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  • 1.
    Abrikosov, Alexei I.
    et al.
    Linköpings universitet, Institutionen för teknik och naturvetenskap, Medie- och Informationsteknik. Linköpings universitet, Tekniska fakulteten.
    Masood, Talha Bin
    Linköpings universitet, Institutionen för teknik och naturvetenskap, Medie- och Informationsteknik. Linköpings universitet, Tekniska fakulteten.
    Falk, Martin
    Linköpings universitet, Institutionen för teknik och naturvetenskap, Medie- och Informationsteknik. Linköpings universitet, Tekniska fakulteten.
    Hotz, Ingrid
    Linköpings universitet, Institutionen för teknik och naturvetenskap, Medie- och Informationsteknik. Linköpings universitet, Tekniska fakulteten.
    Topological analysis of density fields: An evaluation of segmentation methods2021Ingår i: Computers & graphics, ISSN 0097-8493, E-ISSN 1873-7684, Vol. 98, s. 231-241Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    Topological and geometric segmentation methods provide powerful concepts for detailed field analysis and visualization. However, when it comes to a quantitative analysis that requires highly accurate geometric segmentation, there is a large discrepancy between the promising theory and the available computational approaches. In this paper, we compare and evaluate various segmentation methods with the aim to identify and quantify the extent of these discrepancies. Thereby, we focus on an application from quantum chemistry: the analysis of electron density fields. It is a scalar quantity that can be experimentally measured or theoretically computed. In the evaluation we consider methods originating from the domain of quantum chemistry and computational topology. We apply the methods to the charge density of a set of crystals and molecules. Therefore, we segment the volumes into atomic regions and derive and compare quantitative measures such as total charge and dipole moments from these regions. As a result, we conclude that an accurate geometry determination can be crucial for correctly segmenting and analyzing a scalar field, here demonstrated on the electron density field.

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  • 2.
    Dieckmann, Mark E
    et al.
    Linköpings universitet, Institutionen för teknik och naturvetenskap, Medie- och Informationsteknik. Linköpings universitet, Tekniska fakulteten.
    Falk, Martin
    Linköpings universitet, Institutionen för teknik och naturvetenskap, Medie- och Informationsteknik. Linköpings universitet, Tekniska fakulteten.
    Folini, Doris
    Ecole Normale Supérieure, Lyon, CRAL, UMR CNRS 5574, Université de Lyon, 69622 Lyon, France.
    Walder, Rolf
    Ecole Normale Supérieure, Lyon, CRAL, UMR CNRS 5574, Université de Lyon, 69622 Lyon, France.
    Steneteg, Peter
    Linköpings universitet, Institutionen för teknik och naturvetenskap, Medie- och Informationsteknik. Linköpings universitet, Tekniska fakulteten.
    Hotz, Ingrid
    Linköpings universitet, Institutionen för teknik och naturvetenskap, Medie- och Informationsteknik. Linköpings universitet, Tekniska fakulteten.
    Ynnerman, Anders
    Linköpings universitet, Institutionen för teknik och naturvetenskap, Medie- och Informationsteknik. Linköpings universitet, Tekniska fakulteten.
    Collisionless Rayleigh–Taylor-like instability of the boundary between a hot pair plasma and an electron–proton plasma: The undular mode2020Ingår i: Physics of Plasmas, ISSN 1070-664X, E-ISSN 1089-7674, Vol. 27, nr 11, s. 1-14, artikel-id 112106Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    We study with a two-dimensional particle-in-cell simulation the stability of a discontinuity or piston, which separates an electron–positron cloud from a cooler electron–proton plasma. Such a piston might be present in the relativistic jets of accreting black holes separating the jet material from the surrounding ambient plasma and when pair clouds form during an x-ray flare and expand into the plasma of the accretion disk corona. We inject a pair plasma at a simulation boundary with a mildly relativistic temperature and mean speed. It flows across a spatially uniform electron–proton plasma, which is permeated by a background magnetic field. The magnetic field is aligned with one simulation direction and oriented orthogonally to the mean velocity vector of the pair cloud. The expanding pair cloud expels the magnetic field and piles it up at its front. It is amplified to a value large enough to trap ambient electrons. The current of the trapped electrons, which is carried with the expanding cloud front, drives an electric field that accelerates protons. A solitary wave grows and changes into a piston after it saturated. Our simulations show that this piston undergoes a collisionless instability similar to a Rayleigh–Taylor instability. The undular mode grows and we observe fingers in the proton density distribution. The effect of the instability is to deform the piston but it cannot destroy it.

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  • 3.
    Dieckmann, Mark E
    et al.
    Linköpings universitet, Institutionen för teknik och naturvetenskap, Medie- och Informationsteknik. Linköpings universitet, Tekniska fakulteten.
    Falk, Martin
    Linköpings universitet, Institutionen för teknik och naturvetenskap, Medie- och Informationsteknik. Linköpings universitet, Tekniska fakulteten.
    Steneteg, Peter
    Linköpings universitet, Institutionen för teknik och naturvetenskap, Medie- och Informationsteknik. Linköpings universitet, Tekniska fakulteten.
    Folini, Doris
    CRAL, École Normale Supérieure, 69622 Lyon, France.
    Hotz, Ingrid
    Linköpings universitet, Institutionen för teknik och naturvetenskap, Medie- och Informationsteknik. Linköpings universitet, Tekniska fakulteten.
    Nordman, Aida
    Linköpings universitet, Institutionen för teknik och naturvetenskap, Medie- och Informationsteknik. Linköpings universitet, Tekniska fakulteten.
    Dell'Acqua, Pierangelo
    Linköpings universitet, Institutionen för teknik och naturvetenskap, Medie- och Informationsteknik. Linköpings universitet, Tekniska fakulteten.
    Ynnerman, Anders
    Linköpings universitet, Institutionen för teknik och naturvetenskap, Medie- och Informationsteknik. Linköpings universitet, Tekniska fakulteten.
    Walder, Rolf
    CRAL, École Normale Supérieure, 69622 Lyon, France.
    Structure of a collisionless pair jet in a magnetized electron-proton plasma: Flow-aligned magnetic field2019Ingår i: High Energy Phenomena in Relativistic Outflows VII (HEPRO VII): Formation and propagation of relativistic outflows, 2019, artikel-id 006Konferensbidrag (Refereegranskat)
    Abstract [en]

    We present the results from a particle-in-cell (PIC) simulation that models the interaction between a spatially localized electron-positron cloud and an electron-ion plasma. The latter is permeated by a magnetic field that is initially spatially uniform and aligned with the mean velocity vector of the pair cloud. The pair cloud expels the magnetic field and piles it up into an electromagnetic piston. Its electromagnetic field is strong enough to separate the pair cloud from the ambient plasma in the direction that is perpendicular to the cloud propagation direction. The piston propagates away from the spine of the injected pair cloud and it accelerates the protons to a high nonrelativistic speed. The accelerated protons form an outer cocoon that will eventually become separated from the unperturbed ambient plasma by a fast magnetosonic shock. No electromagnetic piston forms at the front of the cloud and a shock is mediated here by the filamentation instability. The final plasma distribution resembles that of a hydrodynamic jet. Collisionless plasma jets may form in the coronal plasma of accreting black holes and the interaction between the strong magnetic field of the piston and the hot pair cloud may contribute to radio emissions by such objects.

  • 4.
    Dieckmann, Mark E
    et al.
    Linköpings universitet, Institutionen för teknik och naturvetenskap, Medie- och Informationsteknik. Linköpings universitet, Tekniska fakulteten.
    Folini, D.
    Univ Lyon, France.
    Falk, Martin
    Linköpings universitet, Institutionen för teknik och naturvetenskap, Medie- och Informationsteknik. Linköpings universitet, Tekniska fakulteten.
    Bock, Alexander
    Linköpings universitet, Institutionen för teknik och naturvetenskap, Medie- och Informationsteknik. Linköpings universitet, Tekniska fakulteten.
    Steneteg, Peter
    Linköpings universitet, Institutionen för teknik och naturvetenskap, Medie- och Informationsteknik. Linköpings universitet, Tekniska fakulteten.
    Walder, R.
    Univ Lyon, France.
    Three-dimensional structure and stability of discontinuities between unmagnetized pair plasma and magnetized electron-proton plasma2023Ingår i: New Journal of Physics, E-ISSN 1367-2630, Vol. 25, nr 6, artikel-id 063017Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    We study with a 3D particle-in-cell simulation discontinuities between an electron-positron pair plasma and magnetized electrons and protons. A pair plasma is injected at one simulation boundary with a speed 0.6c along its normal. It expands into an electron-proton plasma and a magnetic field that points orthogonally to the injection direction. Diamagnetic currents expel the magnetic field from within the pair plasma and pile it up in front of it. It pushes electrons, which induces an electric field pulse ahead of the magnetic one. This initial electromagnetic pulse (EMP) confines the pair plasma magnetically and accelerates protons electrically. The fast flow of the injected pair plasma across the protons behind the initial EMP triggers the filamentation instability. Some electrons and positrons cross the injection boundary and build up a second EMP. Electron-cyclotron drift instabilities perturb the plasma ahead of both EMPs seeding a Rayleigh-Taylor (RT)-type instability. Despite equally strong perturbations ahead of both EMPs, the second EMP is much more stable than the initial one. We attribute the rapid collapse of the initial EMP to the filamentation instability, which perturbed the plasma behind it. The RT-type instability transforms the planar EMPs into transition layers, in which magnetic flux ropes and electrostatic forces due to uneven numbers of electrons and positrons slow down and compress the pair plasma and accelerate protons. In our simulation, the expansion speed of the pair cloud decreased by about an order of magnitude and its density increased by the same factor. Its small thickness implies that it is capable of separating a relativistic pair outflow from an electron-proton plasma, which is essential for collimating relativistic jets of pair plasma in collisionless astrophysical plasma.

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  • 5.
    Dieckmann, Mark E
    et al.
    Linköpings universitet, Institutionen för teknik och naturvetenskap, Medie- och Informationsteknik. Linköpings universitet, Tekniska fakulteten.
    Spencer, Selina-Jane
    Centre for Fusion, Space and Astrophysics, University of Warwick, Coventry, CV4 7AL, UK.
    Falk, Martin
    Linköpings universitet, Institutionen för teknik och naturvetenskap, Medie- och Informationsteknik. Linköpings universitet, Tekniska fakulteten.
    Rowlands, George
    Centre for Fusion, Space and Astrophysics, University of Warwick, Coventry, CV4 7AL, UK.
    Preferential acceleration of positrons by a filamentation instability between an electron–proton beam and a pair plasma beam2020Ingår i: Physics of Plasmas, ISSN 1070-664X, E-ISSN 1089-7674, Vol. 27, nr 12, artikel-id 122102Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    Particle-in-cell simulations of jets of electrons and positrons in an ambient electron–proton plasma have revealed an acceleration of positrons at the expense of electron kinetic energy. We show that a filamentation instability, between an unmagnetized ambient electron–proton plasma at rest and a beam of pair plasma that moves through it at a non-relativistic speed, indeed results in preferential positron acceleration. Filaments form that are filled predominantly with particles with the same direction of their electric current vector. Positron filaments are separated by electromagnetic fields from beam electron filaments. Some particles can cross the field boundary and enter the filament of the other species. Positron filaments can neutralize their net charge by collecting the electrons of the ambient plasma, while protons cannot easily follow the beam electron filaments. Positron filaments can thus be compressed to a higher density and temperature than the beam electron filaments. Filament mergers, which take place after the exponential growth phase of the instability has ended, lead to an expansion of the beam electron filaments, which amplifies the magnetic field they generate and induces an electric field in this filament. Beam electrons lose a substantial fraction of their kinetic energy to the electric field. Some positrons in the beam electron filament are accelerated by the induced electric field to almost twice their initial speed. The simulations show that a weaker electric field is induced in the positron filament and particles in this filament hardly change their speed.

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  • 6.
    Falk, Martin
    Visualization Research Center, University of Stuttgart, Germany.
    Visualization and mesoscopic simulation in systems biology2013Doktorsavhandling, monografi (Övrigt vetenskapligt)
    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.

  • 7.
    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 Membrane2011Ingår i: IEEE Symposium on Biological Data Visualization (BioVis 2011), IEEE, 2011, s. 9-15Konferensbidrag (Refereegranskat)
    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.

  • 8.
    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 Simulations2010Ingår i: Proceedings of SIGRAD 2010: Content Aggregation and Visualization / [ed] Kai-Mikael Jää-Aro Thomas Larsson, Linköping University Electronic Press, 2010, s. 35-43Konferensbidrag (Refereegranskat)
    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.

  • 9.
    Falk, Martin
    et al.
    Linköpings universitet, Institutionen för teknik och naturvetenskap, Medie- och Informationsteknik. Linköpings universitet, Tekniska fakulteten.
    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 Data2016Bok (Refereegranskat)
    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.

  • 10.
    Falk, Martin
    et al.
    Linköpings universitet, Institutionen för teknik och naturvetenskap, Medie- och Informationsteknik. Linköpings universitet, Tekniska fakulteten.
    Hotz, Ingrid
    Linköpings universitet, Institutionen för teknik och naturvetenskap, Medie- och Informationsteknik. Linköpings universitet, Tekniska fakulteten.
    Ljung, Patric
    Linköpings universitet, Institutionen för teknik och naturvetenskap, Medie- och Informationsteknik. Linköpings universitet, Tekniska fakulteten.
    Treanor, Darren
    Linköpings universitet, Centrum för medicinsk bildvetenskap och visualisering, CMIV. Leeds Teaching Hospitals NHS Trust, United Kingdom.
    Ynnerman, Anders
    Linköpings universitet, Institutionen för teknik och naturvetenskap, Medie- och Informationsteknik. Linköpings universitet, Tekniska fakulteten. Linköpings universitet, Centrum för medicinsk bildvetenskap och visualisering, CMIV.
    Lundström, Claes
    Linköpings universitet, Institutionen för teknik och naturvetenskap, Medie- och Informationsteknik. Linköpings universitet, Tekniska fakulteten. Linköpings universitet, Centrum för medicinsk bildvetenskap och visualisering, CMIV. Sectra AB.
    Transfer Function Design Toolbox for Full-Color Volume Datasets2017Ingår i: 2017 IEEE PACIFIC VISUALIZATION SYMPOSIUM (PACIFICVIS), IEEE, IEEE, 2017, s. 171-179Konferensbidrag (Refereegranskat)
    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.

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  • 11.
    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 Simulations2010Ingår i: Biomedical Imaging: From Nano to Macro, 2010 IEEE International Symposium on: From Nano to Macro (ISBI 2010), IEEE, 2010, s. 1301-1304Konferensbidrag (Refereegranskat)
    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.

  • 12.
    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 Cell2009Ingår i: IEEE Pacific Visualization Symposium (PacificVis 2009), 2009, s. 169-176Konferensbidrag (Refereegranskat)
    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.

  • 13.
    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 Simulations2012Ingår i: 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, s. 123-130Konferensbidrag (Refereegranskat)
    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.

  • 14.
    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 Instancing2013Ingår i: Computer graphics forum (Print), ISSN 0167-7055, E-ISSN 1467-8659, Vol. 32, nr 8, s. 195-206Artikel i tidskrift (Refereegranskat)
    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.

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  • 15.
    Falk, Martin
    et al.
    Linköpings universitet, Institutionen för teknik och naturvetenskap, Medie- och Informationsteknik. Linköpings universitet, Tekniska fakulteten.
    Ljung, Patric
    Linköpings universitet, Institutionen för teknik och naturvetenskap, Medie- och Informationsteknik. Linköpings universitet, Tekniska fakulteten.
    Lundström, Claes
    Linköpings universitet, Institutionen för teknik och naturvetenskap, Medie- och Informationsteknik. Linköpings universitet, Tekniska fakulteten. Linköpings universitet, Centrum för medicinsk bildvetenskap och visualisering, CMIV.
    Ynnerman, Anders
    Linköpings universitet, Institutionen för teknik och naturvetenskap, Medie- och Informationsteknik. Linköpings universitet, Tekniska fakulteten. Linköpings universitet, Centrum för medicinsk bildvetenskap och visualisering, CMIV.
    Hotz, Ingrid
    Linköpings universitet, Institutionen för teknik och naturvetenskap, Medie- och Informationsteknik. Linköpings universitet, Tekniska fakulteten.
    Feature Exploration in Medical Volume Data using Local Frequency Distributions2020Ingår i: / [ed] B. Kozlíková, M. Krone, and N. N. Smit, 2020Konferensbidrag (Refereegranskat)
    Abstract [en]

    Frequency distributions (FD) are an important instrument when analyzing and investigating scientific data. In volumetric visualization, for example, frequency distributions visualized as histograms, often assist the user in the process of designing transfer function (TF) primitives. Yet a single point in the distribution can correspond to multiple features in the data, particularly in low-dimensional TFs that dominate time-critical domains such as health care. In this paper, we propose contributions to the area of medical volume data exploration, in particular Computed Tomography (CT) data, based on the decomposition of local frequency distributions (LFD). By considering the local neighborhood utilizing LFDs we can incorporate a measure for neighborhood similarity to differentiate features thereby enhancing the classification abilities of existing methods. This also allows us to link the attribute space of the histogram with the spatial properties of the data to improve the user experience and simplify the exploration step. We propose three approaches for data exploration which we illustrate with several visualization cases highlighting distinct features that are not identifiable when considering only the global frequency distribution. We demonstrate the power of the method on selected datasets.

  • 16.
    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 Biology2011Ingår i: Proceedings of the 9th International Conference on Computational Methods in Systems Biology, CMSB'112011, ACM Press, 2011, s. 73-82Konferensbidrag (Refereegranskat)
    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.

  • 17.
    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 tracing2007Ingår i: GRAPHITE '07: Proceedings of the 5th international conference on Computer graphics and interactive techniques in Australia and Southeast Asia, ACM Digital Library, 2007, s. 9-16Konferensbidrag (Refereegranskat)
    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.

  • 18.
    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 Flow2010Ingår i: International Symposium on Flow Visualization (ISFV14), 2010Konferensbidrag (Övrigt vetenskapligt)
    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.

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  • 19.
    Falk, Martin
    et al.
    Linköpings universitet, Institutionen för teknik och naturvetenskap, Medie- och Informationsteknik. Linköpings universitet, Tekniska fakulteten. Swedish e-Science Research Centre (SeRC), Sweden.
    Tobiasson, Victor
    Science for Life Laboratory, Department of Biochemistry and Biophysics, Stockholm University, Solna, Sweden.
    Bock, Alexander
    Linköpings universitet, Institutionen för teknik och naturvetenskap, Medie- och Informationsteknik. Linköpings universitet, Tekniska fakulteten. Swedish e-Science Research Centre (SeRC), Sweden.
    Hansen, Charles
    Linköpings universitet, Institutionen för teknik och naturvetenskap, Medie- och Informationsteknik. Linköpings universitet, Tekniska fakulteten. Kahlert School of Computing, University of Utah.
    Ynnerman, Anders
    Linköpings universitet, Institutionen för teknik och naturvetenskap, Medie- och Informationsteknik. Linköpings universitet, Tekniska fakulteten. Swedish e-Science Research Centre (SeRC), Sweden.
    A Visual Environment for Data Driven Protein Modeling and Validation2023Ingår i: IEEE Transactions on Visualization and Computer Graphics, ISSN 1077-2626, E-ISSN 1941-0506Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    In structural biology, validation and verification of new atomic models are crucial and necessary steps which limit the production of reliable molecular models for publications and databases. An atomic model is the result of meticulous modeling and matching and is evaluated using a variety of metrics that provide clues to improve and refine the model so it fits our understanding of molecules and physical constraints. In cryo electron microscopy (cryo-EM) the validation is also part of an iterative modeling process in which there is a need to judge the quality of the model during the creation phase. A shortcoming is that the process and results of the validation are rarely communicated using visual metaphors.

    This work presents a visual framework for molecular validation. The framework was developed in close collaboration with domain experts in a participatory design process. Its core is a novel visual representation based on 2D heatmaps that shows all available validation metrics in a linear fashion, presenting a global overview of the atomic model and provide domain experts with interactive analysis tools. Additional information stemming from the underlying data, such as a variety of local quality measures, is used to guide the user's attention toward regions of higher relevance. Linked with the heatmap is a three-dimensional molecular visualization providing the spatial context of the structures and chosen metrics. Additional views of statistical properties of the structure are included in the visual framework. We demonstrate the utility of the framework and its visual guidance with examples from cryo-EM.

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  • 20.
    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 Convolution2008Ingår i: IEEE Transactions on Visualization and Computer Graphics, ISSN 1077-2626, E-ISSN 1941-0506, Vol. 14, nr 4, s. 820-834Artikel i tidskrift (Refereegranskat)
    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.

  • 21.
    Falk, Martin
    et al.
    Linköpings universitet, Institutionen för teknik och naturvetenskap, Medie- och Informationsteknik. Linköpings universitet, Tekniska fakulteten.
    Ynnerman, Anders
    Linköpings universitet, Institutionen för teknik och naturvetenskap, Medie- och Informationsteknik. Linköpings universitet, Tekniska fakulteten.
    Treanor, Darren
    Linköpings universitet, Centrum för medicinsk bildvetenskap och visualisering, CMIV. Leeds Teaching Hospitals NHS Trust, United Kingdom.
    Lundström, Claes
    Linköpings universitet, Centrum för medicinsk bildvetenskap och visualisering, CMIV. Sectra, Linköping, Sweden.
    Interactive Visualization of 3D Histopathology in Native Resolution2019Ingår i: IEEE Transactions on Visualization and Computer Graphics, ISSN 1077-2626, E-ISSN 1941-0506, Vol. 25, nr 1, s. 1008-1017Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    We present a visualization application that enables effective interactive visual analysis of large-scale 3D histopathology, that is, high-resolution 3D microscopy data of human tissue. Clinical work flows and research based on pathology have, until now, largely been dominated by 2D imaging. As we will show in the paper, studying volumetric histology data will open up novel and useful opportunities for both research and clinical practice. Our starting point is the current lack of appropriate visualization tools in histopathology, which has been a limiting factor in the uptake of digital pathology. Visualization of 3D histology data does pose difficult challenges in several aspects. The full-color datasets are dense and large in scale, on the order of 100,000 x 100,000 x 100 voxels. This entails serious demands on both rendering performance and user experience design. Despite this, our developed application supports interactive study of 3D histology datasets at native resolution. Our application is based on tailoring and tuning of existing methods, system integration work, as well as a careful study of domain specific demands emanating from a close participatory design process with domain experts as team members. Results from a user evaluation employing the tool demonstrate a strong agreement among the 14 participating pathologists that 3D histopathology will be a valuable and enabling tool for their work.

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  • 22.
    Friederici, Anke
    et al.
    Otto-von-Guericke-University Magdeburg, Magdeburg, Germany.
    Falk, Martin
    Linköpings universitet, Institutionen för teknik och naturvetenskap, Medie- och Informationsteknik. Linköpings universitet, Tekniska fakulteten.
    Hotz, Ingrid
    Linköpings universitet, Institutionen för teknik och naturvetenskap, Medie- och Informationsteknik. Linköpings universitet, Tekniska fakulteten.
    A Winding Angle Framework for Tracking and Exploring Eddy Transport in Oceanic Ensemble Simulations2021Ingår i: Workshop on Visualisation in Environmental Sciences (EnvirVis), The Eurographics Association , 2021Konferensbidrag (Refereegranskat)
    Abstract [en]

    Oceanic eddies, which are highly mass-coherent vortices traveling through the earth's waters, are of special interest for their mixing properties. Therefore, large-scale ensemble simulations are performed to approximate their possible evolution. Analyzing their development and transport behavior requires a stable extraction of both their shape and properties of water masses within. We present a framework for extracting the time series of full 3D eddy geometries based on an winding angle criterion. Our analysis tools enables users to explore the results in-depth by linking extracted volumes to extensive statistics collected across several ensemble members. The methods are showcased on an ensemble simulation of the Red Sea. We show that our extraction produces stable and coherent geometries even for highly irregular eddies in the Red Sea. These capabilities are utilized to evaluate the stability of our method with respect to variations of user-defined parameters. Feedback gathered from domain experts was very positive and indicates that our methods will be considered for newly simulated, even larger data sets.

  • 23.
    Hotz, Ingrid
    et al.
    Linköpings universitet, Institutionen för teknik och naturvetenskap, Medie- och Informationsteknik. Linköpings universitet, Tekniska fakulteten.
    Falk, MartinLinköpings universitet, Institutionen för teknik och naturvetenskap, Medie- och Informationsteknik. Linköpings universitet, Tekniska fakulteten.
    Proceedings of SIGRAD 2017, August 17-18, 2017 Norrköping, Sweden2017Proceedings (redaktörskap) (Refereegranskat)
    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

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  • 24.
    Jönsson, Daniel
    et al.
    Linköpings universitet, Institutionen för teknik och naturvetenskap, Medie- och Informationsteknik. Linköpings universitet, Tekniska fakulteten.
    Falk, Martin
    Linköpings universitet, Institutionen för teknik och naturvetenskap, Medie- och Informationsteknik. Linköpings universitet, Tekniska fakulteten.
    Ynnerman, Anders
    Linköpings universitet, Institutionen för teknik och naturvetenskap, Medie- och Informationsteknik. Linköpings universitet, Tekniska fakulteten. Linköpings universitet, Centrum för medicinsk bildvetenskap och visualisering, CMIV.
    Intuitive Exploration of Volumetric Data Using Dynamic Galleries2016Ingår i: IEEE Transactions on Visualization and Computer Graphics, ISSN 1077-2626, E-ISSN 1941-0506, Vol. 22, nr 1, s. 896-905Artikel i tidskrift (Refereegranskat)
    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.

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  • 25.
    Jönsson, Daniel
    et al.
    Linköpings universitet, Institutionen för teknik och naturvetenskap, Medie- och Informationsteknik. Linköpings universitet, Tekniska fakulteten.
    Steneteg, Peter
    Linköpings universitet, Institutionen för teknik och naturvetenskap, Medie- och Informationsteknik. Linköpings universitet, Tekniska fakulteten.
    Sundén, Erik
    Linköpings universitet, Institutionen för teknik och naturvetenskap, Medie- och Informationsteknik. Linköpings universitet, Tekniska fakulteten.
    Englund, Rickard
    Linköpings universitet, Institutionen för teknik och naturvetenskap, Medie- och Informationsteknik. Linköpings universitet, Tekniska fakulteten.
    Kottravel, Sathish
    Linköpings universitet, Institutionen för teknik och naturvetenskap, Medie- och Informationsteknik. Linköpings universitet, Tekniska fakulteten.
    Falk, Martin
    Linköpings universitet, Institutionen för teknik och naturvetenskap, Medie- och Informationsteknik. Linköpings universitet, Tekniska fakulteten.
    Ynnerman, Anders
    Linköpings universitet, Institutionen för teknik och naturvetenskap, Medie- och Informationsteknik. Linköpings universitet, Tekniska fakulteten.
    Hotz, Ingrid
    Linköpings universitet, Institutionen för teknik och naturvetenskap, Medie- och Informationsteknik. Linköpings universitet, Tekniska fakulteten.
    Ropinski, Timo
    Linköpings universitet, Institutionen för teknik och naturvetenskap, Medie- och Informationsteknik. Linköpings universitet, Tekniska fakulteten.
    Inviwo - A Visualization System with Usage Abstraction Levels2020Ingår i: IEEE Transactions on Visualization and Computer Graphics, ISSN 1077-2626, Vol. 26, nr 11, s. 3241-3254Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    The complexity of todays visualization applications demands specific visualization systems tailored for the development of these applications. Frequently, such systems utilize levels of abstraction to improve the application development process, for insta

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  • 26.
    Kauker, Daniel
    et al.
    VISUS, University of Stuttgart.
    Falk, Martin
    Linköpings universitet, Institutionen för teknik och naturvetenskap, Medie- och Informationsteknik. Linköpings universitet, Tekniska fakulteten.
    Reina, Guido
    VISUS, University of Stuttgart.
    Ynnerman, Anders
    Linköpings universitet, Institutionen för teknik och naturvetenskap, Medie- och Informationsteknik. Linköpings universitet, Tekniska fakulteten. Linköpings universitet, Centrum för medicinsk bildvetenskap och visualisering, CMIV.
    Ertl, Thomas
    VISUS, University of Stuttgart.
    VoxLink—Combining sparse volumetric data and geometry for efficient rendering2016Ingår i: Computational Visual Media, ISSN 2096-0662, Vol. 2, nr 1, s. 45-56Artikel i tidskrift (Refereegranskat)
    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.

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  • 27.
    Kottravel, Sathish
    et al.
    Linköpings universitet, Institutionen för teknik och naturvetenskap, Medie- och Informationsteknik. Linköpings universitet, Tekniska fakulteten.
    Falk, Martin
    Linköpings universitet, Institutionen för teknik och naturvetenskap, Medie- och Informationsteknik. Linköpings universitet, Tekniska fakulteten.
    Sundén, Erik
    Linköpings universitet, Institutionen för teknik och naturvetenskap, Medie- och Informationsteknik. Linköpings universitet, Tekniska fakulteten.
    Ropinski, Timo
    Visual Computing Research Group, Ulm University, Germany.
    Coverage-Based Opacity Estimation for Interactive Depth of Field in Molecular Visualization2015Ingår i: IEEE Pacific Visualization Symposium (PacificVis 2015), IEEE Computer Society, 2015, s. 255-262Konferensbidrag (Refereegranskat)
    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.

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  • 28.
    Kozlíková, Barbora
    et al.
    Masaryk University, Czech Republic.
    Krone, Michael
    VISUS, University of Stuttgart, Germany.
    Lindow, Norbert
    Zuse Institute Berlin, Germany.
    Falk, Martin
    Linköpings universitet, Institutionen för teknik och naturvetenskap, Medie- och Informationsteknik. Linköpings universitet, Tekniska fakulteten.
    Baaden, Marc
    Laboratoire de Biochimie Théorique, France.
    Baum, Daniel
    Zuse Institute Berlin, Germany.
    Viola, Ivan
    Institute of Computer Graphics and Algorithms, Vienna University of Technology, Austria.
    Parulek, Julius
    Department of Informatics, University of Bergen, Norway.
    Hege, Hans-Christian
    Zuse Institute Berlin, Germany.
    Visualization of Molecular Structure: The State of the Art2015Ingår i: Eurographics Conference on Visualization (EuroVis) - STARs / [ed] R. Borgo and F. Ganovelli and I. Viola, Eurographics - European Association for Computer Graphics, 2015Konferensbidrag (Refereegranskat)
    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.

  • 29.
    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 Cavities2011Ingår i: Computer graphics forum (Print), ISSN 0167-7055, E-ISSN 1467-8659, Vol. 30, nr 3, s. 673-682Artikel i tidskrift (Refereegranskat)
    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.

  • 30.
    Lindholm, Stefan
    et al.
    Linköpings universitet, Institutionen för teknik och naturvetenskap, Medie- och Informationsteknik. Linköpings universitet, Tekniska högskolan.
    Falk, Martin
    Linköpings universitet, Institutionen för teknik och naturvetenskap, Medie- och Informationsteknik. Linköpings universitet, Tekniska högskolan.
    Sundén, Erik
    Linköpings universitet, Institutionen för teknik och naturvetenskap, Medie- och Informationsteknik. Linköpings universitet, Tekniska högskolan.
    Bock, Alexander
    Linköpings universitet, Institutionen för teknik och naturvetenskap, Medie- och Informationsteknik. Linköpings universitet, Tekniska högskolan.
    Ynnerman, Anders
    Linköpings universitet, Institutionen för teknik och naturvetenskap, Medie- och Informationsteknik. Linköpings universitet, Centrum för medicinsk bildvetenskap och visualisering, CMIV. Linköpings universitet, Tekniska högskolan.
    Ropinski, Timo
    Linköpings universitet, Institutionen för teknik och naturvetenskap, Medie- och Informationsteknik. Linköpings universitet, Tekniska högskolan.
    Hybrid Data Visualization Based On Depth Complexity Histogram Analysis2015Ingår i: Computer graphics forum (Print), ISSN 0167-7055, E-ISSN 1467-8659, Vol. 34, nr 1, s. 74-85Artikel i tidskrift (Refereegranskat)
    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.

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  • 31.
    Lukasczyk, Jonas
    et al.
    Technische Universität Kaiserslautern, Kaiserslautern, Germany.
    Beran, Jakob
    Stockholm University, Stockholm, Sweden.
    Engelke, Wito
    Linköpings universitet, Institutionen för teknik och naturvetenskap, Medie- och Informationsteknik. Linköpings universitet, Tekniska fakulteten.
    Falk, Martin
    Linköpings universitet, Institutionen för teknik och naturvetenskap, Medie- och Informationsteknik. Linköpings universitet, Tekniska fakulteten.
    Friederici, Anke
    KTH Royal Institute of Technology, Stockholm, Sweden.
    Garth, Christoph
    Technische Universität Kaiserslautern, Kaiserslautern, Germany.
    Hofmann, Lutz
    Heidelberg University, Heidelberg, Germany.
    Hotz, Ingrid
    Linköpings universitet, Institutionen för teknik och naturvetenskap, Medie- och Informationsteknik. Linköpings universitet, Tekniska fakulteten.
    Hristov, Petar
    University of Leeds, Leeds, UK.
    Köpp, Wiebke
    KTH Royal Institute of Technology, Stockholm, Sweden.
    Masood, Talha Bin
    Linköpings universitet, Institutionen för teknik och naturvetenskap, Medie- och Informationsteknik. Linköpings universitet, Tekniska fakulteten.
    Olejniczak, Małgorzata
    University of Warsaw, Warsaw, Poland.
    Rosen, Paul
    University of South Florida, Tampa, USA.
    Sohns, Jan-Tobias
    Technische Universität Kaiserslautern, Kaiserslautern, Germany.
    Weinkauf, Tino
    KTH Royal Institute of Technology, Stockholm, Sweden.
    Werner, Kilian
    Technische Universität Kaiserslautern, Kaiserslautern, Germany.
    Tierny, Julien
    CNRS, Sorbonne Universite, Paris, France.
    Report of the TopoInVis TTK Hackathon: Experiences, Lessons Learned, and Perspectives2021Ingår i: Topological Methods in Data Analysis and Visualization VI: Theory, Applications, and Software / [ed] Ingrid Hotz, Talha Bin Masood, Filip Sadlo and Julien Tierny, Springer, 2021, s. 359-373Kapitel i bok, del av antologi (Refereegranskat)
    Abstract [en]

    This paper documents the organization, the execution, and the results of the Topology ToolKit (TTK) hackathon that took place at the TopoInVis 2019 conference. The primary goal of the hackathon was to promote TTK in our research community as a unified software development platform for topology-based data analysis algorithms. To this end, participants were first introduced to the structure and capabilities of TTK, and then worked on their own TTK-related projects while being mentored by senior TTK developers. Notable outcomes of the hackathon were first steps towards Python and Docker packages, further integration of TTK in Inviwo, the extension of TTK with new algorithms, and the discovery of current limitations of TTK as well as future development directions.

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  • 32.
    Masood, Talha Bin
    et al.
    Linköpings universitet, Institutionen för teknik och naturvetenskap, Medie- och Informationsteknik. Linköpings universitet, Tekniska fakulteten.
    Budin, Joseph
    Sorbonne Université, Paris, France.
    Falk, Martin
    Linköpings universitet, Institutionen för teknik och naturvetenskap, Medie- och Informationsteknik. Linköpings universitet, Tekniska fakulteten.
    Favelier, Guillaume
    INRIA Saclay - Île-de-France, Palaiseau, France.
    Garth, Christoph
    TU Kaiserslautern, Kaiserslautern, Germany.
    Gueunet, Charles
    Kitware, New York, USA.
    Guillou, Pierre
    Sorbonne Université, Paris, France.
    Hofmann, Lutz
    Heidelberg University, Heidelberg, Germany.
    Hristov, Petar
    University of Leeds, Leeds, UK.
    Kamakshidasan, Adhitya
    INRIA Saclay - Île-de-France, Palaiseau, France.
    Kappe, Christopher
    TU Kaiserslautern, Kaiserslautern, Germany.
    Klacansky, Pavol
    SCI Institute, University of Utah, Salt Lake City, USA.
    Laurin, Patrick
    ShapeShift3D, Montreal, Canada.
    Levine, Joshua A.
    University of Arizona, Tucson, USA.
    Lukasczyk, Jonas
    Arizona State University, Phoenix, USA.
    Sakurai, Daisuke
    Kyushu University, Fukuoka, Japan.
    Soler, Maxime
    Total / Sorbonne Université, Paris, France.
    Steneteg, Peter
    Linköpings universitet, Institutionen för teknik och naturvetenskap, Medie- och Informationsteknik. Linköpings universitet, Tekniska fakulteten.
    Tierny, Julien
    CNRS / Sorbonne Université, Paris, France.
    Usher, Will
    SCI Institute, University of Utah, Salt Lake City, USA.
    Vidal, Jules
    Sorbonne Université, Paris, France.
    Wozniak, Michal
    ShapeShift3D, Montreal, Canada.
    An Overview of the Topology ToolKit2021Ingår i: Topological Methods in Data Analysis and Visualization VI: Theory, Applications, and Software / [ed] Ingrid Hotz, Talha Bin Masood, Filip Sadlo and Julien Tierny, Springer, 2021, s. 327-342Kapitel i bok, del av antologi (Refereegranskat)
    Abstract [en]

    This software paper gives an overview of the features supported by the Topology ToolKitTopology ToolKit (TTK), which is an  Open-sourceopen-source library for  Topological data analysistopological data analysis (TDA). TTK implements, in a generic and efficient way, a substantial collection of reference algorithms in TDA. Since its initial public release in 2017, both its user and developer bases have grown, resulting in a significant increase in the number of supported features. In contrast to the original paper introducing TTK [40] (which detailed the core algorithms and data structures of TTK), the purpose of this Softwaresoftware paper is to describe the list of features currently supported by TTK, ranging from image segmentation tools to advanced topological analysis of high-dimensional data, with concrete usage examples available on the TTK website [42].

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  • 33.
    Menges, Anna-Leonie
    et al.
    Univ Hosp Zurich, Switzerland.
    Nackenhorst, Maja
    Med Univ Vienna, Austria.
    Mueller, Johannes R.
    Tech Univ Dresden, Germany.
    Engl, Marie-Luise
    Tech Univ Munich, Germany.
    Hegenloh, Renate
    Tech Univ Munich, Germany.
    Pelisek, Jaroslav
    Univ Hosp Zurich, Switzerland.
    Geibelt, Ellen
    Tech Univ Dresden, Germany.
    Hofmann, Anja
    TUD Dresden Univ Technol, Germany; TUD Dresden Univ Technol, Germany.
    Reeps, Christian
    TUD Dresden Univ Technol, Germany; TUD Dresden Univ Technol, Germany.
    Biro, Gabor
    Tech Univ Munich, Germany.
    Eckstein, Hans-Henning
    Tech Univ Munich, Germany; Munich Heart Alliance, Germany.
    Zimmermann, Alexander
    Univ Hosp Zurich, Switzerland.
    Magee, Derek
    HeteroGenius Ltd, England; Univ Leeds, England.
    Falk, Martin
    Linköpings universitet, Institutionen för teknik och naturvetenskap, Medie- och Informationsteknik. Linköpings universitet, Tekniska fakulteten.
    Sachs, Nadja
    Tech Univ Munich, Germany; Munich Heart Alliance, Germany.
    Busch, Albert
    Tech Univ Munich, Germany; TUD Dresden Univ Technol, Germany; TUD Dresden Univ Technol, Germany.
    Correction: Completing the view - histologic insights from circular AAA specimen including 3D imaging (vol 18, 73, 2023)2023Ingår i: Diagnostic Pathology, E-ISSN 1746-1596, Vol. 18, nr 1, artikel-id 130Artikel i tidskrift (Övrigt vetenskapligt)
  • 34.
    Menges, Anna-Leonie
    et al.
    Univ Hosp Zurich, Switzerland.
    Nackenhorst, Maja
    Med Univ Vienna, Austria.
    Müller, Johannes R.
    Tech Univ Dresden, Germany.
    Engl, Marie-Luise
    Tech Univ Munich, Germany.
    Hegenloh, Renate
    Tech Univ Munich, Germany.
    Pelisek, Jaroslav
    Univ Hosp Zurich, Switzerland.
    Geibelt, Ellen
    Tech Univ Dresden, Germany.
    Hofmann, Anja
    Tech Univ Dresden, Germany.
    Reeps, Christian
    Tech Univ Dresden, Germany.
    Biro, Gabor
    Tech Univ Munich, Germany.
    Eckstein, Hans-Henning
    Tech Univ Munich, Germany; German Ctr Cardiovasc Res DZHK, Germany.
    Zimmermann, Alexander
    Univ Hosp Zurich, Switzerland.
    Magee, Derek
    HeteroGenius Ltd, England; Univ Leeds, England.
    Falk, Martin
    Linköpings universitet, Institutionen för teknik och naturvetenskap, Medie- och Informationsteknik. Linköpings universitet, Tekniska fakulteten.
    Sachs, Nadja
    Tech Univ Munich, Germany; German Ctr Cardiovasc Res DZHK, Germany.
    Busch, Albert
    Tech Univ Munich, Germany; Tech Univ Dresden, Germany.
    Completing the view – histologic insights from circular AAA specimen including 3D imaging2023Ingår i: Diagnostic Pathology, E-ISSN 1746-1596, Vol. 18, nr 1, artikel-id 73Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    Abdominal aortic aneurysm (AAA) is a pathologic enlargement of the infrarenal aorta with an associated risk of rupture. However, the responsible mechanisms are only partially understood. Based on murine and human samples, a heterogeneous distribution of characteristic pathologic features across the aneurysm circumference is expected. Yet, complete histologic workup of the aneurysm sac is scarcely reported. Here, samples from five AAAs covering the complete circumference partially as aortic rings are investigated by histologic means (HE, EvG, immunohistochemistry) and a new method embedding the complete ring. Additionally, two different methods of serial histologic section alignment are applied to create a 3D view. The typical histopathologic features of AAA, elastic fiber degradation, matrix remodeling with collagen deposition, calcification, inflammatory cell infiltration and thrombus coverage were distributed without recognizable pattern across the aneurysm sac in all five patients. Analysis of digitally scanned entire aortic rings facilitates the visualization of these observations. Immunohistochemistry is feasible in such specimen, however, tricky due to tissue disintegration. 3D image stacks were created using open-source and non-generic software correcting for non-rigid warping between consecutive sections. Secondly, 3D image viewers allowed visualization of in-depth changes of the investigated pathologic hallmarks. In conclusion, this exploratory descriptive study demonstrates a heterogeneous histomorphology around the AAA circumference. Warranting an increased sample size, these results might need to be considered in future mechanistic research, especially in reference to intraluminal thrombus coverage. 3D histology of such circular specimen could be a valuable visualization tool for further analysis.

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  • 35.
    Skånberg, Robin
    et al.
    Linköpings universitet, Institutionen för teknik och naturvetenskap, Medie- och Informationsteknik. Linköpings universitet, Tekniska fakulteten. Swedish e-Science Research Centre (SeRC), Stockholm, Sweden.
    Falk, Martin
    Linköpings universitet, Institutionen för teknik och naturvetenskap, Medie- och Informationsteknik. Linköpings universitet, Tekniska fakulteten. Swedish e-Science Research Centre (SeRC), Stockholm, Sweden.
    Linares, Mathieu
    Linköpings universitet, Institutionen för teknik och naturvetenskap, Laboratoriet för organisk elektronik. Linköpings universitet, Tekniska fakulteten. Swedish e-Science Research Centre (SeRC), Stockholm, Sweden.
    Ynnerman, Anders
    Linköpings universitet, Institutionen för teknik och naturvetenskap, Medie- och Informationsteknik. Linköpings universitet, Tekniska fakulteten. Swedish e-Science Research Centre (SeRC), Stockholm, Sweden.
    Hotz, Ingrid
    Linköpings universitet, Institutionen för teknik och naturvetenskap, Medie- och Informationsteknik. Linköpings universitet, Tekniska fakulteten. Swedish e-Science Research Centre (SeRC), Stockholm, Sweden.
    Tracking Internal Frames of Reference for Consistent Molecular Distribution Functions2022Ingår i: IEEE Transactions on Visualization and Computer Graphics, ISSN 1077-2626, E-ISSN 1941-0506, Vol. 28, nr 9, s. 3126-3137Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    In molecular analysis, Spatial Distribution Functions (SDF) are fundamental instruments in answering questions related to spatial occurrences and relations of atomic structures over time. Given a molecular trajectory, SDFs can, for example, reveal the occurrence of water in relation to particular structures and hence provide clues of hydrophobic and hydrophilic regions. For the computation of meaningful distribution functions, the definition of molecular reference structures is essential. Therefore we introduce the concept of an internal frame of reference (IFR) for labeled point sets that represent selected molecular structures, and we propose an algorithm for tracking the IFR over time and space using a variant of Kabschs algorithm. This approach lets us generate a consistent space for the aggregation of the SDF for molecular trajectories and molecular ensembles. We demonstrate the usefulness of the technique by applying it to temporal molecular trajectories as well as ensemble datasets. The examples include different docking scenarios with DNA, insulin, and aspirin.

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  • 36.
    Skånberg, Robin
    et al.
    Linköpings universitet, Institutionen för teknik och naturvetenskap, Medie- och Informationsteknik. Linköpings universitet, Tekniska fakulteten. Swedish e-Science Research Centre (SeRC).
    Linares, Mathieu
    Linköpings universitet, Tekniska fakulteten. Linköpings universitet, Institutionen för teknik och naturvetenskap, Medie- och Informationsteknik. Swedish e-Science Research Centre (SeRC).
    Falk, Martin
    Linköpings universitet, Institutionen för teknik och naturvetenskap, Medie- och Informationsteknik. Linköpings universitet, Tekniska fakulteten. Swedish e-Science Research Centre (SeRC).
    Hotz, Ingrid
    Linköpings universitet, Institutionen för teknik och naturvetenskap, Medie- och Informationsteknik. Linköpings universitet, Tekniska fakulteten. Swedish e-Science Research Centre (SeRC).
    Ynnerman, Anders
    Linköpings universitet, Institutionen för teknik och naturvetenskap, Medie- och Informationsteknik. Linköpings universitet, Tekniska fakulteten. Swedish e-Science Research Centre (SeRC).
    MolFind - Integrated Multi-Selection Schemes for Complex Molecular Structures2019Ingår i: Workshop on Molecular Graphics and Visual Analysis of Molecular Data (MolVA) / [ed] J. Byška, M. Krone, and B. Sommer, The Eurographics Association , 2019Konferensbidrag (Refereegranskat)
    Abstract [en]

    Selecting components and observing changes ofproperties and configurations over time is an important step in the analysis of molecular dynamics (MD) data. In this paper, we present a selection tool combining text-based queries with spatial selection and filtering. Morphological operations facilitate refinement of the selection by growth operators, e.g. across covalent bonds. The combination of different selection paradigms enables flexible and intuitive analysis on different levels of detail and visual depiction of molecular events. Immediate visual feedback during interactions ensures a smooth exploration of the data. We demonstrate the utility of our selection framework by analyzing temporal changes in the secondary structure of poly-alanineand the binding ofaspirin to phospholipase A2.

  • 37.
    Steneteg, Peter
    et al.
    Linköpings universitet, Institutionen för teknik och naturvetenskap, Medie- och Informationsteknik. Linköpings universitet, Tekniska fakulteten.
    Jönsson, Daniel
    Linköpings universitet, Institutionen för teknik och naturvetenskap, Medie- och Informationsteknik. Linköpings universitet, Tekniska fakulteten. Linköpings universitet, Centrum för medicinsk bildvetenskap och visualisering, CMIV.
    Falk, Martin
    Linköpings universitet, Institutionen för teknik och naturvetenskap, Medie- och Informationsteknik. Linköpings universitet, Tekniska fakulteten.
    Hotz, Ingrid
    Linköpings universitet, Institutionen för teknik och naturvetenskap, Medie- och Informationsteknik. Linköpings universitet, Tekniska fakulteten.
    Volume Raycasting Sampling Revisited2019Konferensbidrag (Refereegranskat)
    Abstract [en]

    We investigate the effects of practical sample placement strategies when solving the volume rendering integral for interactive volume raycasting with fixed step lengths for each ray. Different sample placements have been used in previous work but they have not been compared with respect to their correctness or visual quality. In this work, the different sampling strategies are presented visually and practical implementation details are provided using algorithmic descriptions of each strategy. A thorough analysis based on comparisons with analytic solutions and real-world data shows that visual artifacts, especially at volume borders, can appear if samples are not placed correctly. Our analysis and comparison results in a sample placement strategy that easily can be integrated into existing implementations, has no impact on performance, and decreases visual artifacts of the rendered image compared to other fixed step size sample strategies.

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