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  • 1. Falk, Martin
    Visualization and mesoscopic simulation in systems biology2013Doctoral thesis, monograph (Other academic)
    Abstract [en]

    Biological cells appear everywhere on earth. They might live on their own as unicellular organism, like bacteria, or might form complex organisms consisting of several thousands or millions of cells. Despite their small size of only a few micrometers, they are complex little miracles. A better understanding of the internal mechanisms and interplays within a single cell is the key to the understanding of life. In the context of this thesis, the mechanism of cellular signal transduction, i.e. relaying a signal from outside the cell by different means of transport toward its target inside the cell, is employed. Understanding and adjusting parts of the cellular signaling mechanism will eventually lead to the design of new drugs with less or even without any side-effects. Besides experiments, understanding can also be achieved by numerical simulations of cellular behavior. This is where systems biology closely relates and depends on recent research results in computer science in order to deal with the modeling, the simulation, and the analysis of the computational results.

    Since a single cell can consist of billions of molecules, the simulation of intracellular processes requires a simplifiedmodel. Typically, mesoscopic models are used containing only parts that are believed to be necessary for the processes. The simulation domain has to be three dimensional to consider the spatial, possibly asymmetric, intracellular architecture filled with individual particles representing signaling molecules. In contrast to continuous models defined by systems of partial differential equations, a particle-based model allows tracking individual molecules moving through the cell. This particle-based approach, however, demands for a higher computational effort than, e.g., non-spatial models that can be solved with ordinary differential equations. The overall process of signal propagation usually requires between minutes and hours to complete, but the movement of molecules and the interactions between them have to be computed in the range of microseconds. Hence, the computation of thousands of consecutive time steps is necessary, requiring several hours or even days of computational time for a sequential simulation. The need for several simulation runs with different parameter settings, a higher level of detail including more particles, or a generally more precise simulation, i.e. smaller time steps, demands for short execution times of the simulation. To speed up the simulation, the parallel hardware of current central processing units (CPUs) and graphics processing units (GPUs) can be employed. The parallelization of interacting particles, however, is non-trivial and requires special care when utilizing modern manycore architectures like the GPU. Finally, the resulting data has to be analyzed by domain experts and, therefore, has to be represented in meaningful ways. Typical prevalent analysis methods include the aggregation of the data in tables or simple 2D graph plots, sometimes 3D plots for continuous data. Despite the fact that techniques for the interactive visualization of data in 3D are well-known, so far none of the methods have been applied to the biological context of single cell models and specialized visualizations fitted to the experts’ need are missing. Another issue is the hardware available to the domain experts that can be used for the task of visualizing the increasing amount of time-dependent data resulting from simulations. Exa-scale visualization still seems to be a long way off, but even the data sets available today are pushing the rendering capability of current graphics hardware to its limits. However, it is important that the visualization keeps up with the simulations to ensure that domain experts can still analyze their data sets. To deal with the massive amount of data to come, compute clusters will be necessary with specialized hardware dedicated to data visualization. It is, thus, important, to develop visualization algorithms for this dedicated hardware, which is currently available as GPU.

    In this thesis, the computational power of recent many-core architectures (CPUs as well as GPUs) is harnessed for both the simulation and the visualizations. Novel parallel algorithms are introduced to parallelize the spatio-temporal, mesoscopic particle simulation to fit the architectures of CPU and GPU in a similar way, easing the portability between both. Besides molecular diffusion, the simulation considers extracellular effects on the signal propagation as well as the import of molecules into the nucleus and a dynamic cytoskeleton. An extensive comparison between different configurations is performed leading to the conclusion that the usage of GPUs is not always beneficial. Depending on the simulation setup, however, the GPU implementation can be up to ten times faster than the parallel simulation on the CPU. For the visual data analysis, novel interactive visualization techniques were developed to visualize the 3D simulation results. Existing glyph-based approaches are combined in a new way facilitating the visualization of the individual molecules in the interior of the cell as well as their trajectories. A novel implementation of the depth of field effect, as known from photography, combined with additional depth cues and coloring aid the visual perception and reduce visual clutter. To obtain a continuous signal distribution from the discrete particles, techniques known from volume rendering are employed. The visualization of the underlying atomic structures provides new detailed insights and can be used for educational purposes besides showing the original data. The proposed technique allows for the interactive visualization of data sets containing several billion atoms per time step. A microscope-like visualization allows for the first time to generate images of synthetic data similar to images obtained in wet lab experiments. The simulation and the visualizations are merged into a prototypical framework, thereby supporting the domain expert during the different stages of model development, i.e. design, parallel simulation, and analysis.

    Although the proposed methods for both simulation and visualization were developed with the study of single-cell signal transduction processes in mind, they are also applicable to models consisting of several cells and other particle-based scenarios. Examples in this thesis include the diffusion of drugs into a tumor, the detection of protein cavities, and molecular dynamics data from laser ablation simulations, among others.

  • 2.
    Falk, Martin
    et al.
    VISUS - Visualization Research Center, University of Stuttgart, Germany.
    Daub, Markus
    Institute of Analysis, Dynamics, and Modeling, University of Stuttgart, Germany.
    Schneider, Guido
    Institute of Analysis, Dynamics, and Modeling, University of Stuttgart, Germany.
    Ertl, Thomas
    VISUS - Visualization Research Center, University of Stuttgart, Germany.
    Modeling and Visualization of Receptor Clustering on the Cellular Membrane2011In: IEEE Symposium on Biological Data Visualization (BioVis 2011), IEEE, 2011, p. 9-15Conference paper (Refereed)
    Abstract [en]

    In cell biology, apopotosis is a very important cellular process. Apopotosis, or programmed cell death, allows an organism to remove damaged or unneeded cells in a structured manner in contrast to necrosis. Ligands bind to the death receptors located on the cellular membrane forming ligand-receptor clusters. In this paper, we develop a novel mathematical model describing the stochastic process of the ligand-receptor clustering. To study the structure and the size of the receptor clusters, a stochastic particle simulation is employed. Besides the translation of the particles on the plasma membrane, we also take the particle rotation into account as we model binding sites explicitly. Glyph-based visualization techniques are used to validate and analyze the results of our in-silico model. Information on the individual clusters as well as particle-specific data can be selected by the user and are mapped to colors to highlight certain properties of the data. The preliminary results of our model look very promising. The visualization supports the process of model development by visual data analysis containing the identification of cluster components as well as the illustration of particle trajectories.

  • 3.
    Falk, Martin
    et al.
    VISUS – Visualization Research Center, University of Stuttgart, Germany.
    Grottel, S.
    VISUS – Visualization Research Center, University of Stuttgart, Germany.
    Ertl, T.
    VISUS – Visualization Research Center, University of Stuttgart, Germany.
    Interactive Image-Space Volume Visualization for Dynamic Particle Simulations2010In: Proceedings of SIGRAD 2010: Content Aggregation and Visualization / [ed] Kai-Mikael Jää-Aro Thomas Larsson, Linköping University Electronic Press, 2010, p. 35-43Conference paper (Refereed)
    Abstract [en]

    Particle-based simulation plays an important role in many different fields of science and engineering. Two common visualization approaches for the resulting data are glyph-based rendering and density sampling employing volume rendering. Fine geometric features are inherently captured by glyph-based methods. However, they might suffer from aliasing and the global structure is often poorly conveyed. Volume rendering preserves the global structure but is limited due to the sampling resolution. To avoid aliasing artifacts and large memory footprints, we propose a direct volume rendering technique with on-demand density sampling of the particle data, as combination of splatting, texture slicing, and ray casting. We optimized our system with a novel ray cast termination employing early-z-test culling and hardware occlusion queries utilizing inter-frame coherency. Our system contains a fully-featured volume renderer and captures all geometric features of the data set representable at the available display resolution. Since no pre-computation is required, the proposed method can be used easily to visualize time-dependent data sets. The effectiveness of our approach is shown with examples from different application fields.

  • 4.
    Falk, Martin
    et al.
    Linköping University, Department of Science and Technology, Media and Information Technology. Linköping University, Faculty of Science & Engineering.
    Grottel, Sebastian
    Technische Universität Dresden, Germany.
    Krone, Michael
    University of Stuttgart, Germany.
    Reina, Guido
    University of Stuttgart, Germany.
    Interactive GPU-based Visualization of Large Dynamic Particle Data2016Book (Refereed)
    Abstract [en]

    Prevalent types of data in scientific visualization are volumetric data, vector field data, and particle-based data. Particle data typically originates from measurements and simulations in various fields, such as life sciences or physics. The particles are often visualized directly, that is, by simple representants like spheres. Interactive rendering facilitates the exploration and visual analysis of the data. With increasing data set sizes in terms of particle numbers, interactive high-quality visualization is a challenging task. This is especially true for dynamic data or abstract representations that are based on the raw particle data.

    This book covers direct particle visualization using simple glyphs as well as abstractions that are application-driven such as clustering and aggregation. It targets visualization researchers and developers who are interested in visualization techniques for large, dynamic particle-based data. Its explanations focus on GPU-accelerated algorithms for high-performance rendering and data processing that run in real-time on modern desktop hardware. Consequently, the implementation of said algorithms and the required data structures to make use of the capabilities of modern graphics APIs are discussed in detail. Furthermore, it covers GPU-accelerated methods for the generation of application-dependent abstract representations. This includes various representations commonly used in application areas such as structural biology, systems biology, thermodynamics, and astrophysics.

  • 5.
    Falk, Martin
    et al.
    Linköping University, Department of Science and Technology, Media and Information Technology. Linköping University, Faculty of Science & Engineering.
    Hotz, Ingrid
    Linköping University, Department of Science and Technology, Media and Information Technology. Linköping University, Faculty of Science & Engineering.
    Ljung, Patric
    Linköping University, Department of Science and Technology, Media and Information Technology. Linköping University, Faculty of Science & Engineering.
    Treanor, Darren
    Linköping University, Center for Medical Image Science and Visualization (CMIV). Leeds Teaching Hospitals NHS Trust, United Kingdom.
    Ynnerman, Anders
    Linköping University, Department of Science and Technology, Media and Information Technology. Linköping University, Faculty of Science & Engineering. Linköping University, Center for Medical Image Science and Visualization (CMIV).
    Lundström, Claes
    Linköping University, Department of Science and Technology, Media and Information Technology. Linköping University, Faculty of Science & Engineering. Linköping University, Center for Medical Image Science and Visualization (CMIV). Sectra AB.
    Transfer Function Design Toolbox for Full-Color Volume Datasets2017In: 2017 IEEE PACIFIC VISUALIZATION SYMPOSIUM (PACIFICVIS), IEEE, IEEE, 2017, p. 171-179Conference paper (Refereed)
    Abstract [en]

    In this paper, we tackle the challenge of effective Transfer Function (TF) design for Direct Volume Rendering (DVR) of full-color datasets. We propose a novel TF design toolbox based on color similarity which is used to adjust opacity as well as replacing colors. We show that both CIE L*u*v* chromaticity and the chroma component of YCbCr are equally suited as underlying color space for the TF widgets. In order to maximize the area utilized in the TF editor, we renormalize the color space based on the histogram of the dataset. Thereby, colors representing a higher share of the dataset are depicted more prominently, thus providing a higher sensitivity for fine-tuning TF widgets. The applicability of our TF design toolbox is demonstrated by volume ray casting challenging full-color volume data including the visible male cryosection dataset and examples from 3D histology.

  • 6.
    Falk, Martin
    et al.
    VISUS - Visualization Research Center, Universität Stuttgart, Germany.
    Klann, Michael
    Institute of Biochemical Engineering and Center Systems Biology, Universität Stuttgart, Germany.
    Reuss, Matthias
    Institute of Biochemical Engineering and Center Systems Biology, Universität Stuttgart, Germany.
    Ertl, Thomas
    VISUS - Visualization Research Center, Universität Stuttgart, Germany.
    3D Visualization of Concentrations from Stochastic Agent-based Signal Transduction Simulations2010In: Biomedical Imaging: From Nano to Macro, 2010 IEEE International Symposium on: From Nano to Macro (ISBI 2010), IEEE, 2010, p. 1301-1304Conference paper (Refereed)
    Abstract [en]

    Cellular signal transduction involves a transport step from the plasma membrane towards the nucleus, during which the signaling molecules are partly deactivated in control loops. This leads to a gradient in the concentration of active signaling molecules. The low number of molecules introduces spatio-temporal fluctuations and the asymmetric cellular architecture further increases the complexity. We propose a technique to represent this pattern in a continuous three-dimensional concentration map. The local concentration is computed and visualized with volume rendering techniques at interactive frame rates and is therefore well-suited for time-dependent data. Our approach allows the transition from the nano-scale of single and discrete signaling proteins to a continuous signal on the cell level. In the application context of this paper, we employ an agent-based Monte Carlo simulation to calculate the actual particle positions depending on reaction and transport parameters in the cell. The applicability of the proposed technique is demonstrated by an investigation of the effects of different transport parameters in Mitogen-activated protein kinase (MAPK) signaling.

  • 7.
    Falk, Martin
    et al.
    VISUS - Visualization Research Center, Universität Stuttgart, Germany.
    Klann, Michael
    Institute of Biochemical Engineering and Center Systems Biology, Universität Stuttgart, Germany.
    Reuss, Matthias
    Institute of Biochemical Engineering and Center Systems Biology, Universität Stuttgart, Germany.
    Ertl, Thomas
    VISUS - Visualization Research Center, Universität Stuttgart, Germany.
    Visualization of Signal Transduction Processes in the Crowded Environment of the Cell2009In: IEEE Pacific Visualization Symposium (PacificVis 2009), 2009, p. 169-176Conference paper (Refereed)
    Abstract [en]

    In this paper, we propose a stochastic simulation to model and analyze cellular signal transduction. The high number of objects in a simulation requires advanced visualization techniques: first to handle the large data sets, second to support the human perception in the crowded environment, and third to provide an interactive exploration tool. To adjust the state of the cell to an external signal, a specific set of signaling molecules transports the information to the nucleus deep inside the cell. There, key molecules regulate gene expression. In contrast to continuous ODE models we model all signaling molecules individually in a more realistic crowded and disordered environment. Beyond spatiotemporal concentration profiles our data describes the process on a mesoscopic, molecular level, allowing a detailed view of intracellular events. In our proposed schematic visualization individual molecules, their tracks, or reactions can be selected and brought into focus to highlight the signal transduction pathway. Segmentation, depth cues and depth of field are applied to reduce the visual complexity. We also provide a virtual microscope to display images for comparison with wet lab experiments. The method is applied to distinguish different transport modes of MAPK (mitogen-activated protein kinase) signaling molecules in a cell. In addition, we simulate the diffusion of drug molecules through the extracellular space of a solid tumor and visualize the challenges in cancer related therapeutic drug delivery.

  • 8.
    Falk, Martin
    et al.
    Visualization Research Center (VISUS), University of Stuttgart, Germany..
    Krone, Michael
    Visualization Research Center (VISUS), University of Stuttgart, Germany..
    Ertl, Thomas
    Visualization Research Center (VISUS), University of Stuttgart, Germany..
    Atomistic Visualization of Mesoscopic Whole-Cell Simulations2012In: VCBM 12: Eurographics Workshop on Visual Computing for Biology and Medicine / [ed] Timo Ropinski and Anders Ynnerman and Charl Botha and Jos Roerdink}, The Eurographics Association , 2012, Vol. 2, p. 123-130Conference paper (Refereed)
    Abstract [en]

    Molecular visualizations are a principal tool for analyzing the results of biochemical simulations. With modern GPU ray casting approaches it is only possible to render several millions of atoms at interactive frame rates unless advanced acceleration methods are employed. But even simplified cell models of whole-cell simulations consist of at least several billion atoms. However, many instances of only a few different proteins occur in the intracellular environment, which is beneficial in order to fit the data into the graphics memory. One model is stored for each protein species and rendered once per instance. The proposed method exploits recent algorithmic advances for particle rendering and the repetitive nature of intracellular proteins to visualize dynamic results from mesoscopic simulations of cellular transport processes. We present two out-of-core optimizations for the interactive visualization of data sets composed of billions of atoms as well as details on the data preparation and the employed rendering techniques. Furthermore, we apply advanced shading methods to improve the image quality including methods to enhance depth and shape perception besides non-photorealistic rendering methods.

  • 9.
    Falk, Martin
    et al.
    Visualization Research Center (VISUS), University of Stuttgart, Germany.
    Krone, Michael
    Visualization Research Center (VISUS), University of Stuttgart, Germany.
    Ertl, Thomas
    Visualization Research Center (VISUS), University of Stuttgart, Germany.
    Atomistic Visualization of Mesoscopic Whole-Cell Simulations Using Ray-Casted Instancing2013In: Computer graphics forum (Print), ISSN 0167-7055, E-ISSN 1467-8659, Vol. 32, no 8, p. 195-206Article in journal (Refereed)
    Abstract [en]

    Molecular visualization is an important tool for analysing the results of biochemical simulations. With modern GPU ray casting approaches, it is only possible to render several million of atoms interactively unless advanced acceleration methods are employed. Whole-cell simulations consist of at least several billion atoms even for simplified cell models. However, many instances of only a few different proteins occur in the intracellular environment, which can be exploited to fit the data into the graphics memory. For each protein species, one model is stored and rendered once per instance. The proposed method exploits recent algorithmic advances for particle rendering and the repetitive nature of intracellular proteins to visualize dynamic results from mesoscopic simulations of cellular transport processes. We present two out-of-core optimizations for the interactive visualization of data sets composed of billions of atoms as well as details on the data preparation and the employed rendering techniques. Furthermore, we apply advanced shading methods to improve the image quality including methods to enhance depth and shape perception besides non-photorealistic rendering methods. We also show that the method can be used to render scenes that are composed of triangulated instances, not only implicit surfaces.

  • 10.
    Falk, Martin
    et al.
    VISUS - Visualization Research Center, University of Stuttgart, Germany.
    Ott, Michael
    VISUS - Visualization Research Center, University of Stuttgart, Germany.
    Ertl, Thomas
    VISUS - Visualization Research Center, University of Stuttgart, Germany.
    Klann, Michael
    Automatic Control Laboratory, BISON Group, ETH Zürich,Switzerland.
    Koeppl, Heinz
    Automatic Control Laboratory, BISON Group, ETH Zürich,Switzerland.
    Parallelized Agent-based Simulation on CPU and Graphics Hardware for Spatial and Stochastic Models in Biology2011In: Proceedings of the 9th International Conference on Computational Methods in Systems Biology, CMSB'112011, ACM Press, 2011, p. 73-82Conference paper (Refereed)
    Abstract [en]

    The complexity of biological systems is enormous, even when considering a single cell where a multitude of highly parallel and intertwined processes take place on the molecular level. This paper focuses on the parallel simulation of signal transduction processes within a cell carried out solely on the graphics processing unit (GPU). Each signaling molecule is represented by an agent performing a discretetime continuous-space random walk to model its diffusion through the cell. Since the interactions and reactions between the agents can be competitive and are interdependent, we propose spatial partitioning for the reaction detection to overcome the data dependencies in the parallel execution of reactions. In addition, we present a simple way to simulate the Michaelis-Menten kinetics in our particle-based method using a per-particle delay. We apply this agent-based simulation to model signal transduction in the MAPK (Mitogen-Activated Protein Kinase) cascade both with and without cytoskeletal filaments. Finally, we compare the speed-up of our GPU simulation with a parallelized CPU version resulting in a twelvefold speedup.

  • 11.
    Falk, Martin
    et al.
    VISUS – Visualization Research Center, Universitat Stuttgart, Germany .
    Schafhitzel, Tobias
    Graphical Systems, Institut VIS, Universitat Stuttgart, Germany .
    Weiskopf, Daniel
    VISUS – Visualization Research Center, Universitat Stuttgart, Germany .
    Ertl, Thomas
    Graphical Systems, Institut VIS, Universitat Stuttgart, Germany .
    Panorama maps with non-linear ray tracing2007In: GRAPHITE '07: Proceedings of the 5th international conference on Computer graphics and interactive techniques in Australia and Southeast Asia, ACM Digital Library, 2007, p. 9-16Conference paper (Refereed)
    Abstract [en]

    We present a framework for the interactive generation of 3D panorama maps. Our approach addresses the main issue that occurs during panorama map construction: non-linear projection or deformation of the terrain in order to minimize the occlusion of important information such as roads and trails. Traditionally, panorama maps are hand-drawn by skilled illustrators. In contrast, our approach provides computer support for the rendering of non-occluded views of 3D panorama maps, where deformations are modeled by nonlinear ray tracing. The deflection of rays is influenced by 2D and 3D force fields that directly consider the shape of the terrain. In addition, our framework allows the user to further modify the force fields to have fine control over the deformations of the panorama map. User interaction is facilitated by our real-time rendering system in terms of linked multiple views of both linear and non-linear projected terrain and the deformed view rays. Fast rendering is achieved by GPU-based non-linear ray tracing. We demonstrate the usefulness of our modeling and visualization method by several examples.

  • 12.
    Falk, Martin
    et al.
    VISUS – Visualization Research Center, Universität Stuttgart.
    Seizinger, A.
    VISUS – Visualization Research Center, Universität Stuttgart.
    Sadlo, F.
    VISUS – Visualization Research Center, Universität Stuttgart.
    Üffinger, M.
    VISUS – Visualization Research Center, Universität Stuttgart.
    Weiskopf, D.
    VISUS – Visualization Research Center, Universität Stuttgart.
    Trajectory-Augmented Visualization of Lagrangian Coherent Structures in Unsteady Flow2010In: International Symposium on Flow Visualization (ISFV14), 2010Conference paper (Other academic)
    Abstract [en]

    The finite-time Lyapunov exponent (FTLE) field can be used for many purposes, from the analysis of the predictability in dynamical systems to the topological analysis of timedependent vector fields. In the topological context, the topic of this work, FTLE ridges represent Lagrangian coherent structures (LCS), a counterpart to separatrices in vector field topology. Since the explicit vector field behavior cannot be deduced from these representations, they may be augmented by line integral convolution patterns, a computational flow visualization counterpart to the surface oil flow method. This is, however, strictly meaningful only in stationary vector fields. Here, we propose an augmentation that visualizes the LCS-inducing flow behavior by means of complete trajectories but avoids occlusion and visual clutter. For this we exploit the FTLE for both the selection of significant trajectories as well as their individual representation. This results in 3D line representations for 2D vector fields by treating 2D time-dependent vector fields in 3D space-time. We present two variants of the approach, one easing the choice of the finite advection time for FTLE analysis and one for investigating the flow once the time is chosen.

  • 13.
    Falk, Martin
    et al.
    Visualization Res. Center (VISUS), Univ. Stuttgart, Stuttgart.
    Weiskopf, Daniel
    Visualization Res. Center (VISUS), Univ. Stuttgart, Stuttgart.
    Output-Sensitive 3D Line Integral Convolution2008In: IEEE Transactions on Visualization and Computer Graphics, ISSN 1077-2626, E-ISSN 1941-0506, Vol. 14, no 4, p. 820-834Article in journal (Refereed)
    Abstract [en]

    We propose a largely output-sensitive visualization method for 3D line integral convolution (LIC) whose rendering speed is mainly independent of the data set size and mostly governed by the complexity of the output on the image plane. Our approach of view-dependent visualization tightly links the LIC generation with the volume rendering of the LIC result in order to avoid the computation of unnecessary LIC points: early-ray termination and empty-space leaping techniques are used to skip the computation of the LIC integral in a lazy-evaluation approach; both ray casting and texture slicing can be used as volume-rendering techniques. The input noise is modeled in object space to allow for temporal coherence under object and camera motion. Different noise models are discussed, covering dense representations based on filtered white noise all the way to sparse representations similar to oriented LIC. Aliasing artifacts are avoided by frequency control over the 3D noise and by employing a 3D variant of MlPmapping. A range of illumination models is applied to the LIC streamlines: different codimension-2 lighting models and a novel gradient-based illumination model that relies on precomputed gradients and does not require any direct calculation of gradients after the LIC integral is evaluated. We discuss the issue of proper sampling of the LIC and volume-rendering integrals by employing a frequency-space analysis of the noise model and the precomputed gradients. Finally, we demonstrate that our visualization approach lends itself to a fast graphics processing unit (GPU) implementation that supports both steady and unsteady flow. Therefore, this 3D LIC method allows users to interactively explore 3D flow by means of high-quality, view-dependent, and adaptive LIC volume visualization. Applications to flow visualization in combination with feature extraction and focus-and-context visualization are described, a comparison to previous methods is provided, and a detailed performance analysis is included.

  • 14.
    Hotz, Ingrid
    et al.
    Linköping University, Department of Science and Technology, Media and Information Technology. Linköping University, Faculty of Science & Engineering.
    Falk, MartinLinköping University, Department of Science and Technology, Media and Information Technology. Linköping University, Faculty of Science & Engineering.
    Proceedings of SIGRAD 2017, August 17-18, 2017 Norrköping, Sweden2017Conference proceedings (editor) (Refereed)
    Abstract [en]

    The annual meeting 2017 of the Swedish Computer Graphics Association (SIGRAD) took place at Linköping University, Campus Norrköping in Norrköping, Sweden in August 2017. SIGRAD is an event where researchers and industry professionals meet to discuss novel visions and developments in the field of computer graphics and related areas, such as visualization and human-computer interaction (HCI). Since SIGRAD was started in 1976, it has developed into the major annual appointment for the Nordic community of graphics and visual computing experts with a broad range of backgrounds. It thereby addresses the increasing need for visual computing solutions in both commercial and academic areas. SIGRAD 2017 offered a strong scientific program consisting of international keynote speakers from research and industry, presentations of recent scientific achievements in the field within Sweden, and novel technological results from international contributors. The topics covered present a nice cross-section across the diverse research efforts in the domains.

    Five original papers have been accepted for presentation after being peer-reviewed by an International Program Committee consisting of 22 highly qualified scientists. Each paper was reviewed, on average, by three reviewers from the committee. The accepted papers range from general computer graphics practices to practical applications and services that may benefit from the use of visualizations and computer graphics technologies. The extended participation of students at all levels of academia in research has been encouraged this year and 2 papers were selected which are first-authored by students studying at Master's Degree level.

    This year, we continued the “Swedish Research Overview Session” introduced at last year’s conference. In this session, Swedish research groups are given the opportunity to present their academically outstanding, previously published work at the annual conference. All papers in this session have been published in an academically outstanding journals or conferences not more than two years prior to the SIGRAD conference.

    We especially wish to thank our invited keynote speakers: Christoph Garth, University of Kaiserslautern, Germany, Ivan Viola, Vienna University of Technology, Austria, Claes Lundström, CMIV, Linköping University, and Samuel Ranta Eskola, Microsoft. Finally, we want to express our thanks to Gun-Britt Löfgren for helping us in organizing this event.

    The SIGRAD 2017 organizers

    Martin Falk, Daniel Jönsson, Ingrid Hotz

  • 15.
    Jönsson, Daniel
    et al.
    Linköping University, Department of Science and Technology, Media and Information Technology. Linköping University, Faculty of Science & Engineering.
    Falk, Martin
    Linköping University, Department of Science and Technology, Media and Information Technology. Linköping University, Faculty of Science & Engineering.
    Ynnerman, Anders
    Linköping University, Department of Science and Technology, Media and Information Technology. Linköping University, Faculty of Science & Engineering. Linköping University, Center for Medical Image Science and Visualization (CMIV).
    Intuitive Exploration of Volumetric Data Using Dynamic Galleries2016In: IEEE Transactions on Visualization and Computer Graphics, ISSN 1077-2626, E-ISSN 1941-0506, Vol. 22, no 1, p. 896-905Article in journal (Refereed)
    Abstract [en]

    In this work we present a volume exploration method designed to be used by novice users and visitors to science centers and museums. The volumetric digitalization of artifacts in museums is of rapidly increasing interest as enhanced user experience through interactive data visualization can be achieved. This is, however, a challenging task since the vast majority of visitors are not familiar with the concepts commonly used in data exploration, such as mapping of visual properties from values in the data domain using transfer functions. Interacting in the data domain is an effective way to filter away undesired information but it is difficult to predict where the values lie in the spatial domain. In this work we make extensive use of dynamic previews instantly generated as the user explores the data domain. The previews allow the user to predict what effect changes in the data domain will have on the rendered image without being aware that visual parameters are set in the data domain. Each preview represents a subrange of the data domain where overview and details are given on demand through zooming and panning. The method has been designed with touch interfaces as the target platform for interaction. We provide a qualitative evaluation performed with visitors to a science center to show the utility of the approach.

  • 16.
    Kauker, Daniel
    et al.
    VISUS, University of Stuttgart.
    Falk, Martin
    Linköping University, Department of Science and Technology, Media and Information Technology. Linköping University, Faculty of Science & Engineering.
    Reina, Guido
    VISUS, University of Stuttgart.
    Ynnerman, Anders
    Linköping University, Department of Science and Technology, Media and Information Technology. Linköping University, Faculty of Science & Engineering. Linköping University, Center for Medical Image Science and Visualization (CMIV).
    Ertl, Thomas
    VISUS, University of Stuttgart.
    VoxLink—Combining sparse volumetric data and geometry for efficient rendering2016In: Computational Visual Media, ISSN 2096-0662, Vol. 2, no 1, p. 45-56Article in journal (Refereed)
    Abstract [en]

    Processing and visualizing large scale volumetric and geometric datasets is mission critical in an increasing number of applications in academic research as well as in commercial enterprise. Often the datasets are, or can be processed to become, sparse. In this paper, we present VoxLink, a novel approach to render sparse volume data in a memory-efficient manner enabling interactive rendering on common, offthe- shelf graphics hardware. Our approach utilizes current GPU architectures for voxelizing, storing, and visualizing such datasets. It is based on the idea of perpixel linked lists (ppLL), an A-buffer implementation for order-independent transparency rendering. The method supports voxelization and rendering of dense semi-transparent geometry, sparse volume data, and implicit surface representations with a unified data structure. The proposed data structure also enables efficient simulation of global lighting effects such as reflection, refraction, and shadow ray evaluation.

  • 17.
    Kottravel, Sathish
    et al.
    Linköping University, Department of Science and Technology, Media and Information Technology. Linköping University, Faculty of Science & Engineering.
    Falk, Martin
    Linköping University, Department of Science and Technology, Media and Information Technology. Linköping University, Faculty of Science & Engineering.
    Sundén, Erik
    Linköping University, Department of Science and Technology, Media and Information Technology. Linköping University, Faculty of Science & Engineering.
    Ropinski, Timo
    Visual Computing Research Group, Ulm University. Germany.
    Coverage-Based Opacity Estimation for Interactive Depth of Field in Molecular Visualization2015In: IEEE Pacific Visualization Symposium (PacificVis 2015), IEEE Computer Society, 2015, p. 255-262Conference paper (Refereed)
    Abstract [en]

    In this paper, we introduce coverage-based opacity estimation to achieve Depth of Field (DoF) effects when visualizing molecular dynamics (MD) data. The proposed algorithm is a novel object-based approach which eliminates many of the shortcomings of state-of-the-art image-based DoF algorithms. Based on observations derived from a physically-correct reference renderer, coverage-based opacity estimation exploits semi-transparency to simulate the blur inherent to DoF effects. It achieves high quality DoF effects, by augmenting each atom with a semi-transparent shell, which has a radius proportional to the distance from the focal plane of the camera. Thus, each shell represents an additional coverage area whose opacity varies radially, based on our observations derived from the results of multi-sampling DoF algorithms. By using the proposed technique, it becomes possible to generate high quality visual results, comparable to those achieved through ground-truth multi-sampling algorithms. At the same time, we obtain a significant speedup which is essential for visualizing MD data as it enables interactive rendering. In this paper, we derive the underlying theory, introduce coverage-based opacity estimation and demonstrate how it can be applied to real world MD data in order to achieve DoF effects. We further analyze the achieved results with respect to performance as well as quality and show that they are comparable to images generated with modern distributed ray tracing engines.

  • 18.
    Kozlikova, B.
    et al.
    Masaryk University, Czech Republic.
    Krone, M.
    University of Stuttgart, Germany.
    Falk, Martin
    Linköping University, Department of Science and Technology, Media and Information Technology. Linköping University, Faculty of Science & Engineering.
    Lindow, N.
    ZIB, Germany.
    Baaden, M.
    CNRS, France.
    Baum, D.
    ZIB, Germany.
    Viola, I.
    University of Bergen, Norway; TU Wien, Austria.
    Parulek, J.
    University of Bergen, Norway.
    Hege, H-C.
    ZIB, Germany.
    Visualization of Biomolecular Structures: State of the Art Revisited2017In: Computer graphics forum (Print), ISSN 0167-7055, E-ISSN 1467-8659, Vol. 36, no 8, p. 178-204Article in journal (Refereed)
    Abstract [en]

    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 survey concludes with an outlook on promising and important research topics to foster further success in the development of tools that help to reveal molecular secrets.

  • 19.
    Kozlíková, Barbora
    et al.
    Masaryk University.
    Krone, Michael
    VISUS, University of Stuttgart.
    Lindow, Norbert
    Zuse Institute Berlin.
    Falk, Martin
    Linköping University, Department of Science and Technology, Media and Information Technology. Linköping University, Faculty of Science & Engineering.
    Baaden, Marc
    Laboratoire de Biochimie Théorique.
    Baum, Daniel
    Zuse Institute Berlin.
    Viola, Ivan
    Institute of Computer Graphics and Algorithms, Vienna University of Technology.
    Parulek, Julius
    Department of Informatics, University of Bergen.
    Hege, Hans-Christian
    Zuse Institute Berlin.
    Visualization of Molecular Structure: The State of the Art2015In: Eurographics Conference on Visualization (EuroVis) - STARs / [ed] R. Borgo and F. Ganovelli and I. Viola, Eurographics - European Association for Computer Graphics, 2015Conference paper (Refereed)
    Abstract [en]

    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.

  • 20.
    Krone, Michael
    et al.
    Visualization Research Center (VISUS), University of Stuttgart, Germany.
    Falk, Martin
    Visualization Research Center (VISUS), University of Stuttgart, Germany.
    Rehm, Sascha
    Institute for Technical Biochemistry (ITB), University of Stuttgart, Germany.
    Pleiss, Jürgen
    Institute for Technical Biochemistry (ITB), University of Stuttgart, Germany.
    Ertl, Thomas
    Visualization Research Center (VISUS), University of Stuttgart, Germany.
    Interactive Exploration of Protein Cavities2011In: Computer graphics forum (Print), ISSN 0167-7055, E-ISSN 1467-8659, Vol. 30, no 3, p. 673-682Article in journal (Refereed)
    Abstract [en]

    We present a novel application for the interactive exploration of cavities within proteins in dynamic data sets. Inside a protein, cavities can often be found close to the active center. Therefore, when analyzing a molecular dynamics simulation trajectory it is of great interest to find these cavities and determine if such a cavity opens up to the environment, making the binding site accessible to the surrounding substrate. Our user-driven approach enables expert users to select a certain cavity and track its evolution over time. The user is supported by different visualizations of the extracted cavity to facilitate the analysis. The boundary of the protein and its cavities is obtained by means of volume ray casting, where the volume is computed in real-time for each frame, therefore allowing the examination of time-dependent data sets. A fast, partial segmentation of the volume is applied to obtain the selected cavity and trace it over time. Domain experts found our method useful when they applied it exemplarily on two trajectories of lipases from Rhizomucor miehei and Candida antarctica. In both data sets cavities near the active center were easily identified and tracked over time until they reached the surface and formed an open substrate channel.

  • 21.
    Lindholm, Stefan
    et al.
    Linköping University, Department of Science and Technology, Media and Information Technology. Linköping University, The Institute of Technology.
    Falk, Martin
    Linköping University, Department of Science and Technology, Media and Information Technology. Linköping University, The Institute of Technology.
    Sundén, Erik
    Linköping University, Department of Science and Technology, Media and Information Technology. Linköping University, The Institute of Technology.
    Bock, Alexander
    Linköping University, Department of Science and Technology, Media and Information Technology. Linköping University, The Institute of Technology.
    Ynnerman, Anders
    Linköping University, Department of Science and Technology, Media and Information Technology. Linköping University, Center for Medical Image Science and Visualization (CMIV). Linköping University, The Institute of Technology.
    Ropinski, Timo
    Linköping University, Department of Science and Technology, Media and Information Technology. Linköping University, The Institute of Technology.
    Hybrid Data Visualization Based On Depth Complexity Histogram Analysis2014In: Computer graphics forum (Print), ISSN 0167-7055, E-ISSN 1467-8659, Vol. 34, no 1, p. 74-85Article in journal (Refereed)
    Abstract [en]

    In many cases, only the combination of geometric and volumetric data sets is able to describe a single phenomenon under observation when visualizing large and complex data. When semi-transparent geometry is present, correct rendering results require sorting of transparent structures. Additional complexity is introduced as the contributions from volumetric data have to be partitioned according to the geometric objects in the scene. The A-buffer, an enhanced framebuffer with additional per-pixel information, has previously been introduced to deal with the complexity caused by transparent objects. In this paper, we present an optimized rendering algorithm for hybrid volume-geometry data based on the A-buffer concept. We propose two novel components for modern GPUs that tailor memory utilization to the depth complexity of individual pixels. The proposed components are compatible with modern A-buffer implementations and yield performance gains of up to eight times compared to existing approaches through reduced allocation and reuse of fast cache memory. We demonstrate the applicability of our approach and its performance with several examples from molecular biology, space weather, and medical visualization containing both, volumetric data and geometric structures.

  • 22.
    Sundén, Erik
    et al.
    Linköping University, Department of Science and Technology, Media and Information Technology. Linköping University, Faculty of Science & Engineering.
    Steneteg, Peter
    Linköping University, Department of Science and Technology, Media and Information Technology. Linköping University, Faculty of Science & Engineering.
    Kottravel, Sathish
    Linköping University, Department of Science and Technology, Media and Information Technology. Linköping University, Faculty of Science & Engineering.
    Jönsson, Daniel
    Linköping University, Department of Science and Technology, Media and Information Technology. Linköping University, Faculty of Science & Engineering.
    Englund, Rickard
    Linköping University, Department of Science and Technology, Media and Information Technology. Linköping University, Faculty of Science & Engineering.
    Falk, Martin
    Linköping University, Department of Science and Technology, Media and Information Technology. Linköping University, Faculty of Science & Engineering.
    Ropinski, Timo
    University of Ulm, Germany.
    Inviwo - An Extensible, Multi-Purpose Visualization Framework2015In: 2015 IEEE Scientific Visualization Conference (SciVis), IEEE , 2015, p. 163-164Conference paper (Refereed)
    Abstract [en]

    To enable visualization research impacting other scientific domains, the availability of easy-to-use visualization frameworks is essential. Nevertheless, an easy-to-use system also has to be adapted to the capabilities of modern hardware architectures, as only this allows for realizing interactive visualizations. With this trade-off in mind, we have designed and realized the cross-platform Inviwo (Interactive Visualization Workshop) visualization framework, that supports both interactive visualization research as well as efficient visualization application development and deployment. In this poster we give an overview of the architecture behind Inviwo, and show how its design enables us and other researchers to realize their visualization ideas efficiently. Inviwo consists of a modern and lightweight, graphics independent core, which is extended by optional modules that encapsulate visualization algorithms, well-known utility libraries and commonly used parallel-processing APIs (such as OpenGL and OpenCL). The core enables a simplistic structure for creating bridges between the different modules regarding data transfer across architecture and devices with an easy-to-use screen graph and minimalistic programming. Making the base structures in a modern way while providing intuitive methods of extending the functionality and creating modules based on other modules, we hope that Inviwo can help the visualization community to perform research through a rapid-prototyping design and GUI, while at the same time allowing users to take advantage of the results implemented in the system in any way they desire later on. Inviwo is publicly available at www.inviwo.org, and can be used freely by anyone under a permissive free software license (Simplified BSD).

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