can increase the classification performance of the model. Experiments were performed on an extensive collection of 297,541 chest X-ray images from 86,876 patients, leading to a state-of-the-art performance level of 0.883 AUC on average for 12 different abnormalities. We also conducted a detailed performance analysis and compared the accuracy of our system with 3 board-certified radiologists. In this context, we highlight the high level of label noise inherent to this problem. On a reduced subset containing only cases with high confidence reference labels based on the consensus of the 3 radiologists, our system reached an average AUC of 0.945.

cs.CV↗