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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DockVis: Visual Analysis of Molecular Docking Data
(The Eurographics Association, 2019) Furmanová, Katarína; Kozlíková, Barbora; Vonásek, Vojtěch; Byška, Jan; Kozlíková, Barbora and Linsen, Lars and Vázquez, Pere-Pau and Lawonn, Kai and Raidou, Renata Georgia
Molecular docking is one of the key mechanisms for predicting possible interactions between ligands and proteins. This highly complex task can be simulated by several software tools, providing the biochemists with possible ligand trajectories, which have to be subsequently explored and evaluated for their biochemical relevance. This paper focuses on aiding this exploration process by introducing DockVis visual analysis tool. DockVis operates primarily with the multivariate output data from one of the latest available tools for molecular docking, CaverDock. CaverDock output consists of several parameters and properties, which have to be subsequently studied and understood. DockVis was designed in tight collaboration with protein engineers using the CaverDock tool. However, we believe that the concept of DockVis can be extended to any other molecular docking tool providing the users with corresponding computation results.
Evolutionary Pathlines for Blood Flow Exploration in Cerebral Aneurysms
(The Eurographics Association, 2019) Behrendt, Benjamin; Engelke, Wito; Berg, Philipp; Beuing, Oliver; Preim, Bernhard; Hotz, Ingrid; Saalfeld, Sylvia; Kozlíková, Barbora and Linsen, Lars and Vázquez, Pere-Pau and Lawonn, Kai and Raidou, Renata Georgia
Blood flow simulations play an important role for the understanding of vascular diseases, such as aneurysms. However, analysis of the resulting flow patterns, especially comparisons across patient groups, are challenging. Typically, the hemodynamic analysis relies on trial and error inspection of the flow data based on pathline visualizations and surface renderings. Visualizing too many pathlines at once may obstruct interesting features, e.g., embedded vortices, whereas with too little pathlines, particularities such as flow characteristics in aneurysm blebs might be missed. While filtering and clustering techniques support this task, they require the pre-computation of pathlines densely sampled in the space-time domain. Not only does this become prohibitively expensive for large patient groups, but the results often suffer from undersampling artifacts. In this work, we propose the usage of evolutionary algorithms to reduce the overhead of computing pathlines that do not contribute to the analysis, while simultaneously reducing the undersampling artifacts. Integrated in an interactive framework, it efficiently supports the evaluation of hemodynamics for clinical research and treatment planning in case of cerebral aneurysms. The specification of general optimization criteria for entire patient groups allows the blood flow data to be batch-processed. We present clinical cases to demonstrate the benefits of our approach especially in presence of aneurysm blebs. Furthermore, we conducted an evaluation with four expert neuroradiologists. As a result, we report advantages of our method for treatment planning to underpin its clinical potential.
Hybrid Visualization of Protein-Lipid and Protein-Protein Interaction
(The Eurographics Association, 2019) Alharbi, Naif; Krone, Michael; Chavent, Matthieu; Laramee, Robert S.; Kozlíková, Barbora and Linsen, Lars and Vázquez, Pere-Pau and Lawonn, Kai and Raidou, Renata Georgia
In the Molecular Dynamics (MD) visualization literature, different approaches are utilized to study protein-lipid interactions (PLI) and protein-protein interaction (PPI) in decoupled contexts. However, the two types of interaction occur in the same space-time domain. It is beneficial to study the PLI and PPI in a unified context. Nevertheless, the simulation's size, length, and complexity increase the challenge of understanding the dynamic behavior. We propose a novel framework consisting of four linked views, a time-dependent 3D view, a novel hybrid view, a clustering timeline, and a details-on-demand window. We introduce a selection of visual designs to convey the behavior of PLI and PPI through a unified coordinate system. Abstraction is used to present proteins in hybrid 2D space, a projected tiled space is used to present both PLI and PPI at the particle level in a heat-map style visual design while glyphs are used to represent PPI at the molecular level. We couple visually separable visual designs in a unified coordinate space. The result lets the user study both PLI and PPI separately or together in a unified visual analysis framework. We also exemplify its use with case studies focusing on protein clustering and we report domain expert feedback.
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.
Interactive Exploded Views for Molecular Structures
(The Eurographics Association, 2019) Sbardellati, Maximilian; Miao, Haichao; WU, Hsiang-Yun; Groeller, Eduard; Barisic, Ivan; Viola, Ivan; Kozlíková, Barbora and Linsen, Lars and Vázquez, Pere-Pau and Lawonn, Kai and Raidou, Renata Georgia
We propose an approach to interactively create exploded views of molecular structures with the goal to help domain experts in their design process and provide them with a meaningful visual representation of component relationships. Exploded views are excellently suited to manage visual occlusion of structure components, which is one of the main challenges when visualizing complex 3D data. In this paper, we discuss four key parameters of an exploded view: explosion distance, direction, order, and the selection of explosion components. We propose two strategies, namely the structure-derived exploded view and the interactive free-form exploded view, for computing these four parameters systematically. The first strategy allows scientists to automatically create exploded views by computing the parameters from the given object structures. The second strategy further supports them to design and customize detailed explosion paths through user interaction. Our approach features the possibility to animate exploded views, to incorporate ease functions into these animations and to display the explosion path of components via arrows. Finally, we demonstrate three use cases with various challenges that we investigated in collaboration with a domain scientist. Our approach, therefore, provides interesting new ways of investigating and presenting the design layout and composition of complex molecular structures.
Layer-Aware iOCT Volume Rendering for Retinal Surgery
(The Eurographics Association, 2019) Weiss, Jakob; Eck, Ulrich; Nasseri, Muhamad Ali; Maier, Mathias; Eslami, Abouzar; Navab, Nassir; Kozlíková, Barbora and Linsen, Lars and Vázquez, Pere-Pau and Lawonn, Kai and Raidou, Renata Georgia
Retinal microsurgery is one of the most challenging types of surgery, yet in practice, intraoperative digital assistance is rare. The introduction of fast, microscope integrated Optical Coherence Tomography (iOCT) has enabled intraoperative imaging of subsurface structures. However, effective intraoperative visualization of this data poses a challenging problem both in terms of performance and engineering as well as for creating easily interpretable visualizations of this data. Most existing research focuses on visualization of diagnostic OCT data where imaging quality is higher and processing times are not an issue. We introduce a perceptually linear color map for a separated encoding of tissue reflectivity and positional information as chrominance and luminance. Based on this color mapping, we propose a Direct Volume Rendering (DVR) method that aids structure perception. To aid subretinal injection tasks, we introduce a novel Layer-Adjusted Maximum Intensity Projection (LA-MIP), correcting for the natural curvature of the retinal tissue. Expert feedback suggests our methods are preferred over baseline methods. Further research is needed to confirm the benefits of our approach in routine clinical applications.
MedUse: A Visual Analysis Tool for Medication Use Data in the ABCD Study
(The Eurographics Association, 2019) Bartsch, Hauke; Garrison, Laura; Bruckner, Stefan; Wang, Ariel; Tapert, Susan F.; Grüner, Renate; Kozlíková, Barbora and Linsen, Lars and Vázquez, Pere-Pau and Lawonn, Kai and Raidou, Renata Georgia
The RxNorm vocabulary is a yearly-published biomedical resource providing normalized names for medications. It is used to capture medication use in the Adolescent Brain Cognitive Development (ABCD) study, an active and publicly available longitudinal research study following 11,800 children over 10 years. In this work, we present medUse, a visual tool allowing researchers to explore and analyze the relationship of drug category to cognitive or imaging derived measures using ABCD study data. Our tool provides position-based context for tree traversal and selection granularity of both study participants and drug category. Developed as part of the Data Exploration and Analysis Portal (DEAP), medUse is available to more than 600 ABCD researchers world-wide. By integrating medUse into an actively used research product we are able to reach a wide audience and increase the practical relevance of visualization for the biomedical field.
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.
Robustness Evaluation of CFD Simulations to Mesh Deformation
(The Eurographics Association, 2019) Scheid-Rehder, Alexander; Lawonn, Kai; Meuschke, Monique; Kozlíková, Barbora and Linsen, Lars and Vázquez, Pere-Pau and Lawonn, Kai and Raidou, Renata Georgia
CFD simulations are an increasingly important method for the non-invasive analysis of risk factors for aneurysm rupture. Their robustness, however, has to be examined more thoroughly before clinical use is possible. We present a novel framework that enables robustness evaluation of CFD simulation according to mesh deformation on patient-specific blood vessel geometry. Our tool offers a guided workflow to generate, run, and visualize OpenFOAM simulations, which significantly decreases the usual overhead of CFD simulations with OpenFOAM. Besides, the deformation of the original geometry allows the user to evaluate the robustness of the simulation without the need to repeat expensive operations of the data pre-processing phase. We assessed the robustness of CFD simulations by applying our framework to several aneurysm data sets.
SpectraMosaic: An Exploratory Tool for the Interactive Visual Analysis of Magnetic Resonance Spectroscopy Data
(The Eurographics Association, 2019) Garrison, Laura; Vašíček, Jakub; Grüner, Renate; Smit, Noeska N.; Bruckner, Stefan; Kozlíková, Barbora and Linsen, Lars and Vázquez, Pere-Pau and Lawonn, Kai and Raidou, Renata Georgia
Magnetic resonance spectroscopy (MRS) allows for assessment of tissue metabolite characteristics used often for early detection and treatment evaluation of brain-related pathologies. However, a steep learning curve for metabolite interpretation, paired with limited visualization tools, have constrained the more widespread adoption of MRS in clinical practice. In this design study, we collaborated with domain experts to design a novel visualization tool for the exploration of tissue metabolite concentration ratios in MRS clinical and research studies. We present a data and task analysis for this domain, with categorization of MRS data attributes into tiers of visual priority. We furthermore introduce a novel set of visual encodings for these attributes. Our result is SpectraMosaic (Figure 1), an interactive insight-generation tool for rapid exploration and comparison of metabolite ratios. We validate our approach with two case studies from MR spectroscopy experts, providing early qualitative evidence of the efficacy of the system and affording deeper insights into these complex data.
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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