Eurovis: Eurographics Conference on Visualization

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https://diglib.eg.org/handle/10.2312/392

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AmniVis - A System for Qualitative Exploration of Near-Wall Hemodynamics in Cerebral Aneurysms
(The Eurographics Association and Blackwell Publishing Ltd., 2013) Neugebauer, Mathias; Lawonn, Kai; Beuing, Oliver; Berg, Philipp; Janiga, Gabor; Preim, Bernhard; B. Preim, P. Rheingans, and H. Theisel
The qualitative exploration of near-wall hemodynamics in cerebral aneurysms provides important insights for risk assessment. For instance, a direct relation between complex flow patterns and aneurysm formation could be observed. Due to the high complexity of the underlying time-dependent flow data, the exploration is challenging, in particular for medical researchers not familiar with such data. We present the AmniVis-Explorer, a system that is designed for the preparation of a qualitative medical study. The provided features were developed in close collaboration with medical researchers involved in the study. This comprises methods for a purposeful selection of surface regions of interest and a novel approach to provide a 2D overview of flow patterns that are represented by streamlines at these regions. Furthermore, we present a specialized interface that supports binary classification of patterns and temporal exploration as well as methods for selection, highlighting and automatic 3D navigation to particular patterns. Based on eight representative datasets, we conducted informal interviews with two bordcertified radiologists and a flow expert to evaluate the system. It was confirmed that the AmniVis-Explorer allows for an easy selection, qualitative exploration and classification of near-wall flow patterns that are represented by streamlines.
Anatomy-Guided Multi-Level Exploration of Blood Flow in Cerebral Aneurysms
(The Eurographics Association and Blackwell Publishing Ltd., 2011) Neugebauer, Mathias; Janiga, Gabor; Beuing, Oliver; Skalej, Martin; Preim, Bernhard; H. Hauser, H. Pfister, and J. J. van Wijk
For cerebral aneurysms, the ostium, the area of inflow, is an important anatomic landmark, since it separates the pathological vessel deformation from the healthy parent vessel. A better understanding of the inflow characteristics, the flow inside the aneurysm and the overall change of pre- and post-aneurysm flow in the parent vessel provide insights for medical research and the development of new risk-reduced treatment options. We present an approach for a qualitative, visual flow exploration that incorporates the ostium and derived anatomical landmarks. It is divided into three scopes: a global scope for exploration of the in- and outflow, an ostium scope that provides characteristics of the flow profile close to the ostium and a local scope for a detailed exploration of the flow in the parent vessel and the aneurysm. The approach was applied to five representative datasets, including measured and simulated blood flow. Informal interviews with two board-certified radiologists confirmed the usefulness of the provided exploration tools and delivered input for the integration of the ostium-based flow analysis into the overall exploration workflow.
Cell Lineage Visualisation
(The Eurographics Association and John Wiley & Sons Ltd., 2015) Pretorius, A. Johannes; Khan, Imtiaz A.; Errington, Rachel J.; H. Carr, K.-L. Ma, and G. Santucci
Cell lineages describe the developmental history of cell populations and are produced by combining time-lapse imaging and image processing. Biomedical researchers study cell lineages to understand fundamental processes such as cell differentiation and the pharmacodynamic action of anticancer agents. Yet, the interpretation of cell lineages is hindered by their complexity and insufficient capacity for visual analysis. We present a novel approach for interactive visualisation of cell lineages. Based on an understanding of cellular biology and live-cell imaging methodology, we identify three requirements: multimodality (cell lineages combine spatial, temporal, and other properties), symmetry (related to lineage branching structure), and synchrony (related to temporal alignment of cellular events). We address these by combining visual summaries of the spatiotemporal behaviour of an arbitrary number of lineages, including variation from average behaviour, with node-link representations that emphasise the presence or absence of symmetry and synchrony. We illustrate the merit of our approach by presenting a real-world case study where the cytotoxic action of the anticancer drug topotecan was determined.
Comparative Visualization of Tracer Uptake in In Vivo Small Animal PET/CT Imaging of the Carotid Arteries
(The Eurographics Association and Blackwell Publishing Ltd., 2013) Diepenbrock, Stefan; Hermann, Sven; Schäfers, Michael; Kuhlmann, Michael; Hinrichs, Klaus; B. Preim, P. Rheingans, and H. Theisel
Cardiovascular diseases are the main cause of death in the western world. Medical research on atherosclerosis is therefore of great interest and a very active research topic. We present a visualization system that supports scientists in exploring plaque development and evaluating the applicability of PET tracers for early diagnosis of cardiovascular diseases. In our application case a cone shaped cuff has been implanted around the carotid artery of ApoE knockout mice, fed with a high cholesterol western type diet. As a result, vascular lesions develop upstream and downstream from the cuff. Tracer uptake induced by these lesions needs to be analyzed in order to evaluate the effectiveness of different PET tracers. We discuss the approach previously utilized to perform this kind of analysis, the problems arising from in vivo image acquisition (in contrast to ex vivo) and the design process of our application. In close cooperation with domain experts we have developed new visualization techniques that display PET activity in the vessel wall and surrounding tissue in a single image. We use the vessel wall detected in the CT image to perform a normalized circular projection which allows the user to judge PET signal distribution in relation to the deformed vessel. Based on this projection a quantitative analysis of a defined region adjacent to the vessel wall can be performed and compared to the artery without the cuff.
Cytosplore: Interactive Immune Cell Phenotyping for Large Single-Cell Datasets
(The Eurographics Association and John Wiley & Sons Ltd., 2016) Höllt, Thomas; Pezzotti, Nicola; Unen, Vincent van; Koning, Frits; Eisemann, Elmar; Lelieveldt, Boudewijn P. F.; Vilanova, Anna; Kwan-Liu Ma and Giuseppe Santucci and Jarke van Wijk
To understand how the immune system works, one needs to have a clear picture of its cellular compositon and the cells' corresponding properties and functionality. Mass cytometry is a novel technique to determine the properties of single-cells with unprecedented detail. This amount of detail allows for much finer differentiation but also comes at the cost of more complex analysis. In this work, we present Cytosplore, implementing an interactive workflow to analyze mass cytometry data in an integrated system, providing multiple linked views, showing different levels of detail and enabling the rapid definition of known and unknown cell types. Cytosplore handles millions of cells, each represented as a high-dimensional data point, facilitates hypothesis generation and confirmation, and provides a significant speed up of the current workflow. We show the effectiveness of Cytosplore in a case study evaluation.
Decoupled Shading for Real-time Heterogeneous Volume Illumination
(The Eurographics Association and John Wiley & Sons Ltd., 2016) Zhang, Yubo; Ma, Kwan-Liu; Kwan-Liu Ma and Giuseppe Santucci and Jarke van Wijk
Existing real-time volume rendering techniques which support global illumination are limited in modeling distinct realistic appearances for classified volume data, which is a desired capability in many fields of study for illustration and education. Directly extending the emission-absorption volume integral with heterogeneous material shading becomes unaffordable for real-time applications because the high-frequency view-dependent global lighting needs to be evaluated per sample along the volume integral. In this paper, we present a decoupled shading algorithm for multi-material volume rendering that separates global incident lighting evaluation from per-sample material shading under multiple light sources. We show how the incident lighting calculation can be optimized through a sparse volume integration method. The quality, performance and usefulness of our new multi-material volume rendering method is demonstrated through several examples.
dPSO-Vis: Topology-based Visualization of Discrete Particle Swarm Optimization
(The Eurographics Association and Blackwell Publishing Ltd., 2013) Volke, Sebastian; Middendorf, Martin; Hlawitschka, Mario; Kasten, Jens; Zeckzer, Dirk; Scheuermann, Gerik; B. Preim, P. Rheingans, and H. Theisel
Particle swarm optimization (PSO) is a metaheuristic that has been applied successfully to many continuous and combinatorial optimization problems, e.g., in the fields of economics, engineering, and natural sciences. In PSO, a swarm of particles moves within a search space in order to find an optimal solution. Unfortunately, it is hard to understand in detail why and how changes in the design of PSO algorithms affect the optimization behavior. Visualizing the particle states could provide substantially better insight into PSO algorithms. Though in case of combinatorial optimization problems, it often raises the problem of illustrating the states within the discrete search space that cannot be embedded spatially. We propose a visualization approach to depict the optimization problem topologically using a landscape metaphor. This visualization is augmented by an illustration of the time-dependent states of the particles. Thus, the user of dPSO-Vis is able to analyze the swarm's behavior within the search space. In principle, our method can be used for any optimization algorithm where a swarm of individuals searches within a discrete search space. Our approach is verified with a case study for the PSO algorithm HelixPSO that predicts the secondary structure of RNA molecules.
Energy-scale Aware Feature Extraction for Flow Visualization
(The Eurographics Association and Blackwell Publishing Ltd., 2011) Pobitzer, A.; Tutkun, M.; Andreassen, Ø.; Fuchs, R.; Peikert, R.; Hauser, H.; H. Hauser, H. Pfister, and J. J. van Wijk
In the visualization of flow simulation data, feature detectors often tend to result in overly rich response, making some sort of filtering or simplification necessary to convey meaningful images. In this paper we present an approach that builds upon a decomposition of the flow field according to dynamical importance of different scales of motion energy. Focusing on the high-energy scales leads to a reduction of the flow field while retaining the underlying physical process. The presented method acknowledges the intrinsic structures of the flow according to its energy and therefore allows to focus on the energetically most interesting aspects of the flow. Our analysis shows that this approach can be used for methods based on both local feature extraction and particle integration and we provide a discussion of the error caused by the approximation. Finally, we illustrate the use of the proposed approach for both a local and a global feature detector and in the context of numerical flow simulations.
Enhancing Scatterplots with Multi-Dimensional Focal Blur
(The Eurographics Association and John Wiley & Sons Ltd., 2016) Staib, Joachim; Grottel, Sebastian; Gumhold, Stefan; Kwan-Liu Ma and Giuseppe Santucci and Jarke van Wijk
Scatterplots directly depict two dimensions of multi-dimensional data points, discarding all other information. To visualize all data, these plots are extended to scatterplot matrices, which distribute the information of each data point over many plots. Problems arising from the resulting visual complexity are nowadays alleviated by concepts like filtering and focus and context. We present a method based on depth of field that contains both aspects and injects information from all dimensions into each scatterplot. Our approach is a natural generalization of the commonly known focus effects from optics. It is based on a multidimensional focus selection body. Points outside of this body are defocused depending on their distance. Our method allows for a continuous transition from data points in focus, over regions of blurry points providing contextual information, to visually filtered data. Our algorithm supports different focus selection bodies, blur kernels, and point shapes. We present an optimized GPU-based implementation for interactive exploration and show the usefulness of our approach on several data sets.
Evaluating 2D Flow Visualization Using Eye Tracking
(The Eurographics Association and John Wiley & Sons Ltd., 2015) Ho, Hsin-Yang; Yeh, I-Cheng; Lai, Yu-Chi; Lin, Wen-Chieh; Cherng, Fu-Yin; H. Carr, K.-L. Ma, and G. Santucci
Flow visualization is recognized as an essential tool for many scientific research fields and different visualization approaches are proposed. Several studies are also conducted to evaluate their effectiveness but these studies rarely examine the performance from the perspective of visual perception. In this paper, we aim at exploring how users' visual perception is influenced by different 2D flow visualization methods. An eye tracker is used to analyze users' visual behaviors when they perform the free viewing, advection prediction, flow feature detection, and flow feature identification tasks on the flow field images generated by different visualizations methods. We evaluate the illustration capability of five representative visualization algorithms. Our results show that the eye-tracking-based evaluation provides more insights to quantitatively analyze the effectiveness of these visualization methods.
An Evaluation of Visualization Techniques to Illustrate Statistical Deformation Models
(The Eurographics Association and Blackwell Publishing Ltd., 2011) Caban, Jesus J.; Rheingans, Penny; Yoo, T.; H. Hauser, H. Pfister, and J. J. van Wijk
As collections of 2D/3D images continue to grow, interest in effective ways to visualize and explore the statistical morphological properties of a group of images has surged. Recently, deformation models have emerged as simple methods to capture the variability and statistical properties of a collection of images. Such models have proven to be effective in tasks such as image classification, generation, registration, segmentation, and analysis of modes of variation. A crucial element missing from most statistical models has been an effective way to summarize and visualize the statistical morphological properties of a group of images. This paper evaluates different visualization techniques that can be extended and used to illustrate the information captured by such statistical models. First, four illustration techniques are described as methods to summarize the statistical morphological properties as captured by deformation models. Second, results of a user study conducted to compare the effectiveness of each visualization technique are presented. After comparing the performance of 40 subjects, we found that statistical annotation techniques present significant benefits when analyzing the structural properties of a group of images.
GEMSe: Visualization-Guided Exploration of Multi-channel Segmentation Algorithms
(The Eurographics Association and John Wiley & Sons Ltd., 2016) Fröhler, Bernhard; Möller, Torsten; Heinzl, Christoph; Kwan-Liu Ma and Giuseppe Santucci and Jarke van Wijk
We present GEMSe, an interactive tool for exploring and analyzing the parameter space of multi-channel segmentation algorithms. Our targeted user group are domain experts who are not necessarily segmentation specialists. GEMSe allows the exploration of the space of possible parameter combinations for a segmentation framework and its ensemble of results. Users start with sampling the parameter space and computing the corresponding segmentations. A hierarchically clustered image tree provides an overview of variations in the resulting space of label images. Details are provided through exemplary images from the selected cluster and histograms visualizing the parameters and the derived output in the selected cluster. The correlation between parameters and derived output as well as the effect of parameter changes can be explored through interactive filtering and scatter plots. We evaluate the usefulness of GEMSe through expert reviews and case studies based on three different kinds of datasets: A synthetic dataset emulating the combination of 3D X-ray computed tomography with data from K-Edge spectroscopy, a three-channel scan of a rock crystal acquired by a Talbot-Lau grating interferometer X-ray computed tomography device, as well as a hyperspectral image.
Glyphs for Asymmetric Second-Order 2D Tensors
(The Eurographics Association and John Wiley & Sons Ltd., 2016) Seltzer, Nicholas; Kindlmann, Gordon; Kwan-Liu Ma and Giuseppe Santucci and Jarke van Wijk
Tensors model a wide range of physical phenomena. While symmetric tensors are sufficient for some applications (such as diffusion), asymmetric tensors are required, for example, to describe differential properties of fluid flow. Glyphs permit inspecting individual tensor values, but existing tensor glyphs are fully defined only for symmetric tensors. We propose a glyph to visualize asymmetric second-order two-dimensional tensors. The glyph includes visual encoding for physically significant attributes of the tensor, including rotation, anisotropic stretching, and isotropic dilation. Our glyph design conserves the symmetry and continuity properties of the underlying tensor, in that transformations of a tensor (such as rotation or negation) correspond to analogous transformations of the glyph. We show results with synthetic data from computational fluid dynamics.
HiFiVE: A Hilbert Space Embedding of Fiber Variability Estimates for Uncertainty Modeling and Visualization
(The Eurographics Association and Blackwell Publishing Ltd., 2013) Schultz, Thomas; Schlaffke, Lara; Schölkopf, Bernhard; Schmidt-Wilcke, Tobias; B. Preim, P. Rheingans, and H. Theisel
Obtaining reproducible fiber direction estimates from diffusion MRI is crucial for successful fiber tracking. Modeling and visualizing the probability distribution of the inferred fiber directions is an important step in evaluating and comparing different acquisition schemes and fiber models. However, this distribution is usually strongly dominated by its main direction, which makes it difficult to examine when plotted naively. In this work, we propose a new visualization of the fiber probability distribution. It is based on embedding the probability measure into a particular reproducing kernel Hilbert space. This permits a decomposition into an embedded delta peak, representing the main direction, and a non-negative residual. They are then combined into a new glyph representation which visually enhances the residual, in order to highlight even subtle differences. Moreover, the magnitude of the delta peak component quantifies precision of the main fiber direction. We demonstrate that our new glyph provides a more detailed impression of the uncertainty than the current standard method, cones that contain 95% of the estimated directions. We use our new method to contribute to the validation of different ways of resampling the data (bootstrapping), and to visualize the differences between alternative acquisition schemes and models for high angular resolution diffusion imaging (HARDI).
In-situ Sampling of a Large-Scale Particle Simulation for Interactive Visualization and Analysis
(The Eurographics Association and Blackwell Publishing Ltd., 2011) Woodring, Jonathan; Ahrens, J.; Figg, J.; Wendelberger, J.; Habib, S.; Heitmann, K.; H. Hauser, H. Pfister, and J. J. van Wijk
We describe a simulation-time random sampling of a large-scale particle simulation, the RoadRunner Universe MC3 cosmological simulation, for interactive post-analysis and visualization. Simulation data generation rates will continue to be far greater than storage bandwidth rates by many orders of magnitude. This implies that only a very small fraction of data generated by a simulation can ever be stored and subsequently post-analyzed. The limiting factors in this situation are similar to the problem in many population surveys: there aren't enough human resources to query a large population. To cope with the lack of resources, statistical sampling techniques are used to create a representative data set of a large population. Following this analogy, we propose to store a simulationtime random sampling of the particle data for post-analysis, with level-of-detail organization, to cope with the bottlenecks. A sample is stored directly from the simulation in a level-of-detail format for post-visualization and analysis, which amortizes the cost of post-processing and reduces workflow time. Additionally by sampling during the simulation, we are able to analyze the entire particle population to record full population statistics and quantify sample error.
Interactive 3D Force-Directed Edge Bundling
(The Eurographics Association and John Wiley & Sons Ltd., 2016) Zielasko, Daniel; Weyers, Benjamin; Hentschel, Bernd; Kuhlen, Torsten W.; Kwan-Liu Ma and Giuseppe Santucci and Jarke van Wijk
Interactive analysis of 3D relational data is challenging. A common way of representing such data are node-link diagrams as they support analysts in achieving a mental model of the data. However, naïve 3D depictions of complex graphs tend to be visually cluttered, even more than in a 2D layout. This makes graph exploration and data analysis less efficient. This problem can be addressed by edge bundling. We introduce a 3D cluster-based edge bundling algorithm that is inspired by the force-directed edge bundling (FDEB) algorithm [HvW09b] and fulfills the requirements to be embedded in an interactive framework for spatial data analysis. It is parallelized and scales with the size of the graph regarding the runtime. Furthermore, it maintains the edge's model and thus supports rendering the graph in different structural styles. We demonstrate this with a graph originating from a simulation of the function of a macaque brain.
An Interactive Analysis and Exploration Tool for Epigenomic Data
(The Eurographics Association and Blackwell Publishing Ltd., 2013) Younesy, Hamidreza; Nielsen, Cydney B.; Möller, Torsten; Alder, Olivia; Cullum, Rebecca; Lorincz, Matthew C.; Karimi, Mohammad M.; Jones, Steven J. M.; B. Preim, P. Rheingans, and H. Theisel
In this design study, we present an analysis and abstraction of the data and tasks related to the domain of epigenomics, and the design and implementation of an interactive tool to facilitate data analysis and visualization in this domain. Epigenomic data can be grouped into subsets either by k-means clustering or by querying for combinations of presence or absence of signal (on/off) in different epigenomic experiments. These steps can easily be interleaved and the comparison of different workflows is explicitly supported. We took special care to contain the exponential expansion of possible on/off combinations by creating a novel querying interface. An interactive heat map facilitates the exploration and comparison of different clusters. We validated our iterative design by working closely with two groups of biologists on different biological problems. Both groups quickly found new insight into their data as well as claimed that our tool would save them several hours or days of work over using existing tools.
Prostate Cancer Visualization from MR Imagery and MR Spectroscopy
(The Eurographics Association and Blackwell Publishing Ltd., 2011) Marino, Joseph; Kaufman, Arie; H. Hauser, H. Pfister, and J. J. van Wijk
Prostate cancer is one of the most prevalent cancers among males, and the use of magnetic resonance imaging (MRI) has been suggested for its detection. A framework is presented for scoring and visualizing various MR data in an efficient and intuitive manner. A classification method is introduced where a cumulative score volume is created which takes into account each of three acquisition types. This score volume is integrated into a volume rendering framework which allows the user to view the prostate gland, the multi-modal score values, and the sur- rounding anatomy. A visibility persistence mode is introduced to automatically avoid full occlusion of a selected score and indicate overlaps. The use of GPU-accelerated multi-modal single-pass ray casting provides an inter- active experience. User driven importance rendering allows the user to gain insight into the data and can assist in localization of the disease and treatment planning. We evaluate our results against pathology and radiologists' determinations.
Semi-automatic Vortex Flow Classification in 4D PC-MRI Data of the Aorta
(The Eurographics Association and John Wiley & Sons Ltd., 2016) Meuschke, Monique; Köhler, Benjamin; Preim, Uta; Preim, Bernhard; Lawonn, Kai; Kwan-Liu Ma and Giuseppe Santucci and Jarke van Wijk
We present an Aortic Vortex Classification (AVOCLA) that allows to classify vortices in the human aorta semi-automatically. Current medical studies assume a strong relation between cardiovascular diseases and blood flow patterns such as vortices. Such vortices are extracted and manually classified according to specific, unstandardized properties. We employ an agglomerative hierarchical clustering to group vortex-representing path lines as basis for the subsequent classification. Classes are based on the vortex' size, orientation and shape, its temporal occurrence relative to the cardiac cycle as well as its spatial position relative to the vessel course. The classification results are presented by a 2D and 3D visualization technique. To confirm the usefulness of both approaches, we report on the results of a user study. Moreover, AVOCLA was applied to 15 datasets of healthy volunteers and patients with different cardiovascular diseases. The results of the semi-automatic classification were qualitatively compared to a manually generated ground truth of two domain experts considering the vortex number and five specific properties.
Topology-based Visualization of Transformation Pathways in Complex Chemical Systems
(The Eurographics Association and Blackwell Publishing Ltd., 2011) Beketayev, Kenes; Weber, G. H.; Haranczyk, M.; Bremer, P.-T.; Hlawitschka, M.; Hamann, B.; H. Hauser, H. Pfister, and J. J. van Wijk
Studying transformation in a chemical system by considering its energy as a function of coordinates of the system's components provides insight and changes our understanding of this process. Currently, a lack of effective visualization techniques for high-dimensional energy functions limits chemists to plot energy with respect to one or two coordinates at a time. In some complex systems, developing a comprehensive understanding requires new visualization techniques that show relationships between all coordinates at the same time. We propose a new visualization technique that combines concepts from topological analysis, multi-dimensional scaling, and graph layout to enable the analysis of energy functions for a wide range of molecular structures. We demonstrate our technique by studying the energy function of a dimer of formic and acetic acids and a LTA zeolite structure, in which we consider diffusion of methane.

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