VCBM 19: Eurographics Workshop on Visual Computing for Biology and Medicine

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https://diglib.eg.org/handle/10.2312/2632802

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InkVis: A High-Particle-Count Approach for Visualization of Phase-Contrast Magnetic Resonance Imaging Data
(The Eurographics Association, 2019) de Hoon, Niels; Lawonn, Kai; Jalba, Andrei; Eisemann, Elmar; Vilanova, Anna; Kozlíková, Barbora and Linsen, Lars and Vázquez, Pere-Pau and Lawonn, Kai and Raidou, Renata Georgia
Phase-Contrast Magnetic Resonance Imaging (PC-MRI) measures volumetric and time-varying blood flow data, unsurpassed in quality and completeness. Such blood-flow data have been shown to have the potential to improve both diagnosis and risk assessment of cardiovascular diseases (CVDs) uniquely. Typically PC-MRI data is visualized using stream- or pathlines. However, time-varying aspects of the data, e.g., vortex shedding, breakdown, and formation, are not sufficiently captured by these visualization techniques. Experimental flow visualization techniques introduce a visible medium, like smoke or dye, to visualize flow aspects including time-varying aspects. We propose a framework that mimics such experimental techniques by using a high number of particles. The framework offers great flexibility which allows for various visualization approaches. These include common traditional flow visualizations, but also streak visualizations to show the temporal aspects, and uncertainty visualizations. Moreover, these patient-specific measurements suffer from noise artifacts and a coarse resolution, causing uncertainty. Traditional flow visualizations neglect uncertainty and, therefore, may give a false sense of certainty, which can mislead the user yielding incorrect decisions. Previously, the domain experts had no means to visualize the effect of the uncertainty in the data. Our framework has been adopted by domain experts to visualize the vortices present in the sinuses of the aorta root showing the potential of the framework. Furthermore, an evaluation among domain experts indicated that having the option to visualize the uncertainty contributed to their confidence on the analysis.
Interactive CPU-based Ray Tracing of Solvent Excluded Surfaces
(The Eurographics Association, 2019) Rau, Tobias; Zahn, Sebastian; Krone, Michael; Reina, Guido; Ertl, Thomas; Kozlíková, Barbora and Linsen, Lars and Vázquez, Pere-Pau and Lawonn, Kai and Raidou, Renata Georgia
Depictions of molecular surfaces such as the Solvent Excluded Surface (SES) can provide crucial insight into functional molecular properties, such as the molecule's potential to react. The interactive visualization of single and multiple molecule surfaces is essential for the data analysis by domain experts. Nowadays, the SES can be rendered at high frame rates using shader-based ray casting on the GPU. However, rendering large molecules or larger molecule complexes requires large amounts of memory that has the potential to exceed the memory limitations of current hardware. Here we show that rendering using CPU ray tracing also reaches interactive frame rates without hard limitations to memory. In our results large molecule complexes can be rendered with only the precomputation of each individual SES, and no further involved representation or transformation. Additionally, we provide advanced visualization techniques like ambient occlusion opacity mapping (AOOM) to enhance the comprehensibility of the molecular structure. CPU ray tracing not only provides very high image quality and global illumination, which is beneficial for the perception of spatial structures, it also opens up the possibility to visualize larger data sets and to render on any HPC cluster. Our results demonstrate that simple instancing of geometry keeps the memory consumption for rendering large molecule complexes low, so the examination of much larger data is also possible.
Molecular Sombreros: Abstract Visualization of Binding Sites within Proteins
(The Eurographics Association, 2019) Schatz, Karsten; Krone, Michael; Bauer, Tabea L.; Ferrario, Valerio; Pleiss, Jürgen; Ertl, Thomas; Kozlíková, Barbora and Linsen, Lars and Vázquez, Pere-Pau and Lawonn, Kai and Raidou, Renata Georgia
We present a novel abstract visualization for the binding sites of proteins. Binding sites play an essential role in enzymatic reactions and are, thus, often investigated in structural biology. They are typically located within cavities. The shape and properties of the cavity influence whether and how easily a substrate can reach the active site where the reaction is triggered. Molecular surface visualizations can help to analyze the accessibility of binding sites, but are typically prone to visual clutter. Our novel abstract visualization shows the cavity containing the binding site as well as the surface region directly surrounding the cavity entrance in a simplified manner. The resulting visualization resembles a hat, where the brim depicts the surrounding surface region and the crown the cavity. Hence, we dubbed our abstraction Molecular Sombrero, using the Spanish term for 'hat'. Our abstraction is less cluttered than traditional molecular surface visualizations. It highlights important parameters, like cavity diameter, by mapping them to the shape of the sombrero. The visual abstraction also facilitates an easy side-by-side comparison of different data sets. We show the applicability of our Molecular Sombreros to different real-world use cases.
Using Position-Based Dynamics for Simulating the Mitral Valve in a Decision Support System
(The Eurographics Association, 2019) Walczak, Lars; Georgii, Joachim; Tautz, Lennart; Neugebauer, Mathias; Wamala, Isaac; Sündermann, Simon; Falk, Volkmar; Hennemuth, Anja; Kozlíková, Barbora and Linsen, Lars and Vázquez, Pere-Pau and Lawonn, Kai and Raidou, Renata Georgia
In mitral valve interventions, surgeons have to select an optimal combination of techniques for every patient. Especially less experienced physicians would benefit from decision support for this process. To support the visual analysis of the patientspecific valvular dynamics and an in-silico pre-intervention simulation of different therapy options, a real-time simulation of the mitral valve is needed, especially for the use in a time-constrained clinical environment. We develop a simplified model of the mitral valve and propose a novel approach to simulate the mitral valve with position-based dynamics. As input, a mesh representation of the open-state mitral valve, two polygons representing the open and closed annulus states, simplified chordae tendineae, and a set of forces for approximating the surrounding blood are required. The mitral valve model can be deformed to simulate the closing and opening as well as incorporate changes caused by virtual interventions in the simulation. For evaluation, ten mitral valves were reconstructed from transesophageal echocardiogram sequences of patients with normal and abnormal physiology. Experts in cardiac surgery annotated anatomical landmarks for valve reconstruction. The simulation results for closing the valve were qualitatively compared to the anatomy depicted in the image sequences and, if present, the reproduction of a prolapse was verified. In addition, two virtual interventions (annuloplasty and clipping) were performed for one case and provided new insights about changes in valve closure and orifice area after modification. Each simulation ran at interactive frame rates. Our approach enables an efficient simulation of the mitral valve with normal and abnormal valve closing behavior as well as virtual interventions. The simulation results showed good agreements with the image data in general and reproduced valve closure in all cases. In three cases, prolapse was not or not correctly reproduced. Further research is needed to parameterize the model in pathologic cases.
A Visual Environment for Hypothesis Formation and Reasoning in Studies with fMRI and Multivariate Clinical Data
(The Eurographics Association, 2019) Jönsson, Daniel; Bergström, Albin; Forsell, Camilla; Simon, Rozalyn; Engström, Maria; Ynnerman, Anders; Hotz, Ingrid; Kozlíková, Barbora and Linsen, Lars and Vázquez, Pere-Pau and Lawonn, Kai and Raidou, Renata Georgia
We present an interactive visual environment for linked analysis of brain imaging and clinical measurements. The environment is developed in an iterative participatory design process involving neuroscientists investigating the causes of brain-related complex diseases. The hypotheses formation process about correlations between active brain regions and physiological or psychological factors in studies with hundreds of subjects is a central part of the investigation. Observing the reasoning patterns during hypotheses formation, we concluded that while existing tools provide powerful analysis options, they lack effective interactive exploration, thus limiting the scientific scope and preventing extraction of knowledge from available data. Based on these observations, we designed methods that support neuroscientists by integrating their existing statistical analysis of multivariate subject data with interactive visual exploration to enable them to better understand differences between patient groups and the complex bidirectional interplay between clinical measurement and the brain. These exploration concepts enable neuroscientists, for the first time during their investigations, to interactively move between and reason about questions such as 'which clinical measurements are correlated with a specific brain region?' or 'are there differences in brain activity between depressed young and old subjects?'. The environment uses parallel coordinates for effective overview and selection of subject groups, Welch's t-test to filter out brain regions with statistically significant differences, and multiple visualizations of Pearson correlations between brain regions and clinical parameters to facilitate correlation analysis. A qualitative user study was performed with three neuroscientists from different domains. The study shows that the developed environment supports simultaneous analysis of more parameters, provides rapid pathways to insights, and is an effective support tool for hypothesis formation.
The Vitruvian Baby: Interactive Reformation of Fetal Ultrasound Data to a T-Position
(The Eurographics Association, 2019) Mörth, Eric; Raidou, Renata Georgia; Viola, Ivan; Smit, Noeska; Kozlíková, Barbora and Linsen, Lars and Vázquez, Pere-Pau and Lawonn, Kai and Raidou, Renata Georgia
Three-dimensional (3D) ultrasound imaging and visualization is often used in medical diagnostics, especially in prenatal screening. Screening the development of the fetus is important to assess possible complications early on. State of the art approaches involve taking standardized measurements to compare them with standardized tables. The measurements are taken in a 2D slice view, where precise measurements can be difficult to acquire due to the fetal pose. Performing the analysis in a 3D view would enable the viewer to better discriminate between artefacts and representative information. Additionally making data comparable between different investigations and patients is a goal in medical imaging techniques and is often achieved by standardization. With this paper, we introduce a novel approach to provide a standardization method for 3D ultrasound fetus screenings. Our approach is called ''The Vitruvian Baby'' and incorporates a complete pipeline for standardized measuring in fetal 3D ultrasound. The input of the method is a 3D ultrasound screening of a fetus and the output is the fetus in a standardized T-pose. In this pose, taking measurements is easier and comparison of different fetuses is possible. In addition to the transformation of the 3D ultrasound data, we create an abstract representation of the fetus based on accurate measurements. We demonstrate the accuracy of our approach on simulated data where the ground truth is known.

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