@WorkshopTalk{mindek-2018-fyi, title = "Molecular Visualization", author = "Peter Mindek", year = "2018", abstract = "Molecular visualization allows us to display nanoworlds of bacteria and viruses, which would otherwise be impossible to show at such level of fidelity", month = nov, event = "FYI: Informationsdesign Konferenz Wien", location = "Nordbahn-Halle, Vienna", keywords = "molecular visualization, biology, education", URL = "https://www.cg.tuwien.ac.at/research/publications/2018/mindek-2018-fyi/", } @bachelorsthesis{koch-2018-sso, title = "Semantic Screen-Space Occlusion for Multiscale Molecular Visualization", author = "Thomas Bernhard Koch", year = "2018", abstract = "When visualizing large biological data sets the problem of visual clutter arises. This problem is often counteracted with level of detail schemes and appropriate coloring of the visualized structures. Ambient occlusion and shadows are often used in order to improve the depth perception which however promote visual clutter when used excessively. In this work an approach is explored to utilize screen-space shading techniques to reduce the visual clutter by using hierarchy information that is provided with molecular models. This is achieved by selectively applying screen-space shading techniques based on the semantics of the visualized hierarchically structured data. This technique is demonstrated by implementing a hierarchy-aware version of screen-space directional occlusion and screen-space ray traced shadows into Marion, an interactive rendering system to visualize biological data.", month = jan, address = "Favoritenstrasse 9-11/E193-02, A-1040 Vienna, Austria", school = "Institute of Computer Graphics and Algorithms, Vienna University of Technology ", URL = "https://www.cg.tuwien.ac.at/research/publications/2018/koch-2018-sso/", } @bachelorsthesis{lipp-2017-mgpu, title = "Visualization of Fiber Orientation in Glass Fiber Reinforced Polymers", author = "Lukas Lipp", year = "2018", abstract = "Fiber-reinforced composites are materials used for their extraordinary characteristics. The importance of these materials is constantly increasing, therefore, a wide range of variations exists of this material. Types range from Carbon Fiber Reinforced Polymer to Fiber-reinforced Foamed Urethane and more. Fiber-reinforced composites are lightweight, strong, and durable, among others and are therefore used for printed circuit boards, railway sleepers, airplanes or Formula 1 vehicles. To assure that these materials provide the required quality, they need to be tested and analyzed. To analyze these materials or to be more exact, the fibers within, special tools are needed. The first step is to scan the material with a X-ray Computed Tomography (CT) and save it as a volumetric CT-image on a computer. Now this data can be used to analyze the structure and find flaws in the dataset. In this thesis, a program for a later integration in a software called open_iA to extend its range of features, is developed. Purpose of the developed program is to analyze the orientation of fibers in a dataset. The result will be visualized with two different graphs. One shows the orientation of the fibers, while the other shows how many fibers are visible to the analyst. With the option of different configurations, it is possible to further specify these visualizations and get a better understanding of the underlying data.", month = jan, address = "Favoritenstrasse 9-11/E193-02, A-1040 Vienna, Austria", school = "Institute of Computer Graphics and Algorithms, Vienna University of Technology ", URL = "https://www.cg.tuwien.ac.at/research/publications/2018/lipp-2017-mgpu/", } @article{miao_tvcg_2018, title = "Multiscale Visualization and Scale-adaptive Modification of DNA Nanostructures", author = "Haichao Miao and Elisa De Llano and Johannes Sorger and Yasaman Ahmadi and Tadija Kekic and Tobias Isenberg and Eduard Gr\"{o}ller and Ivan Barisic and Ivan Viola", year = "2018", month = jan, journal = "IEEE Transactions on Visualization and Computer Graphics", volume = "24", number = "1", URL = "https://www.cg.tuwien.ac.at/research/publications/2018/miao_tvcg_2018/", } @bachelorsthesis{dietrich-2016-viseq2, title = " Smart Visibility Technique for Linear and Planar Molecular Assemblies", author = "Stefan Dietrich", year = "2018", note = "3", address = "Favoritenstrasse 9-11/E193-02, A-1040 Vienna, Austria", school = "Institute of Computer Graphics and Algorithms, Vienna University of Technology ", URL = "https://www.cg.tuwien.ac.at/research/publications/2018/dietrich-2016-viseq2/", } @phdthesis{waldin-2017-thesis, title = "Using and Adapting to Limits of Human Perception in Visualization", author = "Nicholas Waldin", year = "2017", month = nov, address = "Favoritenstrasse 9-11/E193-02, A-1040 Vienna, Austria", school = "Institute of Computer Graphics and Algorithms, Vienna University of Technology ", URL = "https://www.cg.tuwien.ac.at/research/publications/2017/waldin-2017-thesis/", } @article{mindek-2017-dsn, title = "Data-Sensitive Visual Navigation", author = "Peter Mindek and Gabriel Mistelbauer and Eduard Gr\"{o}ller and Stefan Bruckner", year = "2017", abstract = "In visualization systems it is often the case that the changes of the input parameters are not proportional to the visual change of the generated output. In this paper, we propose a model for enabling data-sensitive navigation for user-interface elements. This model is applied to normalize the user input according to the visual change, and also to visually communicate this normalization. In this way, the exploration of heterogeneous data using common interaction elements can be performed in an efficient way. We apply our model to the field of medical visualization and present guided navigation tools for traversing vascular structures and for camera rotation around 3D volumes. The presented examples demonstrate that the model scales to user-interface elements where multiple parameters are set simultaneously.", month = oct, journal = "Computers & Graphics", volume = "67", number = "C", pages = "77--85", keywords = "navigation, exploration, medical visualization", URL = "https://www.cg.tuwien.ac.at/research/publications/2017/mindek-2017-dsn/", } @inproceedings{Gehrer-2017-molmach, title = "Visualization of molecular machinery using agent-based animation", author = "Daniel Gehrer and Ivan Viola", year = "2017", month = may, event = "Spring Conference on Computer Graphics", booktitle = "Proceedings of SCCG 2017", URL = "https://www.cg.tuwien.ac.at/research/publications/2017/Gehrer-2017-molmach/", } @inproceedings{seyfert-2017, title = "Dynamic word clouds", author = "Ivan Viola and Martin Seyfert", year = "2017", abstract = "Using word clouds to visualize dynamic time-varying data is a field still under-explored. The goal of our approach is to provide a novel way of generating smoothly animated word clouds to show changes in word frequency via font size. Unlike existing methods, a compact layout, inspired by the popular word cloud generation tool Wordle, is preserved during animation and implemented using web technologies.Word size changes in time are also illustrated via color and word rotation. ", month = may, isbn = "978-1-4503-5107-2", location = "Mikulov", event = "SCCG 2017", editor = "ACM", doi = "10.1145/3154353.3154358", booktitle = "Proceedings of SCCG 2017", keywords = " tag cloud, animated, dynamic, time-varying, word cloud ", URL = "https://www.cg.tuwien.ac.at/research/publications/2017/seyfert-2017/", } @mastersthesis{kouril-2015-maya2cellview, title = "Maya2CellVIEW: 3D Package Integrated Tool for Creating Large and Complex Molecular Scenes", author = "David Kou\v{r}il", year = "2017", abstract = "Scientific illustrators communicate the cutting edge of research through their illustrations. There are numerous software tools that assist them with this job. Often they use professional modeling and animation 3D programs which are primarily used in games and movies industry. Because of that however these tools are not suitable for scientific illustration out of the box. There have been attempts to address this issue which brought tremendous results. This work focuses on visualization of structures and processes in biology, focusing mostly on the scales of nano- to micrometers. At this scale we often do not gain much by using hyper-realistic rendering style that the professional software aims for. Instead we want to employ more simplified style which helps to communicate the important story without losing much detail or scientific precision. The aim of this thesis is to push abilities of illustrators working on large scale molecular scenes. This is done by connecting two software packages—Maya and cellVIEW—combining the real-time rendering possibilities of cellVIEW and modeling and animation tools of Maya which results in more effective and efficient workflow.", month = jan, address = "Favoritenstrasse 9-11/E193-02, A-1040 Vienna, Austria", school = "Institute of Computer Graphics and Algorithms, Vienna University of Technology ", URL = "https://www.cg.tuwien.ac.at/research/publications/2017/kouril-2015-maya2cellview/", } @article{miao_tvcg_2017, title = "Placenta Maps: In Utero Placental Health Assessment of the Human Fetus", author = "Haichao Miao and Gabriel Mistelbauer and Alexey Karimov and Amir Alansary and Alice Davidson and David F.A. Lloyd and Mellisa Damodaram and Lisa Story and Jana Hutter and Joseph V. Hajnal and Mary Rutherford and Bernhard Preim and Bernhard Kainz and Eduard Gr\"{o}ller", year = "2017", abstract = "null", journal = "IEEE Transactions on Visualization and Computer Graphics", volume = "23", number = "6", pages = "1612--1623", URL = "https://www.cg.tuwien.ac.at/research/publications/2017/miao_tvcg_2017/", } @article{mindek-2017-marion, title = "Visualization Multi-Pipeline for Communicating Biology", author = "Peter Mindek and David Kou\v{r}il and Johannes Sorger and David Toloudis and Blair Lyons and Graham Johnson and Eduard Gr\"{o}ller and Ivan Viola", year = "2017", abstract = "We propose a system to facilitate biology communication by developing a pipeline to support the instructional visualization of heterogeneous biological data on heterogeneous user-devices. Discoveries and concepts in biology are typically summarized with illustrations assembled manually from the interpretation and application of heterogenous data. The creation of such illustrations is time consuming, which makes it incompatible with frequent updates to the measured data as new discoveries are made. Illustrations are typically non-interactive, and when an illustration is updated, it still has to reach the user. Our system is designed to overcome these three obstacles. It supports the integration of heterogeneous datasets, reflecting the knowledge that is gained from different data sources in biology. After pre-processing the datasets, the system transforms them into visual representations as inspired by scientific illustrations. As opposed to traditional scientific illustration these representations are generated in real-time - they are interactive. The code generating the visualizations can be embedded in various software environments. To demonstrate this, we implemented both a desktop application and a remote-rendering server in which the pipeline is embedded. The remote-rendering server supports multi-threaded rendering and it is able to handle multiple users simultaneously. This scalability to different hardware environments, including multi-GPU setups, makes our system useful for efficient public dissemination of biological discoveries. ", journal = "IEEE Transactions on Visualization and Computer Graphics", volume = "24", number = "1", keywords = "Biological visualization, remote rendering, public dissemination", URL = "https://www.cg.tuwien.ac.at/research/publications/2017/mindek-2017-marion/", } @bachelorsthesis{dworschak-2016-szcm, title = "Semantically Zoomable Choropleth Map", author = "Lucas Dworschak", year = "2016", abstract = "Geographic visualizations, like choropleth maps, are used to visualize data on geographic regions. In this thesis a choropleth map was implemented to display quantities of publications of scientific texts and papers. With the use of a choropleth map the viewer is able to interpret how quantitative data changes on different geographic regions. The main feature that distinguishes the implemented choropleth map from conventional ones is the use of map navigation. The choropleth map can be zoomed and panned to different map regions. What makes this map navigation so special is the use of semantic zooming to allow the level of detail of the map to change on discrete zoom steps. The change of the level of detail means that administrative regions are being divided into smaller administrative regions which are than again colorized individually to create a new, more detailed, choropleth map. Other interactions with the choropleth map are introduced additionally. The other interactions with the map range from the manipulation of the map appearance to filtering the displayed data set.", month = sep, address = "Favoritenstrasse 9-11/E193-02, A-1040 Vienna, Austria", school = "Institute of Computer Graphics and Algorithms, Vienna University of Technology ", URL = "https://www.cg.tuwien.ac.at/research/publications/2016/dworschak-2016-szcm/", } @inproceedings{sorger-2016-fowardabstraction, title = "Illustrative Transitions in Molecular Visualization via Forward and Inverse Abstraction Transform", author = "Johannes Sorger and Peter Mindek and Tobias Klein and Graham Johnson and Ivan Viola", year = "2016", abstract = "A challenging problem in biology is the incompleteness of acquired information when visualizing biological phenomena. Structural biology generates detailed models of viruses or bacteria at different development stages, while the processes that relate one stage to another are often not clear. Similarly, the entire life cycle of a biological entity might be available as a quantitative model, while only one structural model is available. If the relation between two models is specified at a lower level of detail than the actual models themselves, the two models cannot be interpolated correctly. We propose a method that deals with the visualization of incomplete data information in the developmental or evolutionary states of biological mesoscale models, such as viruses or microorganisms. The central tool in our approach is visual abstraction. Instead of directly interpolating between two models that show different states of an organism, we gradually forward transform the models into a level of visual abstraction that matches the level of detail of the modeled relation between them. At this level, the models can be interpolated without conveying false information. After the interpolation to the new state, we apply the inverse transformation to the model’'s original level of abstraction. To show the flexibility of our approach, we demonstrate our method on the basis of molecular data, in particular data of the HIV virion and the mycoplasma bacterium.", month = sep, organization = "Eurographics", location = "Bergen", editor = "S. Bruckner, B. Preim, and A. Vilanova", booktitle = "Eurographics Workshop on Visual Computing for Biology and Medicine (VCBM)", pages = "21--30", keywords = "I.3.3 [Computer Graphics]: Picture/Image Generation-Display algorithms", URL = "https://www.cg.tuwien.ac.at/research/publications/2016/sorger-2016-fowardabstraction/", } @article{bernhard-2016-gft, title = " The Accuracy of Gauge-Figure Tasks in Monoscopic and Stereo Displays", author = "Matthias Bernhard and Manuela Waldner and Pascal Plank and Veronika Solteszova and Ivan Viola", year = "2016", abstract = "The gauge-figure task (GFT) is a widespread method used to study surface perception for evaluating rendering and visualization techniques. The authors investigate how accurately slant angles probed on well-defined objects align with the ground truth (GT) in monoscopic and stereoscopic displays. Their results show that the GFT probes taken with well-defined objects align well with the GT in the all-monoscopic and all-stereoscopic conditions. However, they found that a GF rendered in stereo over a monoscopic stimulus results in a strong slant underestimation and that an overestimation occurred in the inverse case (monoscopic GF andstereoscopic stimulus). They discuss how their findings affect the interpretation of absolute GFT measures, compared to the GT normal.", month = jul, journal = "IEEE Computer Graphics and Applications", number = "4", volume = "36", pages = "56--66", keywords = "computer graphics, gauge-figure task, perceptual visualization, shape perception", URL = "https://www.cg.tuwien.ac.at/research/publications/2016/bernhard-2016-gft/", } @bachelorsthesis{Gadllah_Hani_2016, title = "Comparative Visualization of the Circle of Willis", author = "Hani Gadllah", year = "2016", abstract = "The human brain is supplied with blood by arteries that form a collateral circulation, the so-called Circle of Willis (CoW). The anatomy of the CoW varies considerably among the population. In fact, depending on the study, just 13% to 72% of the population does have the typical textbook illustration of the CoW. Although divergent configurations are usually not pathological, some incomplete configurations increase the risk of stroke. Furthermore, studies suggest an association between certain neurological diseases and abnormal configurations of the CoW. Thus, for the diagnosis and treatment of diverse neurological diseases the assessment of the patient’s CoW is an important issue. This thesis addresses the development of a software for a comparative visualization of the CoWs of a population with the CoWs of a second population. For this purpose, an average CoW is calculated for each of the populations. The two resulting CoWs are then visualized side-by-side, so that the viewer is able to distinguish differences between the CoWs of the two populations with relatively little effort. The aim of this visualization is the support of studies that consider the clinical significance of the different CoW configurations as well as the support of diagnosis and treatment of diseases that are caused by an abnormal configuration of the CoW. The latter can be achieved by comparing the patient’s CoW with datasets of risk groups or with a dataset of a healthy population. ", month = jun, address = "Favoritenstrasse 9-11/E193-02, A-1040 Vienna, Austria", school = "Institute of Computer Graphics and Algorithms, Vienna University of Technology ", URL = "https://www.cg.tuwien.ac.at/research/publications/2016/Gadllah_Hani_2016/", } @WorkshopTalk{mindek-2016-utah-talk, title = "Multi-Scale Molecular Data Visualization", author = "Peter Mindek", year = "2016", month = may, event = "QCB Workshop on Visualizing & Modeling Cell Biology", location = "Salt Lake City, Utah, USA", keywords = "molecular visualization, multiscale", URL = "https://www.cg.tuwien.ac.at/research/publications/2016/mindek-2016-utah-talk/", } @bachelorsthesis{Langer_Maximillian_DMV, title = "Dynamic Multiscale Vector Volumes", author = "Maximilian Langer", year = "2016", abstract = "Dynamic multiscale vector volumes is a solid representation based on signed distance functions to represent object boundaries. Multiscale vector volumes utilize a binary tree and an embedding mechanism to represent structures on different scales in a compact and efficient way. By extending the representation with an analytical formulation to partly replace signed distance functions, an efficient local animation of boundaries can be achieved. The representation uses a markup language for object definition that allows the user to create their own objects. The concept of dynamic multiscale vector volumes is implemented and tested in the Unity3D editor. The complete rendering is done on the graphics card.", month = apr, address = "Favoritenstrasse 9-11/E193-02, A-1040 Vienna, Austria", school = "Institute of Computer Graphics and Algorithms, Vienna University of Technology ", URL = "https://www.cg.tuwien.ac.at/research/publications/2016/Langer_Maximillian_DMV/", } @article{Viola_Ivan_2015_AAM, title = "AnimoAminoMiner: Exploration of Protein Tunnels and their Properties in Molecular Dynamics", author = "Jan Byska and Mathieu Le Muzic and Eduard Gr\"{o}ller and Ivan Viola and Barbora Kozlikova", year = "2016", abstract = "In this paper we propose a novel method for the interactive exploration of protein tunnels. The basic principle of our approach is that we entirely abstract from the 3D/4D space the simulated phenomenon is embedded in. A complex 3D structure and its curvature information is represented only by a straightened tunnel centerline and its width profile. This representation focuses on a key aspect of the studied geometry and frees up graphical estate to key chemical and physical properties represented by surrounding amino acids. The method shows the detailed tunnel profile and its temporal aggregation. The profile is interactively linked with a visual overview of all amino acids which are lining the tunnel over time. In this overview, each amino acid is represented by a set of colored lines depicting the spatial and temporal impact of the amino acid on the corresponding tunnel. This representation clearly shows the importance of amino acids with respect to selected criteria. It helps the biochemists to select the candidate amino acids for mutation which changes the protein function in a desired way. The AnimoAminoMiner was designed in close cooperation with domain experts. Its usefulness is documented by their feedback and a case study, which are included.", month = jan, journal = "IEEE Transactions on Visualization and Computer Graphics", volume = "22", number = "1", issn = "1077-2626", pages = "747--756", keywords = "aggregation, molecular dynamics, Protein, interaction, tunnel", URL = "https://www.cg.tuwien.ac.at/research/publications/2016/Viola_Ivan_2015_AAM/", } @article{lemuzic-mindek-2016-viseq, title = "Visibility Equalizer: Cutaway Visualization of Mesoscopic Biological Models", author = "Mathieu Le Muzic and Peter Mindek and Johannes Sorger and Ludovic Autin and David Goodsell and Ivan Viola", year = "2016", abstract = "In scientific illustrations and visualization, cutaway views are often employed as an effective technique for occlusion management in densely packed scenes.We propose a novel method for authoring cutaway illustrations of mesoscopic biological models. In contrast to the existing cutaway algorithms, we take advantage of the specific nature of the biological models. These models consist of thousands of instances with a comparably smaller number of different types. Our method constitutes a two stage process. In the first step, clipping objects are placed in the scene, creating a cutaway visualization of the model. During this process, a hierarchical list of stacked bars inform the user about the instance visibility distribution of each individual molecular type in the scene. In the second step, the visibility of each molecular type is fine-tuned through these bars, which at this point act as interactive visibility equalizers. An evaluation of our technique with domain experts confirmed that our equalizer-based approach for visibility specification is valuable and effective for both, scientific and educational purposes.", journal = "Computer Graphics Forum", volume = "35", number = "3", keywords = "molecular visualization, visibility, occlusion", URL = "https://www.cg.tuwien.ac.at/research/publications/2016/lemuzic-mindek-2016-viseq/", } @article{Solteszova2016, title = "Output-Sensitive Filtering of Streaming Volume Data", author = "Veronika Solteszova and {\AA}smund Birkeland and Sergej Stoppel and Ivan Viola and Stefan Bruckner", year = "2016", abstract = "Real-time volume data acquisition poses substantial challenges for the traditional visualization pipeline where data enhancement is typically seen as a pre-processing step. In the case of 4D ultrasound data, for instance, costly processing operations to reduce noise and to remove artefacts need to be executed for every frame. To enable the use of high-quality filtering operations in such scenarios, we propose an output-sensitive approach to the visualization of streaming volume data. Our method evaluates the potential contribution of all voxels to the final image, allowing us to skip expensive processing operations that have little or no effect on the visualization. As filtering operations modify the data values which may affect the visibility, our main contribution is a fast scheme to predict their maximum effect on the final image. Our approach prioritizes filtering of voxels with high contribution to the final visualization based on a maximal permissible error per pixel. With zero permissible error, the optimized filtering will yield a result that is identical to filtering of the entire volume. We provide a thorough technical evaluation of the approach and demonstrate it on several typical scenarios that require on-the-fly processing.", journal = "Computer Graphics Forum", volume = "35", URL = "https://www.cg.tuwien.ac.at/research/publications/2016/Solteszova2016/", } @habilthesis{viola-evr, title = "Effective Visual Representations", author = "Ivan Viola", year = "2016", URL = "https://www.cg.tuwien.ac.at/research/publications/2016/viola-evr/", } @article{Krone2016VABC, title = "Visual Analysis of Biomolecular Cavities: State of the Art", author = "Michael Krone and Barbora Kozlikova and Norbert Lindow and Marc Baaden and Daniel Baum and Julius Parulek and Hans-Christian Hege and Ivan Viola", year = "2016", abstract = "In this report we review and structure the branch of molecular visualization that is concerned with the visual analysis of cavities in macromolecular protein structures. First the necessary background, the domain terminology, and the goals of analytical reasoning are introduced. Based on a comprehensive collection of relevant research works, we present a novel classification for cavity detection approaches and structure them into four distinct classes: grid-based, Voronoi-based, surface-based, and probe-based methods. The subclasses are then formed by their combinations. We match these approaches with corresponding visualization technologies starting with direct 3D visualization, followed with non-spatial visualization techniques that for example abstract the interactions between structures into a relational graph, straighten the cavity of interest to see its profile in one view, or aggregate the time sequence into a single contour plot. We also discuss the current state of methods for the visual analysis of cavities in dynamic data such as molecular dynamics simulations. Finally, we give an overview of the most common tools that are actively developed and used in the structural biology and biochemistry research. Our report is concluded by an outlook on future challenges in the field.", journal = "Computer Graphics Forum", volume = "35", number = "3", pages = "527--551", URL = "https://www.cg.tuwien.ac.at/research/publications/2016/Krone2016VABC/", } @bachelorsthesis{glinzner-2016-tex, title = "Texturing of 3D Objects using Simple Physics and Equilateral Triangle Patches", author = "Matthias Glinzner", year = "2016", abstract = "Visualizing cells, in particular cell membranes, is the inspiration for this work. The goal of the presented methods is the efficient visualization of phospholipid membranes. A prominent role hereby plays the concept of seamlessly texturing a surface in threedimensional space. By using suitable texture patches, memory consumption can be kept low. The developed algorithm first creates a texture mesh that stays faithful to the surface structure of a user-provided input-mesh. This texture mesh consists of equilateral triangles. The triangulation is achieved by first simulating repulsion between the vertices making up the texture mesh. This way they are moved around on the surface of the input-mesh until they are uniformly distributed. Mapping texture onto equilateral triangles becomes trivial if triangular texture patches are assumed as well. Thus, seamless texturing is achieved. The implementation is described in detail, followed by the demonstration of results. Also, an exemplary performance-analysis is given, highlighting benefits and shortcomings of the algorithm, especially concerning runtime. Additionally, a short overview of related and prior work is given. The used framework is Unity 3D.", note = "1", address = "Favoritenstrasse 9-11/E193-02, A-1040 Vienna, Austria", school = "Institute of Computer Graphics and Algorithms, Vienna University of Technology ", URL = "https://www.cg.tuwien.ac.at/research/publications/2016/glinzner-2016-tex/", } @article{vad-2016-bre, title = "Generalized box-plot for root growth ensembles", author = "Viktor Vad and Douglas Cedrim and Wolfgang Busch and Peter Filzmoser and Ivan Viola", year = "2016", abstract = "Background In the field of root biology there has been a remarkable progress in root phenotyping, which is the efficient acquisition and quantitative description of root morphology. What is currently missing are means to efficiently explore, exchange and present the massive amount of acquired, and often time dependent root phenotypes. Results In this work, we present visual summaries of root ensembles by aggregating root images with identical genetic characteristics. We use the generalized box plot concept with a new formulation of data depth. In addition to spatial distributions, we created a visual representation to encode temporal distributions associated with the development of root individuals. Conclusions The new formulation of data depth allows for much faster implementation close to interactive frame rates. This allows us to present the statistics from bootstrapping that characterize the root sample set quality. As a positive side effect of the new data-depth formulation we are able to define the geometric median for the curve ensemble, which was well received by the domain experts.", journal = "BMC Bioinformatics", URL = "https://www.cg.tuwien.ac.at/research/publications/2016/vad-2016-bre/", } @bachelorsthesis{Reisacher_Matthias_CPW, title = "CellPathway a Simulation Tool for Illustrative Visualization of Biochemical Networks", author = "Matthias Reisacher", year = "2016", abstract = "The molecular knowledge about complex biochemical reaction networks in biotechnology is crucial and has received a lot of attention lately. As a consequence, multiple visualization programs have been already developed to illustrate the anatomy of a cell. However, since a real cell performs millions of reactions every second to sustain live, it is necessary to move from anatomical to physiological illustrations to communicate knowledge about the behavior of a cell more accurately. In this thesis I propose a reaction system including a collision detection algorithm, which is able to work at the level of single atoms, to enable precise simulation of molecular interactions. To visually explain molecular activities during the simulation process, a real-time glow effect in combination with a clipping object have been implemented. Since intracellular processes are performed with a set of chemical transformations, a hierarchical structure is used to illustrate the impact of one reaction on the entire simulation. The CellPathway system integrates acceleration techniques to render large datasets containing millions of atoms in real-time, while the reaction system is processed directly on the GPU to enable simulation with more than 1000 molecules. Furthermore, a graphical user interface has been implemented to allow the user to control parameters during simulation interactively.", address = "Favoritenstrasse 9-11/E193-02, A-1040 Vienna, Austria", school = "Institute of Computer Graphics and Algorithms, Vienna University of Technology ", URL = "https://www.cg.tuwien.ac.at/research/publications/2016/Reisacher_Matthias_CPW/", } @article{Cornel2016CFM, title = "Composite Flow Maps", author = "Daniel Cornel and Artem Konev and Berhard Sadransky and Zsolt Horvath and Andrea Brambilla and Ivan Viola and J\"{u}rgen Waser", year = "2016", abstract = "Flow maps are widely used to provide an overview of geospatial transportation data. Existing solutions lack the support for the interactive exploration of multiple flow components at once. Flow components are given by different materials being transported, different flow directions, or by the need for comparing alternative scenarios. In this paper, we combine flows as individual ribbons in one composite flow map. The presented approach can handle an arbitrary number of sources and sinks. To avoid visual clutter, we simplify our flow maps based on a force-driven algorithm, accounting for restrictions with respect to application semantics. The goal is to preserve important characteristics of the geospatial context. This feature also enables us to highlight relevant spatial information on top of the flow map such as traffic conditions or accessibility. The flow map is computed on the basis of flows between zones. We describe a method for auto-deriving zones from geospatial data according to application requirements. We demonstrate the method in real-world applications, including transportation logistics, evacuation procedures, and water simulation. Our results are evaluated with experts from corresponding fields.", journal = "Computer Graphics Forum", volume = "35", number = "3", pages = "461--470", URL = "https://www.cg.tuwien.ac.at/research/publications/2016/Cornel2016CFM/", } @inproceedings{Reisacher2016, title = "CellPathway: A Simulation Tool for Illustrative Visualization of Biochemical Networks", author = "Matthias Reisacher and Mathieu Le Muzic and Ivan Viola", year = "2016", abstract = "The molecular knowledge about complex biochemical reaction networks in biotechnology is crucial and has received a lot of attention lately. As a consequence, multiple visualization programs have been already developed to illustrate the anatomy of a cell. However, since a real cell performs millions of reactions every second to sustain live, it is necessary to move from anatomical to physiological illustrations to communicate knowledge about the behavior of a cell more accurately. In this thesis I propose a reaction system including a collision detection algorithm, which is able to work at the level of single atoms, to enable precise simulation of molecular interactions. To visually explain molecular activities during the simulation process, a real-time glow effect in combination with a clipping object have been implemented. Since intracellular processes are performed with a set of chemical transformations, a hierarchical structure is used to illustrate the impact of one reaction on the entire simulation. The CellPathway system integrates acceleration techniques to render large datasets containing millions of atoms in real-time, while the reaction system is processed directly on the GPU to enable simulation with more than 1000 molecules. Furthermore, a graphical user interface has been implemented to allow the user to control parameters during simulation interactively.", location = "Pilsen, Czech Republic", booktitle = "Proceedings of WSCG", URL = "https://www.cg.tuwien.ac.at/research/publications/2016/Reisacher2016/", } @misc{Diehl_2015, title = "Albero: A Visual Analytics Tool for Probabilistic Weather Forecasting.", author = "Alexandra Diehl and Leandro Pelorosso and Kresimir Matkovic and Claudio Delrieux and Marc Ruiz and Eduard Gr\"{o}ller and Stefan Bruckner", year = "2015", month = nov, location = "University of Buenos Aires", event = "Poster at Workshop Big Data & Environment", Conference date = "Poster presented at Poster at Workshop Big Data & Environment (2015-11)", URL = "https://www.cg.tuwien.ac.at/research/publications/2015/Diehl_2015/", } @inproceedings{cellVIEW_2015, title = "cellVIEW: a Tool for Illustrative and Multi-Scale Rendering of Large Biomolecular Datasets", author = "Mathieu Le Muzic and Ludovic Autin and Julius Parulek and Ivan Viola", year = "2015", abstract = "In this article we introduce cellVIEW, a new system to interactively visualize large biomolecular datasets on the atomic level. Our tool is unique and has been specifically designed to match the ambitions of our domain experts to model and interactively visualize structures comprised of several billions atom. The cellVIEW system integrates acceleration techniques to allow for real-time graphics performance of 60 Hz display rate on datasets representing large viruses and bacterial organisms. Inspired by the work of scientific illustrators, we propose a level-of-detail scheme which purpose is two-fold: accelerating the rendering and reducing visual clutter. The main part of our datasets is made out of macromolecules, but it also comprises nucleic acids strands which are stored as sets of control points. For that specific case, we extend our rendering method to support the dynamic generation of DNA strands directly on the GPU. It is noteworthy that our tool has been directly implemented inside a game engine. We chose to rely on a third party engine to reduce software development work-load and to make bleeding-edge graphics techniques more accessible to the end-users. To our knowledge cellVIEW is the only suitable solution for interactive visualization of large bimolecular landscapes on the atomic level and is freely available to use and extend.", month = sep, isbn = "978-3-905674-82-8", publisher = "The Eurographics Association", organization = "EG Digital Library", location = "Chester, United Kingdom", issn = "2070-5786", editor = "Katja B\"{u}hler and Lars Linsen and Nigel W. John", booktitle = "Eurographics Workshop on Visual Computing for Biology and Medicine", pages = "61--70", URL = "https://www.cg.tuwien.ac.at/research/publications/2015/cellVIEW_2015/", } @bachelorsthesis{Plank_Pascal_2015_HVP, title = "Human Visual Perception of 3D Surfaces", author = "Pascal Plank", year = "2015", abstract = "The gauge figure task is a methodological tool to study an observer’s perception of surface orientations in renderings and visualization techniques. Originally developed to probe the perception of paintings, i. e. not veridical stimuli, the gauge figure task has since been used to measure absolute perceptual errors by comparing an observer’s surface estimates with the ground truth surface normals. In this bachelor thesis the accuracy of the gauge figure task was investigated, i. e. how well the probed surface estimates align with the perceived surface normals on an absolute scale. To isolate the probing error a user study was carried out using different primitive objects and several depth cues, including depth-from-motion and stereo disparities, to minimize potential perceptual errors. It was expected that a stereoscopic presentation of the gauge figure would reduce the perceptual error of the gauge figure dramatically. During the experiments I collected about 16.300 probes from 17 participants under different viewing conditions where either the stimuli, the gauge figure, both or none of them were presented in stereo. The results show that the gauge figure estimates for primitive stimuli, e. g. a sphere or a cylinder, align well with the ground truth in modality-consistent conditions, i. e. where stimuli and gauge figure were both presented in stereo or both in mono. In contrast to this, a gauge figure presented in stereo to probe monoscopic stimuli resulted in an enormous slant underestimation. In addition, in the inverse case, where the gauge figure is presented in mono and the stimuli in stereo, an overestimation occurred - even for simple stimulus objects. This bachelor thesis covers the general background and previous work for this subject, the design, setup and procedure of the user study as well as the results and a qualitative assessment. Furthermore, two alternative explanations for the found results are discussed and an outlook for possible future work is given.", month = jun, address = "Favoritenstrasse 9-11/E193-02, A-1040 Vienna, Austria", school = "Institute of Computer Graphics and Algorithms, Vienna University of Technology ", URL = "https://www.cg.tuwien.ac.at/research/publications/2015/Plank_Pascal_2015_HVP/", } @article{Viola_Ivan_2015_MCT, title = "MoleCollar and Tunnel Heat Map Visualizations for Conveying Spatio-Temporo-Chemical Properties Across and Along Protein Voids", author = "Jan Byska and Adam Jurcik and Eduard Gr\"{o}ller and Ivan Viola and Barbora Kozlikova", year = "2015", abstract = "Studying the characteristics of proteins and their inner void space, including their geometry, physico-chemical properties and dynamics are instrumental for evaluating the reactivity of the protein with other small molecules. The analysis of long simulations of molecular dynamics produces a large number of voids which have to be further explored and evaluated. In this paper we propose three new methods: two of them convey important properties along the long axis of a selected void during molecular dynamics and one provides a comprehensive picture across the void. The first two proposed methods use a specific heat map to present two types of information: an overview of all detected tunnels in the dynamics and their bottleneck width and stability over time, and an overview of a specific tunnel in the dynamics showing the bottleneck position and changes of the tunnel length over time. These methods help to select a small subset of tunnels, which are explored individually and in detail. For this stage we propose the third method, which shows in one static image the temporal evolvement of the shape of the most critical tunnel part, i.e., its bottleneck. This view is enriched with abstract depictions of different physicochemical properties of the amino acids surrounding the bottleneck. The usefulness of our newly proposed methods is demonstrated on a case study and the feedback from the domain experts is included. The biochemists confirmed that our novel methods help to convey the information about the appearance and properties of tunnels in a very intuitive and comprehensible manner.", month = may, journal = "Computer Graphics Forum", volume = "3", number = "34", note = "EuroVis 2015 - Conference Proceedings", pages = "1--10", URL = "https://www.cg.tuwien.ac.at/research/publications/2015/Viola_Ivan_2015_MCT/", } @inproceedings{Viola_Ivan_2015_VBS, title = "Visualization of Biomolecular Structures: State of the Art", author = "Barbora Kozlikova and Michael Krone and Norbert Lindow and Martin Falk and Marc Baaden and Daniel Baum and Ivan Viola and Julius Parulek and Hans-Christian Hege", year = "2015", abstract = "Structural properties of molecules are of primary concern in many fields. This report provides a comprehensive overview on techniques that have been developed in the fields of molecular graphics and visualization with a focus on applications in structural biology. The field heavily relies on computerized geometric and visual representations of three-dimensional, complex, large, and time-varying molecular structures. The report presents a taxonomy that demonstrates which areas of molecular visualization have already been extensively investigated and where the field is currently heading. It discusses visualizations for molecular structures, strategies for efficient display regarding image quality and frame rate, covers different aspects of level of detail, and reviews visualizations illustrating the dynamic aspects of molecular simulation data. The report concludes with an outlook on promising and important research topics to enable further success in advancing the knowledge about interaction of molecular structures.", month = may, publisher = "The Eurographics Association", location = "Cagliari, Italy", event = "Eurographics Conference on Visualization (EuroVis) (2015)", editor = "R. Borgo and F. Ganovelli and I. Viola", booktitle = "Eurographics Conference on Visualization (EuroVis) - STARs", pages = "061--081", URL = "https://www.cg.tuwien.ac.at/research/publications/2015/Viola_Ivan_2015_VBS/", } @inproceedings{mindek-2015-mc, title = "Automatized Summarization of Multiplayer Games", author = "Peter Mindek and Ladislav \v{C}mol\'{i}k and Ivan Viola and Eduard Gr\"{o}ller and Stefan Bruckner", year = "2015", abstract = "We present a novel method for creating automatized gameplay dramatization of multiplayer video games. The dramatization serves as a visual form of guidance through dynamic 3D scenes with multiple foci, typical for such games. Our goal is to convey interesting aspects of the gameplay by animated sequences creating a summary of events which occurred during the game. Our technique is based on processing many cameras, which we refer to as a flock of cameras, and events captured during the gameplay, which we organize into a so-called event graph. Each camera has a lifespan with a certain time interval and its parameters such as position or look-up vector are changing over time. Additionally, during its lifespan each camera is assigned an importance function, which is dependent on the significance of the structures that are being captured by the camera. The images captured by the cameras are composed into a single continuous video using a set of operators based on cinematographic effects. The sequence of operators is selected by traversing the event graph and looking for specific patterns corresponding to the respective operators. In this way, a large number of cameras can be processed to generate an informative visual story presenting the gameplay. Our compositing approach supports insets of camera views to account for several important cameras simultaneously. Additionally, we create seamless transitions between individual selected camera views in order to preserve temporal continuity, which helps the user to follow the virtual story of the gameplay.", month = apr, isbn = "978-80-223-3844-8", publisher = "Comenius University, Bratislava", location = "Smolenice, Slovakia", editor = "Joaquim Jorge, Luis Paulo Santos, Roman Durikovic", booktitle = "Proceedings of Spring Conference on Computer Graphics 2015", pages = "93--100", keywords = "storytelling, game visualization, animation", URL = "https://www.cg.tuwien.ac.at/research/publications/2015/mindek-2015-mc/", } @inproceedings{lemuzic_2015_timelapse, title = "Illustrative Timelapse: A Technique for Illustrative Visualization of Particle Simulations on the Mesoscale Level", author = "Mathieu Le Muzic and Manuela Waldner and Julius Parulek and Ivan Viola", year = "2015", abstract = "Animated movies are a popular way to communicate complex phenomena in cell biology to the broad audience. Animation artists apply sophisticated illustration techniques to communicate a story, while trying to maintain a realistic representation of a complex dynamic environment. Since such hand-crafted animations are timeconsuming and cost-intensive to create, our goal is to formalize illustration techniques used by artists to facilitate the automatic creation of visualizations generated from mesoscale particle-based molecular simulations. Our technique Illustrative Timelapse supports visual exploration of complex biochemical processes in dynamic environments by (1) seamless temporal zooming to observe phenomena in different temporal resolutions, (2) visual abstraction of molecular trajectories to ensure that observers are able to visually follow the main actors, (3) increased visual focus on events of interest, and (4) lens effects to preserve a realistic representation of the environment in the context. Results from a first user study indicate that visual abstraction of trajectories improves the ability to follow a story and is also appreciated by users. Lens effects increased the perceived amount of molecular motion in the environment while trading off traceability of individual molecules.", month = apr, publisher = "IEEE", organization = "8th IEEE Pacific Visualization Symposium (PacificVis 2015)", location = "Zijingang Campus, Zhejiang University, Hangzhou, China", booktitle = "Visualization Symposium (PacificVis), 2015 IEEE Pacific", pages = "247--254", URL = "https://www.cg.tuwien.ac.at/research/publications/2015/lemuzic_2015_timelapse/", } @mastersthesis{textures-3d-printing, title = "Projector-Based Textures for 3D-Printed Models - Tangible Molecular Visualization", author = "Simon Brenner", year = "2015", abstract = "The now widely available 3D-printing technology enables structural molecular biologists to easily produce tangible models of large and complex molecules, which can aid them in understanding their spatial structure. Those models, however, are static and often monochrome, therefore their information content cannot compete with existing screenbased visualization solutions. Following the paradigm of spatial augmented reality, we present an approach to dynamically visualize molecular properties directly on the surface of 3D-printed tangible models, using a digital projector. We developed a prototype system consisting of hardware and software, that enables the tracking of the tangible model and the rendering of colorcoded molecular properties, which are then projected onto the tangible surface. Using knowledge about the geometry of the molecular model, the optical properties of the digital projector and the exact spatial relation between projector and model, the rendered projections are updated in real-time, such that they stay registered with the tangible model during user interaction. We evaluated the usability and potential applicability of the developed system by collecting feedback from domain experts from the fields of biochemistry and molecular biology.", address = "Favoritenstrasse 9-11/E193-02, A-1040 Vienna, Austria", school = "Institute of Computer Graphics and Algorithms, Vienna University of Technology ", keywords = "augmented reality, 3D textures, biomedical visualization", URL = "https://www.cg.tuwien.ac.at/research/publications/2015/textures-3d-printing/", } @article{waldner-2014-af, title = " Attractive Flicker: Guiding Attention in Dynamic Narrative Visualizations", author = "Manuela Waldner and Mathieu Le Muzic and Matthias Bernhard and Werner Purgathofer and Ivan Viola", year = "2014", abstract = "Focus+context techniques provide visual guidance in visualizations by giving strong visual prominence to elements of interest while the context is suppressed. However, finding a visual feature to enhance for the focus to pop out from its context in a large dynamic scene, while leading to minimal visual deformation and subjective disturbance, is challenging. This paper proposes Attractive Flicker, a novel technique for visual guidance in dynamic narrative visualizations. We first show that flicker is a strong visual attractor in the entire visual field, without distorting, suppressing, or adding any scene elements. The novel aspect of our Attractive Flicker technique is that it consists of two signal stages: The first “orientation stage” is a short but intensive flicker stimulus to attract the attention to elements of interest. Subsequently, the intensive flicker is reduced to a minimally disturbing luminance oscillation (“engagement stage”) as visual support to keep track of the focus elements. To find a good trade-off between attraction effectiveness and subjective annoyance caused by flicker, we conducted two perceptual studies to find suitable signal parameters. We showcase Attractive Flicker with the parameters obtained from the perceptual statistics in a study of molecular interactions. With Attractive Flicker, users were able to easily follow the narrative of the visualization on a large display, while the flickering of focus elements was not disturbing when observing the context.", month = dec, journal = "IEEE Transactions on Visualization and Computer Graphics", volume = "20", number = "12", pages = "2456--2465", keywords = "Narrative Visualization, Flicker, Visual Attention", URL = "https://www.cg.tuwien.ac.at/research/publications/2014/waldner-2014-af/", } @bachelorsthesis{puenguentzky-2014-ht, title = "HistoryTime: A Chrome history visualization using WebGL", author = "Roman P\"{u}ng\"{u}ntzky2", year = "2014", abstract = "Even though modern web browsers offer history functionalities, only few people use it to re-visit previously visited websites. In this thesis we present HistoryTime, a 3D visualization of the Google Chrome browser history. The goal of this project was to visualize the content of a user’s web browsing history in an aesthetic way, as well as to increase the general motivation to use it. We developed a 3-dimensional, visually appealing extension for Google Chrome that offers various possibilities, sorting-modes and browsing-functionalities which should make exploring and searching for websites in the history more pleasant to use. The data is retrieved via the Chrome history API exclusively, and visualized in a WebGL environment using the three.js JavaScript 3D library. The prototype of HistoryTime was tested and compared to the standard Google Chrome browser history in the scope of a small user study. The results indicated that our extension offered a better usability overall, and also allowed to solve certain tasks that were not possible with the standard history.", month = nov, address = "Favoritenstrasse 9-11/E193-02, A-1040 Vienna, Austria", school = "Institute of Computer Graphics and Algorithms, Vienna University of Technology ", URL = "https://www.cg.tuwien.ac.at/research/publications/2014/puenguentzky-2014-ht/", } @article{birkeland_aasmund_2014_pums, title = "Perceptually Uniform Motion Space", author = "{\AA}smund Birkeland and Cagatay Turkay and Ivan Viola", year = "2014", abstract = "Flow data is often visualized by animated particles inserted into a ?ow ?eld. The velocity of a particle on the screen is typically linearly scaled by the velocities in the data. However, the perception of velocity magnitude in animated particles is not necessarily linear. We present a study on how different parameters affect relative motion perception. We have investigated the impact of four parameters. The parameters consist of speed multiplier, direction, contrast type and the global velocity scale. In addition, we investigated if multiple motion cues, and point distribution, affect the speed estimation. Several studies were executed to investigate the impact of each parameter. In the initial results, we noticed trends in scale and multiplier. Using the trends for the signi?cant parameters, we designed a compensation model, which adjusts the particle speed to compensate for the effect of the parameters. We then performed a second study to investigate the performance of the compensation model. From the second study we detected a constant estimation error, which we adjusted for in the last study. In addition, we connect our work to established theories in psychophysics by comparing our model to a model based on Stevens’ Power Law.", month = nov, journal = "IEEE Transactions on Visualization and Computer Graphics", volume = "20", number = "11", issn = "1077-2626", pages = "1542--1554", keywords = "motion visualization, motion perception, animation, evauation, perceptual model", URL = "https://www.cg.tuwien.ac.at/research/publications/2014/birkeland_aasmund_2014_pums/", } @inproceedings{waldner-2014-ghi, title = "Graphical Histories of Information Foraging", author = "Manuela Waldner and Stefan Bruckner and Ivan Viola", year = "2014", abstract = "During information foraging, knowledge workers iteratively seek, filter, read, and extract information. When using multiple information sources and different applications for information processing, re-examination of activities for validation of previous decisions or re-discovery of previously used information sources is challenging. In this paper, we present a novel representation of cross-application histories to support recall of past operations and re-discovery of information resources. Our graphical history consists of a cross-scale visualization combining an overview node-link diagram of used desktop resources with nested (animated) snapshot sequences, based on a recording of the visual screen output during the users’ desktop work. This representation makes key elements of the users’ tasks visually stand out, while exploiting the power of visual memory to recover subtle details of their activities. In a preliminary study, users found our graphical history helpful to recall details of an information foraging task and commented positively on the ability to expand overview nodes into snapshot and video sequences.", month = oct, isbn = "978-1-4503-2542-4", publisher = "ACM", organization = "NordiCHI’14 - Nordic Conference on Human-Computer Interaction", location = "Helsinki, Finland", booktitle = "Proceedings of the 8th Nordic Conference on Human-Computer Interaction: Fun, Fast, Foundational ", pages = "295--304", keywords = "Graph visualization, Interaction history, Provenance", URL = "https://www.cg.tuwien.ac.at/research/publications/2014/waldner-2014-ghi/", } @article{Viola_Ivan_IIP, title = "Interactively illustrating polymerization using three-level model fusion", author = "Ivan Koles\'{a}r and Julius Parulek and Ivan Viola and Stefan Bruckner and Anne-Kristin Stavrum and Helwig Hauser", year = "2014", abstract = "Background: Research in cell biology is steadily contributing new knowledge about many aspects of physiological processes, both with respect to the involved molecular structures as well as their related function. llustrations of the spatio-temporal development of such processes are not only used in biomedical education, but also can serve scientists as an additional platform for in-silico experiments. Results: In this paper, we contribute a new, three-level modeling approach to illustrate physiological processes from the class of polymerization at different time scales. We integrate physical and empirical modeling, according to which approach best suits the different involved levels of detail, and we additionally enable a form of interactive steering, while the process is illustrated. We demonstrate the suitability of our approach in the context of several polymerization processes and report from a first evaluation with domain experts. Conclusion: We conclude that our approach provides a new, hybrid modeling approach for illustrating the process of emergence in physiology, embedded in a densely filled environment. Our approach of a complementary fusion of three systems combines the strong points from the different modeling approaches and is capable to bridge different spatial and temporal scales.", month = oct, issn = "1471-2105", journal = "BMC Bioinformatics 2014", number = "345", volume = "15", pages = "1--16", keywords = "Multi-agent modeling, L-system modeling, Biochemical visualization, Visualization of physiology, Polymerization", URL = "https://www.cg.tuwien.ac.at/research/publications/2014/Viola_Ivan_IIP/", } @bachelorsthesis{Gehrer_Daniel_CUI, title = "CellUnity an Interactive Tool for Illustrative Visualization of Molecular Reactions", author = "Daniel Gehrer", year = "2014", abstract = "CellUnity is a tool for interactive visualization of molecular reactions using the Unity game engine. Current mesoscale visualizations commonly utilize the results of particle-based simulations, which account for spatial information of each single particle and are supposed to mimic a realistic behavior of the metabolites. However, this approach employs stochastic simulation methods which do not offer any control over the visualized output. CellUnity, on the other hand, exploits the results of deterministic simulations which are purely quantitative and in that way offering full user control over the spatial locations of the reactions. The user is able to trigger reactions on demand instead of having to wait or search for a specific type of reaction event, while the quantities of displayed molecules would still be in accordance with real scientific data. CellUnity exploits the simulation results in real time and allows the user to freely modify simulation parameters while the system is running. The tool was realized in Unity, a cross-platform game engine that also comprises a free version with adequate functionality and therefore enables easy deployment of the project.", month = sep, address = "Favoritenstrasse 9-11/E193-02, A-1040 Vienna, Austria", school = "Institute of Computer Graphics and Algorithms, Vienna University of Technology ", URL = "https://www.cg.tuwien.ac.at/research/publications/2014/Gehrer_Daniel_CUI/", } @inproceedings{Viola_Ivan_VDP, title = "Visibility-Driven Processing of Streaming Volume Data", author = "Veronika Solteszova and {\AA}smund Birkeland and Ivan Viola and Stefan Bruckner", year = "2014", abstract = "In real-time volume data acquisition, such as 4D ultrasound, the raw data is challenging to visualize directly without additional processing. Noise removal and feature detection are common operations, but many methods are too costly to compute over the whole volume when dealing with live streamed data. In this paper, we propose a visibility-driven processing scheme for handling costly on-the-fly processing of volumetric data in real-time. In contrast to the traditional visualization pipeline, our scheme utilizes a fast computation of the potentially visible subset of voxels which significantly reduces the amount of data required to process. As filtering operations modify the data values which may affect their visibility, our method for visibility-mask generation ensures that the set of elements deemed visible does not change after processing. Our approach also exploits the visibility information for the storage of intermediate values when multiple operations are performed in sequence, and can therefore significantly reduce the memory overhead of longer filter pipelines. We provide a thorough technical evaluation of the approach and demonstrate it on several typical scenarios where on-the-fly processing is required.", month = sep, isbn = "978-3-905674-62-0", publisher = "Eurographics Association", location = "Vienna, Austria", issn = "2070-5778", event = "4th EG Workshop on Visual Computing and Biology Medicine", editor = "Ivan Viola and Katja Buehler and Timo Ropinski", booktitle = "Proceedings of EG VCBM 2014", pages = "127--136", URL = "https://www.cg.tuwien.ac.at/research/publications/2014/Viola_Ivan_VDP/", } @incollection{Viola_Ivan_UVP, title = "The Ultrasound Visualization Pipeline", author = "{\AA}smund Birkeland and Veronika Solteszova and Dieter H\"{o}nigmann and Odd Helge Gilja and Svein Brekke and Timo Ropinski and Ivan Viola", year = "2014", abstract = "Radiology is one of the main tools in modern medicine. A numerous set of deceases, ailments and treatments utilize accurate images of the patient. Ultrasound is one of the most frequently used imaging modality in medicine. The high spatial resolution, its interactive nature and non-invasiveness makes it the first choice in many examinations. Image interpretation is one of ultrasound’s main challenges. Much training is required to obtain a confident skill level in ultrasound-based diagnostics. State-of-the-art graphics techniques is needed to provide meaningful visualizations of ultrasound in real-time. In this paper we present the process-pipeline for ultrasound visualization, including an overview of the tasks performed in the specific steps. To provide an insight into the trends of ultrasound visualization research, we have selected a set of significant publications and divided them into a technique-based taxonomy covering the topics pre-processing, segmentation, registration, rendering and augmented reality. For the different technique types we discuss the difference between ultrasound-based techniques and techniques for other modalities.", month = sep, address = "http://link.springer.com/chapter/10.1007%2F978-1-4471-6497-5_24", booktitle = "Scientific Visualization", chapter = "Uncertainty, Multifield, Biomedical, and Scalable Visualization", editor = "Charles D. Hansen, Min Chen, Christopher R. Johnson, Arie E. Kaufman, Hans Hagen", isbn = "978-1-4471-6496-8", publisher = "Springer London", series = "Mathematics and Visualization", URL = "https://www.cg.tuwien.ac.at/research/publications/2014/Viola_Ivan_UVP/", } @inproceedings{Viola_Ivan_DAC, title = "Deriving Anatomical Context from 4D Ultrasound", author = "Markus M\"{u}ller and Linn E. S. Helljesen and Raphael Prevost and Ivan Viola and Kim Nylund and Odd Helge Gilja and Nassir Navab and Wolfgang Wein", year = "2014", abstract = "Real-time three-dimensional (also known as 4D) ultrasound imaging using matrix array probes has the potential to create large-volume information of entire organs such as the liver without external tracking hardware. This information can in turn be placed into the context of a CT or MRI scan of the same patient. However for such an approach many image processing challenges need to be overcome and sources of error addressed, including reconstruction drift, anatomical deformations, varying appearance of anatomy, and imaging artifacts. In this work,we present a fully automatic system including robust image-based ultrasound tracking, a novel learning-based global initialization of the anatomical context, and joint mono- and multi-modal registration. In an evaluation on 4D US sequences and MRI scans of eight volunteers we achieve automatic reconstruction and registration without any user interaction, assess the registration errors based on physician-defined landmarks, and demonstrate realtime tracking of free-breathing sequences.", month = sep, isbn = "978-3-905674-62-0", publisher = "Eurographics Association", note = "The electronic version of the proceedings is available from the Eurographics Digital Library at http://diglib.eg.org", location = "Vienna, Austria", issn = "2070-5778", event = "4th Eurographics Workshop on Visual Computing for Biology and Medicine", editor = "Ivan Viola and Katja Buehler and Timo Ropinski", booktitle = "Proceedings of EG VCBM14", pages = "173--180", URL = "https://www.cg.tuwien.ac.at/research/publications/2014/Viola_Ivan_DAC/", } @article{bernhard-2014-GTOM, title = "Gaze-To-Object Mapping During Visual Search in 3D Virtual Environments ", author = "Matthias Bernhard and Efstathios Stavrakis and Michael Hecher and Michael Wimmer", year = "2014", abstract = "Stimuli obtained from highly dynamic 3D virtual environments and synchronous eye-tracking data are commonly used by algorithms that strive to correlate gaze to scene objects, a process referred to as Gaze-To-Object Mapping (GTOM). We propose to address this problem with a probabilistic approach using Bayesian inference. The desired result of the inference is a predicted probability density function (PDF) specifying for each object in the scene a probability to be attended by the user. To evaluate the quality of a predicted attention PDF, we present a methodology to assess the information value (i.e., likelihood) in the predictions of dierent approaches that can be used to infer object attention. To this end, we propose an experiment based on a visual search task which allows us to determine the object of attention at a certain point in time under controlled conditions. We perform this experiment with a wide range of static and dynamic visual scenes to obtain a ground-truth evaluation data set, allowing us to assess GTOM techniques in a set of 30 particularly challenging cases.", month = aug, journal = "ACM Transactions on Applied Perception (Special Issue SAP 2014)", volume = "11", number = "3", issn = "1544-3558", pages = "14:1--14:17", keywords = "object-based attention, eye-tracking, virtual environments, visual attention", URL = "https://www.cg.tuwien.ac.at/research/publications/2014/bernhard-2014-GTOM/", } @inproceedings{kolesar-ivan-2014-polymers, title = "Illustrating Polymerization using Three-level Model Fusion", author = "Ivan Koles\'{a}r and Julius Parulek and Ivan Viola and Stefan Bruckner and Anne-Kristin Stavrum and Helwig Hauser", year = "2014", abstract = "Research in cell biology is steadily contributing new knowledge about many di?erent aspects of physiological processes like polymerization, both with respect to the involved molecular structures as well as their related function. Illustrations of the spatio-temporal development of such processes are not only used in biomedical education, but also can serve scientists as an additional platform for in-silico experiments. In this paper, we contribute a new, three-level modeling approach to illustrate physiological processes from the class of polymerization at di?erent time scales. We integrate physical and empirical modeling, according to which approach suits the di?erent involved levels of detail best, and we additionally enable a simple form of interactive steering while the process is illustrated. We demonstrate the suitability of our approach in the context of several polymerization processes and report from a ?rst evaluation with domain experts.", month = jul, publisher = "IEEE Digital Library", organization = "4th Symposium on Biological Data Visualization (in Conjunction with the International Conference on Intelligent Systems for Molecular Biology (ISMB 2014)) ", location = "Boston, USA", booktitle = "Proceedings of IEEE BioVis 2014", pages = "1--22", URL = "https://www.cg.tuwien.ac.at/research/publications/2014/kolesar-ivan-2014-polymers/", } @article{lemuzic-2014-ivm, title = "Illustrative Visualization of Molecular Reactions using Omniscient Intelligence and Passive Agents ", author = "Mathieu Le Muzic and Julius Parulek and Anne-Kristin Stavrum and Ivan Viola", year = "2014", abstract = "In this paper we propose a new type of a particle systems, tailored for illustrative visualization purposes, in particular for visualizing molecular reactions in biological networks. Previous visualizations of biochemical processes were exploiting the results of agent-based modeling. Such modeling aims at reproducing accurately the stochastic nature of molecular interactions. However, it is impossible to expect events of interest happening at a certain time and location, which is impractical for storytelling. To obtain the means of controlling molecular interactions, we propose to govern passive agents with an omniscient intelligence, instead of giving to the agents the freedom of initiating reaction autonomously. This makes it possible to generate illustrative animated stories that communicate the functioning of the molecular machinery. The rendering performance delivers for interactive framerates of massive amounts of data, based on the dynamic tessellation capabilities of modern graphics cards. Finally, we report an informal expert feedback we obtained from the potential users.", month = jun, journal = "Computer Graphics Forum", volume = "33", number = "3", note = "Article first published online: 12 JUL 2014", pages = "141--150", URL = "https://www.cg.tuwien.ac.at/research/publications/2014/lemuzic-2014-ivm/", } @article{Viola_Ivan_CLD, title = "Continuous Levels-of-Detail and Visual Abstraction for Seamless Molecular Visualization", author = "Julius Parulek and Daniel J\"{o}nsson and Timo Ropinski and Stefan Bruckner and Anders Ynnerman and Ivan Viola", year = "2014", abstract = "Molecular visualization is often challenged with rendering of large molecular structures in real time. We introduce a novel approach that enables us to show even large protein complexes. Our method is based on the level-of-detail concept, where we exploit three different abstractions combined in one visualization. Firstly, molecular surface abstraction exploits three different surfaces, solvent-excluded surface (SES), Gaussian kernels and van der Waals spheres, combined as one surface by linear interpolation. Secondly, we introduce three shading abstraction levels and a method for creating seamless transitions between these representations. The SES representation with full shading and added contours stands in focus while on the other side a sphere representation of a cluster of atoms with constant shading and without contours provide the context. Thirdly, we propose a hierarchical abstraction based on a set of clusters formed on molecular atoms. All three abstraction models are driven by one importance function classifying the scene into the near-, mid- and far-field. Moreover, we introduce a methodology to render the entire molecule directly using the A-buffer technique, which further improves the performance. The rendering performance is evaluated on series of molecules of varying atom counts.", month = may, issn = "0167-7055", journal = "Computer Graphics Forum", number = "6", volume = "33", pages = "276--287", keywords = "clustering, implicit surfaces, level of detail algorithms, scientific visualization, Computer Applications", URL = "https://www.cg.tuwien.ac.at/research/publications/2014/Viola_Ivan_CLD/", } @bachelorsthesis{boesch_2014_browserHistoryVis, title = "The Chaser: Chrome Extension for History Visualization", author = "Chris B\"{o}sch", year = "2014", abstract = "Revisitation of previously requested URLs happens frequently and the most common list-view-based visualization of the user’s browsing history provided by nearly every internet browser cannot give a compact general view. For this reason we designed and implemented an extension for Chrome called The Chaser, by which an alternative visualization of the content is possible. The currently available add-ons / extensions have other aims to illustrate the history. Some of them are about to show the differences in quantity of called pages. Others give an overview of page paths and the user’s tracks from site to site. Our extension concentrates on helping finding a visited page and giving users a better overview of their called URLs. The user should get the ability to control the time-line with mouse gestures and/or keyboard input. After discarding a 3D prototype we came to the conclusion of designing a simple, self-explanatory time-based illustration with two dimensions. The x-axis represents the time with different levels of detail and the y-axis the visited hosts. After performing an evaluation with six probands where The Chaser’s visualization and its efficiency was compared to the standard list-view, all of them would prefer our extension against the standard history view.", address = "Favoritenstrasse 9-11/E193-02, A-1040 Vienna, Austria", school = "Institute of Computer Graphics and Algorithms, Vienna University of Technology ", URL = "https://www.cg.tuwien.ac.at/research/publications/2014/boesch_2014_browserHistoryVis/", } @bachelorsthesis{koehle-2013-sgv, title = "Spatiotemporal genealogy visualization", author = "Dominik K\"{o}hle", year = "2013", abstract = "The focus of conventional genealogy visualization techniques lies on showing genera- tional and perhaps temporal relationships. A family tree, for instance, perfectly shows dates of birth and death of a person, who is the child of whom, as well as marriages and divorces. But to fully understand an individual’s life, it is important to know some more facts: Where was the person born? When did she or he leave home? How often and where to did that person move? Where did people meet? We propose a combination of a space-time cube and a timeline visualization to be able to actually see a person’s life. The timeline visualization shows generational and temporal relationships, where the space-time cube visualizes spatial relationships and movements of a single person as well as those of whole families. Event clouds (additional information layers for historic events) can further show possible connections between such events and migration of a person/family. ", month = dec, address = "Favoritenstrasse 9-11/E193-02, A-1040 Vienna, Austria", school = "Institute of Computer Graphics and Algorithms, Vienna University of Technology ", keywords = "spatio-temporal visualization, genealogy ", URL = "https://www.cg.tuwien.ac.at/research/publications/2013/koehle-2013-sgv/", } @article{Viola_Ivan_2013_VCA, title = "Visual cavity analysis in molecular simulations", author = "Julius Parulek and Cagatay Turkay and Nathalie Reuter and Ivan Viola", year = "2013", abstract = "Molecular surfaces provide a useful mean for analyzing interactions between biomolecules; such as identification and characterization of ligand binding sites to a host macromolecule. We present a novel technique, which extracts potential binding sites, represented by cavities, and characterize them by 3D graphs and by amino acids. The binding sites are extracted using an implicit function sampling and graph algorithms. We propose an advanced cavity exploration technique based on the graph parameters and associated amino acids. Additionally, we interactively visualize the graphs in the context of the molecular surface. We apply our method to the analysis of MD simulations of Proteinase 3, where we verify the previously described cavities and suggest a new potential cavity to be studied.", month = nov, issn = "1471-2105", journal = "BMC Bioinformatics", number = "Suppl 19:S4 ", volume = "14", pages = "1--15", URL = "https://www.cg.tuwien.ac.at/research/publications/2013/Viola_Ivan_2013_VCA/", } @misc{Viola_2013_IDV, title = "Importance Driven Visualization of Molecular Surfaces", author = "Julius Parulek and Timo Ropinski and Ivan Viola", year = "2013", abstract = "We present a novel rendering method, based on the level-of-detail concept, which shows protein complexes over time in real-time. We exploit three different molecular surface models, solvent excluded surface (SES), Gaussian kernels and van der Waals spheres combined in one seamless visualization. As a general rule, closest to the viewer we aim at providing a maximum of relevant information related to the structure and binding sites. Such information is conveyed by the SES representation. Farther away from the viewer, we are smoothly changing the visual representation to an approximation of SES through Gaussian kernels. The least detailed representation is based on simple sphere splatting and is dedicated to structures farthest away from the viewer. A more general solution leads us to the definition of a 3D importance function that is based on the distance measure from a molecular feature. In order to preserve smoothness in transition areas, we introduce three shading levels that correspond to their geometric counterparts and a method for creating seamless transition between these representations. The SES representation with full shading and added contours stands in focus while on the other side a sphere representation with constant shading and without contours provide the context. Moreover, we introduce a methodology to render the entire molecule directly using the A-buffer technique, which further improves the performance. The rendering performance is evaluated on series of molecules of varying atom counts.", month = oct, publisher = "BioVis website (http://www.biovis.net/year/2013/posters)", location = "Atlanta, GA", event = "3rd IEEE Symposium on Biological Data Visualization", Conference date = "Poster presented at 3rd IEEE Symposium on Biological Data Visualization (2013-10-13--2013-10-14)", URL = "https://www.cg.tuwien.ac.at/research/publications/2013/Viola_2013_IDV/", } @article{Viola_Ivan_2013_GS, title = "Geological storytelling", author = "Endre M. Lidal and Mattia Natali and Daniel Patel and Helwig Hauser and Ivan Viola", year = "2013", abstract = "Developing structural geological models from exploratory subsea imaging is difficult and an ill-posed process. The structural geological processes that take place in the subsurface are both complex and time-dependent. We present Geological Storytelling, a novel graphical system for performing rapid and expressive geomodeling. Geologists can convey geological stories that externalize both their model and the reasoning process behind it through our simple, yet expressive sketch-based, flip-over canvases. This rapid modeling interface makes it easy to construct a large variety of geological stories, and our story tree concept facilitates easy management and the exploration of these alternatives. The stories are then animated and the geologists can examine and compare them to identify the most plausible models. Finally, the geological stories can be presented as illustrative animations of automatically synthesized 3D models, which efficiently communicate the complex geological evolution to non-experts and decision makers. Geological storytelling provides a complete pipeline from the ideas and knowledge in the mind of the geologist, through externalized artifacts specialized for discussion and knowledge dissemination among peer-experts, to automatically rendered illustrative 3D animations for communication to lay audience. We have developed geological storytelling in collaboration with domain experts that work with the modeling challenges on a daily basis. For evaluation, we have developed a geological storytelling prototype and presented it to experts and academics from the geosciences. In their feedback, they acknowledge that the rapid and expressive sketching of stories can make them explore more alternatives and that the 3D illustrative animations assist in communicating their models.", month = aug, issn = "0097-8493", journal = "Computer & Graphics", number = "5", volume = "37", pages = "445--459", URL = "https://www.cg.tuwien.ac.at/research/publications/2013/Viola_Ivan_2013_GS/", } @article{Viola_Ivan_2013_RMA, title = "Rule-based method for automatic scaffold assembly from 3D building models", author = "Tyge Løvset and Dag Magne Ulvang and Tor Christian Bekkvik and K{\aa}re Villanger and Ivan Viola", year = "2013", abstract = "To manually specify an optimal scaffold assembly for a given building geometry is a time consuming task. Our goal is to automate the process of selecting and placing scaffold components in order to design an optimal scaffold assembly for a specific building. The resulting assembly must be possible to construct in practice, should be practical to use for the workers, must satisfy governmental rules and regulations and should ideally result in minimum accumulated component cost. We propose a novel procedural modeling pipeline based on an input house model. First we extract vital coordinates from the house model that define the 3D scaffold placement. These coordinates are the basis for defining the positioning of scaffold cells. In the next step we populate the cells with actual scaffold components geometry. The resulting model is visualized to assist the assembly process. Additionally it is decomposed into elementary building blocks to produce assembly component lists to estimate the scaffold cost estimates, compute the weight for transportation and packing of components from a warehouse. The result from the automated process is compared to scaffold design produced manually by a professional scaffold designer.", month = jun, issn = "0097-8493", journal = "Computer & Graphics", number = "4", volume = "37", pages = "256--268", URL = "https://www.cg.tuwien.ac.at/research/publications/2013/Viola_Ivan_2013_RMA/", } @inproceedings{Viola_Ivan_2013_RSb, title = "Rapid Sketch-based 3D Modeling of Geology", author = "Endre M. Lidal and Morten Bendiksen and Daniel Patel and Ivan Viola", year = "2013", abstract = "We present and compare two different approaches for performing rapid 3D geological modeling. The ad-hoc approach is based on a composition of many specialized modeling functions, while the generic approach provides one powerful, generic modeling function. Our experiences after developing these two approaches are that the solution space of 3D geological modeling is more extensive than we initially expected and most likely larger than for other modeling domains such as architecture. Further, more research is needed to investigate whether it is possible to find one well defined toolset of sketching metaphors that is able to cover all of geological modeling.", month = jun, publisher = "Springer", organization = "Euro Vis 2013", note = "Workshop on Visualisation in Environmental Sciences (EnvirVis) (2013)", location = "Leipzig, Germany", booktitle = "Proceedings of EnvirVis Short Papers 2013, 2013", pages = "1--5", URL = "https://www.cg.tuwien.ac.at/research/publications/2013/Viola_Ivan_2013_RSb/", } @inproceedings{2013_Viola_Ivan_2013_MTS, title = "Modeling Terrains and Subsurface Geology", author = "Mattia Natali and Endre M. Lidal and Julius Parulek and Ivan Viola and Daniel Patel", year = "2013", abstract = "The process of creating terrain and landscape models is important in a variety of computer graphics and visualization applications, from films and computer games, via flight simulators and landscape planning, to scientific visualization and subsurface modelling. Interestingly, the modelling techniques used in this large range of application areas have started to meet in the last years. In this state-of-the-art report, we present two taxonomies of different modelling methods. Firstly we present a data oriented taxonomy, where we divide modelling into three different scenarios: the data-free, the sparse-data and the dense-data scenario. Then we present a workflow oriented taxonomy, where we divide modelling into the separate stages necessary for creating a geological model. We start the report by showing that the new trends in geological modelling are approaching the modelling methods that have been developed in computer graphics. We then give an introduction to the process of geological modelling followed by our two taxonomies with descriptions and comparisons of selected methods. Finally we discuss the challenges and trends in geological modelling.", month = may, publisher = "Eurographics 2013 - State of the Art Reports", organization = "Eurographics", location = "Girona, Spain", booktitle = "INPROCEEDINGS, EuroGraphics 2013 State of the Art Reports (STARs), 2013", pages = "155--173", URL = "https://www.cg.tuwien.ac.at/research/publications/2013/2013_Viola_Ivan_2013_MTS/", } @inproceedings{waldner-2013-ubiWM, title = "Towards Ubiquitous Information Space Management", author = "Manuela Waldner and Dieter Schmalstieg", year = "2013", abstract = "Large, high-resolution display spaces are usually created by carefully aligning multiple monitors or projectors to obtain a perfectly flat, rectangular display. In this paper, we suggest the usage of imperfect surfaces as extension of personal workspaces to create ubiquitous, personalized information spaces. We identify five environmental factors ubiquitous information spaces need to consider: 1) user location and display visibility, 2) display gaps and holes, 3) corners and non-planarity of the display surface, 4) physical objects within and around the display surface, and 5) non-rectangular display shapes. Instead of compensating for fragmentations and non-planarity of the information space, we propose a ubiquitous information space manager, adapting interaction and window rendering techniques to the above mentioned factors. We hypothesize that knowledge workers will benefit from such ubiquitous information spaces due to increased exploitation of spatial cognition. ", month = may, isbn = "978-1-4503-1952-2", publisher = "ACM", location = "Paris, France", booktitle = "POWERWALL: International Workshop on Interactive, Ultra-High-Resolution Displays, part of the SIGCHI Conference on Human Factors in Computing Systems (2013)", pages = "1--6", keywords = "information management, ubiquitous displays", URL = "https://www.cg.tuwien.ac.at/research/publications/2013/waldner-2013-ubiWM/", } @inproceedings{Viola_Ivan_2013_HQ3, title = "High-Quality 3D Visualization of In-Situ Ultrasonography", author = "Ivan Viola and {\AA}smund Birkeland and Veronika Solteszova and Linn Helljesen and Helwig Hauser and Spiros Kotopoulis and Kim Nylund and Dag Magne Ulvang and Ola Kristoffer Øye and Trygve Hausken and Odd Helge Gilja", year = "2013", abstract = "In recent years medical ultrasound has experienced a rapid development in the quality of real-time 3D ultrasound (US) imaging. The image quality of the 3D volume that was previously possible to achieve within the range of a few seconds, is now possible in a fraction of a second. This technological advance offers entirely new opportunities for the use of US in the clinic. In our project, we investigate how real-time 3D US can be combined with high-performance processing of today’s graphics hardware to allow for high-quality 3D visualization and precise navigation during the examination.", month = may, publisher = "Eurogrpahics", note = "1st Prize - Medical Prize Short Paper", location = "Girona, Spain", booktitle = "EG 2013 - Dirk Bartz Prize", pages = "1--4", URL = "https://www.cg.tuwien.ac.at/research/publications/2013/Viola_Ivan_2013_HQ3/", } @inproceedings{waldner-2013-facetCloudsGI, title = "FacetClouds: Exploring Tag Clouds for Multi-Dimensional Data", author = "Manuela Waldner and Johann Schrammel and Michael Klein and Katrin Kristjansdottir and Dominik Unger and Manfred Tscheligi", year = "2013", abstract = "Tag clouds are simple yet very widespread representations of how often certain words appear in a collection. In conventional tag clouds, only a single visual text variable is actively controlled: the tags’ font size. Previous work has demonstrated that font size is indeed the most influential visual text variable. However, there are other variables, such as text color, font style and tag orientation, that could be manipulated to encode additional data dimensions. FacetClouds manipulate intrinsic visual text variables to encode multiple data dimensions within a single tag cloud. We conducted a series of experiments to detect the most appropriate visual text variables for encoding nominal and ordinal values in a cloud with tags of varying font size. Results show that color is the most expressive variable for both data types, and that a combination of tag rotation and background color range leads to the best overall performance when showing multiple data dimensions in a single tag cloud. ", month = may, isbn = "978-1-4822-1680-6 ", publisher = "ACM Publishing House", organization = "ACM Siggraph", location = "Regina, Saskatchewan, Canada", address = "Regina, Saskatchewan, Canada", booktitle = "Proceedings of the 2013 Graphics Interface Conference", pages = "17--24", URL = "https://www.cg.tuwien.ac.at/research/publications/2013/waldner-2013-facetCloudsGI/", } @inproceedings{Viola_Ivan_2013_D3D, title = "Doppler-based 3D Blood Flow Imaging and Visualization", author = "{\AA}smund Birkeland and Dag Magne Ulvang and Kim Nylund and Trygve Hausken and Odd Helge Gilja and Ivan Viola", year = "2013", abstract = "Blood flow is a very important part of human physiology. In this paper, we present a new method for estimating and visualizing 3D blood flow on-the-fly based on Doppler ultrasound. We add semantic information about the geometry of the blood vessels in order to recreate the actual velocities of the blood. Assuming a laminar flow, the flow direction is related to the general direction of the vessel. Based on the center line of the vessel, we create a vector field representing the direction of the vessel at any given point. The actual flow velocity is then estimated from the Doppler ultrasound signal by back-projecting the velocity in the measured direction, onto the vessel direction. Additionally, we estimate the flux at user-selected cross-sections of the vessel by integrating the velocities over the area of the cross-section. In order to visualize the flow and the flux, we propose a visualization design based on traced particles colored by the flux. The velocities are visualized by animating particles in the flow field. Further, we propose a novel particle velocity legend as a means for the user to estimate the numerical value of the current velocity. Finally, we perform an evaluation of the technique where the accuracy of the velocity estimation is measured using a 4D MRI dataset as a basis for the ground truth.", month = may, isbn = "978-80-223-3377-1", publisher = "ACM Publishing House", location = "Smolenice, Slovak Republic", booktitle = "SCCG 2013 - 29th Proceedings Spring conference on Computer Graphics", pages = "128--135", keywords = "Medical Visualization, Biomedical", URL = "https://www.cg.tuwien.ac.at/research/publications/2013/Viola_Ivan_2013_D3D/", } @inproceedings{Viola_Ivan_2013_SVA, title = "Seamless Visual Abstraction of Molecular Surfaces", author = "Julius Parulek and Timo Ropinski and Ivan Viola", year = "2013", abstract = "Molecular visualization is often challenged with rendering of large sequences of molecular simulations in real time. We introduce a novel approach that enables us to show even large protein complexes over time in real-time. Our method is based on the level-ofdetail concept, where we exploit three different molecular surface models, solvent excluded surface (SES), Gaussian kernels and van der Waals spheres combined in one visualization. We introduce three shading levels that correspond to their geometric counterparts and a method for creating seamless transition between these representations. The SES representation with full shading and added contours stands in focus while on the other side a sphere representation with constant shading and without contours provide the context. Moreover, we introduce a methodology to render the entire molecule directly using the A-buffer technique, which further improves the performance. The rendering performance is evaluated on series of molecules of varying atom counts.", month = may, isbn = "978-80-223-3377-1", series = " SCCG '13", publisher = "ACM Publishing House", organization = "Comenius University, Bratislava", location = "Smolenice, Slovak Republic", editor = "Roman Durikovi\v{c}, Holly Rushmeier", booktitle = "SCCG 2013 - 29th Proceedings Spring conference on Computer Graphics", pages = "120--127", keywords = "Implicit Surfaces, Level-of-detail, Visualization of Molecular Surfaces", URL = "https://www.cg.tuwien.ac.at/research/publications/2013/Viola_Ivan_2013_SVA/", } @article{Viola_Ivan_2013_CAI, title = "Computer-aided image geometry analysis and subset selection for optimizing texture quality in photorealistic models", author = "Aleksandra Anna Sima and Xavier Bonaventura and Miquel Feixas and Mateu Sbert and John Anthony Howell and Ivan Viola and Simon John Buckley", year = "2013", abstract = "Photorealistic 3D models are used for visualization, interpretation and spatial measurement in many disciplines, such as cultural heritage, archaeology and geoscience. Using modern image- and laser-based 3D modelling techniques, it is normal to acquire more data than is finally used for 3D model texturing, as images may be acquired from multiple positions, with large overlap, or with different cameras and lenses. Such redundant image sets require sorting to restrict the number of images, increasing the processing efficiency and realism of models. However, selection of image subsets optimized for texturing purposes is an example of complex spatial analysis. Manual selection may be challenging and time-consuming, especially for models of rugose topography, where the user must account for occlusions and ensure coverage of all relevant model triangles. To address this, this paper presents a framework for computer-aided image geometry analysis and subset selection for optimizing texture quality in photorealistic models. The framework was created to offer algorithms for candidate image subset selection, whilst supporting refinement of subsets in an intuitive and visual manner. Automatic image sorting was implemented using algorithms originating in computer science and information theory, and variants of these were compared using multiple 3D models and covering image sets, collected for geological applications. The image subsets provided by the automatic procedures were compared to manually selected sets and their suitability for 3D model texturing was assessed. Results indicate that the automatic sorting algorithms are a promising alternative to manual methods. An algorithm based on a greedy solution to the weighted set-cover problem provided image sets closest to the quality and size of the manually selected sets. The improved automation and more reliable quality indicators make the photorealistic model creation workflow more accessible for application experts, increasing the user’s confidence in the final textured model completeness.", month = mar, journal = "Computers & Geosciences", volume = "52", pages = "281--291", URL = "https://www.cg.tuwien.ac.at/research/publications/2013/Viola_Ivan_2013_CAI/", } @talk{Viola_Ivan_2013_DC, title = "Declarative Visualization", author = "Ivan Viola", year = "2013", abstract = "Visualization algorithms are nowadays formalized in an imperative manner, i.e. the algorithm is explicitly executed on input data and dictates a determined visualization outcome. The efficiency of such an algorithm is measured by means of the computational performance, data-scalability and user studies. In my talk I will speculate on a novel theoretical concept for the development of new visualization methodology that becomes ultimately declarative and algorithm-free, by moving the user study from a validation stage into the center of the iterative design stage. Initial visualization from input data is considered as the first design draft, which will undergo several revisions. This draft can be achieved by executing a traditional imperative algorithm or it can even be hand-crafted by a skilled illustrator. A consequent user study of initial visualization will trigger computational synthesis of a new, quantitatively more effective visualization technique. The visualization designs developed through several iterations of the study-redesign cycle will become declarative, aiming at optimally satisfying the purpose of the visualization, instead of explicit execution of algorithms on the input data. The declarative component will be specified by collected user statistics from completing certain perceptual or cognitive tasks. The user statistics will be analyzed for systematic trends in human perceptual and cognitive performance. These trends will form a basis for visualization redesign. Final satisfactory visualization will evolve over several design iterations.", event = "SCCG 2013", location = "Smolenice castle, Slovakia", URL = "https://www.cg.tuwien.ac.at/research/publications/2013/Viola_Ivan_2013_DC/", } @runmasterthesis{rasch-2016-imgses, title = "Image-Space Solvent-Excluded Surface Visualization", author = "Martina Rasch", URL = "https://www.cg.tuwien.ac.at/research/publications/ongoing/rasch-2016-imgses/", } @talk{Groeller_2016_I7, title = "Visual Computing for the Analysis of Complex Systems", author = "Eduard Gr\"{o}ller", event = "Invited Talk at the Department of Computer Science and Engineering (CSE) at the Hong Kong University of Science and Technology (HKUST)", location = "Invited Talk at the Department of Computer Science and Engineering (CSE) at the Hong Kong University of Science and Technology (HKUST)", URL = "https://www.cg.tuwien.ac.at/research/publications/ongoing/Groeller_2016_I7/", }