Automated cross-sectional view selection in CT angiography of aortic dissections with uncertainty awareness and retrospective clinical annotations.

Surveillance imaging of patients with chronic aortic diseases, such as aneurysms and dissections, relies on obtaining and comparing cross-sectional diameter measurements along the aorta at predefined aortic landmarks, over time. The orientation of the cross-sectional measuring planes at each landmark is currently defined manually by highly trained operators. Centerline-based approaches are unreliable in patients with chronic aortic dissection, because of the asymmetric flow channels, differences in contrast opacification, and presence of mural thrombus, making centerline computations or measurements difficult to generate and reproduce. In this work, we present three alternative approaches - INS, MCDS, MCDbS - based on convolutional neural networks and uncertainty quantification methods to predict the orientation (ϕ,θ) of such cross-sectional planes. For the monitoring of chronic aortic dissections, we show how a dataset of 162 CTA volumes with overall 3273 imperfect manual annotations routinely collected in a clinic can be efficiently used to accomplish this task, despite the presence of non-negligible interoperator variabilities in terms of mean absolute error (MAE) and 95% limits of agreement (LOA). We show how, despite the large limits of agreement in the training data, the trained model provides faster and more reproducible results than either an expert user or a centerline method. The remaining disagreement lies within the variability produced by three independent expert annotators and matches the current state of the art, providing a similar error, but in a fraction of the time.

Enzyme activity profiling for physiological phenotyping within functional phenomics: plant growth and stress responses.

High-throughput profiling of key enzyme activities of carbon, nitrogen, and antioxidant metabolism is emerging as a valuable approach to integrate cell physiological phenotyping into a holistic functional phenomics approach. However, the analyses of the large datasets generated by this method represent a bottleneck, often keeping researchers from exploiting the full potential of their studies. We address these limitations through the exemplary application of a set of data evaluation and visualization tools within a case study. This includes the introduction of multivariate statistical analyses that can easily be implemented in similar studies, allowing researchers to extract more valuable information to identify enzymatic biosignatures. Through a literature meta-analysis, we demonstrate how enzyme activity profiling has already provided functional information on the mechanisms regulating plant development and response mechanisms to abiotic stress and pathogen attack. The high robustness of the distinct enzymatic biosignatures observed during developmental processes and under stress conditions underpins the enormous potential of enzyme activity profiling for future applications in both basic and applied research. Enzyme activity profiling will complement molecular -omics approaches to contribute to the mechanistic understanding required to narrow the genotype-to-phenotype knowledge gap and to identify predictive biomarkers for plant breeding to develop climate-resilient crops.

Critical Aspects of Person Counting and Density Estimation.

Many scientific studies deal with person counting and density estimation from single images. Recently, convolutional neural networks (CNNs) have been applied for these tasks. Even though often better results are reported, it is often not clear where the improvements are resulting from, and if the proposed approaches would generalize. Thus, the main goal of this paper was to identify the critical aspects of these tasks and to show how these limit state-of-the-art approaches. Based on these findings, we show how to mitigate these limitations. To this end, we implemented a CNN-based baseline approach, which we extended to deal with identified problems. These include the discovery of bias in the reference data sets, ambiguity in ground truth generation, and mismatching of evaluation metrics w.r.t. the training loss function. The experimental results show that our modifications allow for significantly outperforming the baseline in terms of the accuracy of person counts and density estimation. In this way, we get a deeper understanding of CNN-based person density estimation beyond the network architecture. Furthermore, our insights would allow to advance the field of person density estimation in general by highlighting current limitations in the evaluation protocols.

A Geometric Perspective on Information Plane Analysis.

Information plane analysis, describing the mutual information between the input and a hidden layer and between a hidden layer and the target over time, has recently been proposed to analyze the training of neural networks. Since the activations of a hidden layer are typically continuous-valued, this mutual information cannot be computed analytically and must thus be estimated, resulting in apparently inconsistent or even contradicting results in the literature. The goal of this paper is to demonstrate how information plane analysis can still be a valuable tool for analyzing neural network training. To this end, we complement the prevailing binning estimator for mutual information with a geometric interpretation. With this geometric interpretation in mind, we evaluate the impact of regularization and interpret phenomena such as underfitting and overfitting. In addition, we investigate neural network learning in the presence of noisy data and noisy labels.

Biomedical image augmentation using Augmentor.

MOTIVATION: Image augmentation is a frequently used technique in computer vision and has been seeing increased interest since the popularity of deep learning. Its usefulness is becoming more and more recognized due to deep neural networks requiring larger amounts of data to train, and because in certain fields, such as biomedical imaging, large amounts of labelled data are difficult to come by or expensive to produce. In biomedical imaging, features specific to this domain need to be addressed. RESULTS: Here we present the Augmentor software package for image augmentation. It provides a stochastic, pipeline-based approach to image augmentation with a number of features that are relevant to biomedical imaging, such as z-stack augmentation and randomized elastic distortions. The software has been designed to be highly extensible meaning an operation that might be specific to a highly specialized task can easily be added to the library, even at runtime. Although it has been designed as a general software library, it has features that are particularly relevant to biomedical imaging and the techniques required for this domain. AVAILABILITY AND IMPLEMENTATION: Augmentor is a Python package made available under the terms of the MIT licence. Source code can be found on GitHub under https://github.com/mdbloice/Augmentor and installation is via the pip package manager (A Julia version of the package, developed in parallel by Christof Stocker, is also available under https://github.com/Evizero/Augmentor.jl).

Exploit fully automatic low-level segmented PET data for training high-level deep learning algorithms for the corresponding CT data.

We present an approach for fully automatic urinary bladder segmentation in CT images with artificial neural networks in this study. Automatic medical image analysis has become an invaluable tool in the different treatment stages of diseases. Especially medical image segmentation plays a vital role, since segmentation is often the initial step in an image analysis pipeline. Since deep neural networks have made a large impact on the field of image processing in the past years, we use two different deep learning architectures to segment the urinary bladder. Both of these architectures are based on pre-trained classification networks that are adapted to perform semantic segmentation. Since deep neural networks require a large amount of training data, specifically images and corresponding ground truth labels, we furthermore propose a method to generate such a suitable training data set from Positron Emission Tomography/Computed Tomography image data. This is done by applying thresholding to the Positron Emission Tomography data for obtaining a ground truth and by utilizing data augmentation to enlarge the dataset. In this study, we discuss the influence of data augmentation on the segmentation results, and compare and evaluate the proposed architectures in terms of qualitative and quantitative segmentation performance. The results presented in this study allow concluding that deep neural networks can be considered a promising approach to segment the urinary bladder in CT images.