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  • 1.
    Axholt, Magnus
    et al.
    Linköping University, Department of Science and Technology, Media and Information Technology. Linköping University, The Institute of Technology.
    Skoglund, Martin A.
    Linköping University, Department of Electrical Engineering, Automatic Control. Linköping University, The Institute of Technology.
    O’Connell, Stephen D.
    Swedish Air Force Combat Simulation Center at the Swedish Defence Research Agency.
    Cooper, Matthew D.
    Linköping University, Department of Science and Technology, Media and Information Technology. Linköping University, The Institute of Technology.
    Ellis, Stephen R.
    Human Systems Integration Division at NASA Ames Research Center.
    Ynnerman, Anders
    Linköping University, Department of Science and Technology, Media and Information Technology. Linköping University, The Institute of Technology.
    Accuracy of Eyepoint Estimation in Optical See-Through Head-Mounted Displays Using the Single Point Active Alignment Method2011Conference paper (Other academic)
    Abstract [en]

    This paper studies the accuracy of the estimated eyepoint of an Optical See-Through Head-Mounted Display (OST HMD) calibrated using the Single Point Active Alignment Method (SPAAM). Quantitative evaluation of calibration procedures for OST HMDs is complicated as it is currently not possible to share the subject’s view. Temporarily replacing the subject’s eye with a camera during the calibration or evaluation stage has been proposed, but the uncertainty of a correct eyepoint estimation remains. In the experiment reported in this paper, subjects were used for all stages of calibration and the results were verified with a 3D measurement device. The nine participants constructed 25 visual alignments per calibration after which the estimated pinhole camera model was decomposed into its intrinsic and extrinsic parameters using two common methods. Unique to this experiment, compared to previous evaluations, is the measurement device used to cup the subject’s eyeball. It measures the eyepoint location relative to the head tracker, thereby establishing the calibration accuracy of the estimated eyepoint location. As the results on accuracy are expressed as individual pinhole camera parameters, rather than a compounded registration error, this paper complements  previously published work on parameter variance as the former denotes bias and the latter represents noise. Results indicate that the calibrated eyepoint is on average 5 cm away from its measured location and exhibits a vertical bias which potentially causes dipvergence for stereoscopic vision for objects located further away than 5.6 m. Lastly, this paper closes with a discussion on the suitability of the traditional pinhole camera model for OST HMD calibration.

  • 2.
    Axholt, Magnus
    et al.
    Linköping University, Department of Science and Technology, Media and Information Technology. Linköping University, The Institute of Technology.
    Skoglund, Martin
    Linköping University, Department of Electrical Engineering, Automatic Control. Linköping University, The Institute of Technology.
    O'Connell, Stephen
    Swedish Defence Research Agency.
    Cooper, Matthew
    Linköping University, Department of Science and Technology, Media and Information Technology. Linköping University, The Institute of Technology.
    Ellis, Stephen
    NASA Ames Research Center.
    Ynnerman, Anders
    Linköping University, Department of Science and Technology, Media and Information Technology. Linköping University, The Institute of Technology.
    Parameter Estimation Variance of the Single Point Active Alignment Method in Optical See-Through Head Mounted Display Calibration2011In: Proceedings of the IEEE Virtual Reality Conference / [ed] Michitaka Hirose, Benjamin Lok, Aditi Majumder and Dieter Schmalstieg, Piscataway, NJ, USA: IEEE , 2011, p. 27-24Conference paper (Refereed)
    Abstract [en]

    The parameter estimation variance of the Single Point Active Alignment Method (SPAAM) is studied through an experiment where 11 subjects are instructed to create alignments using an Optical See-Through Head Mounted Display (OSTHMD) such that three separate correspondence point distributions are acquired. Modeling the OSTHMD and the subject's dominant eye as a pinhole camera, findings show that a correspondence point distribution well distributed along the user's line of sight yields less variant parameter estimates. The estimated eye point location is studied in particular detail. Thefindings of the experiment are complemented with simulated datawhich show that image plane orientation is sensitive to the numberof correspondence points. The simulated data also illustrates someinteresting properties on the numerical stability of the calibrationproblem as a function of alignment noise, number of correspondencepoints, and correspondence point distribution.

  • 3.
    Axholt, Magnus
    et al.
    Linköping University, Department of Science and Technology, Media and Information Technology. Linköping University, The Institute of Technology. Linköping University, Department of Science and Technology, Visual Information Technology and Applications (VITA).
    Skoglund, Martin
    Linköping University, Department of Electrical Engineering, Automatic Control. Linköping University, The Institute of Technology.
    Peterson, Stephen
    Linköping University, Department of Science and Technology, Media and Information Technology. Linköping University, The Institute of Technology. Linköping University, Department of Science and Technology, Visual Information Technology and Applications (VITA).
    Cooper, Matthew
    Linköping University, Department of Science and Technology, Media and Information Technology. Linköping University, The Institute of Technology. Linköping University, Department of Science and Technology, Visual Information Technology and Applications (VITA).
    Schön, Thomas
    Linköping University, Department of Electrical Engineering, Automatic Control. Linköping University, The Institute of Technology.
    Gustafsson, Fredrik
    Linköping University, Department of Electrical Engineering, Automatic Control. Linköping University, The Institute of Technology.
    Ynnerman, Anders
    Linköping University, Department of Science and Technology, Media and Information Technology. Linköping University, The Institute of Technology. Linköping University, Department of Science and Technology, Visual Information Technology and Applications (VITA).
    Ellis, Stephen
    NASA Ames Research Center, USA.
    Optical See-Through Head Mounted Display: Direct Linear Transformation Calibration Robustness in the Presence of User Alignment Noise2010Report (Other academic)
    Abstract [en]

    The correct spatial registration between virtual and real objects in optical see-through augmented reality implies accurate estimates of the user’s eyepoint relative to the location and orientation of the display surface. A common approach is to estimate the display parameters through a calibration procedure involving a subjective alignment exercise. Human postural sway and targeting precision contribute to imprecise alignments, which in turn adversely affect the display parameter estimation resulting in registration errors between virtual and real objects. The technique commonly used has its origin incomputer vision, and calibrates stationary cameras using hundreds of correspondence points collected instantaneously in one video frame where precision is limited only by pixel quantization and image blur. Subsequently the input noise level is several order of magnitudes greater when a human operator manually collects correspondence points one by one. This paper investigates the effect of human alignment noise on view parameter estimation in an optical see-through head mounted display to determine how well astandard camera calibration method performs at greater noise levels than documented in computer vision literature. Through Monte-Carlo simulations we show that it is particularly difficult to estimate the user’s eyepoint in depth, but that a greater distribution of correspondence points in depth help mitigate the effects of human alignment noise.

  • 4.
    Axholt, Magnus
    et al.
    Linköping University, Department of Science and Technology, Media and Information Technology. Linköping University, The Institute of Technology.
    Skoglund, Martin
    Linköping University, Department of Electrical Engineering, Automatic Control. Linköping University, The Institute of Technology.
    Peterson, Stephen
    Linköping University, Department of Science and Technology, Media and Information Technology. Linköping University, The Institute of Technology.
    Cooper, Matthew
    Linköping University, Department of Science and Technology, Media and Information Technology. Linköping University, The Institute of Technology.
    Schön, Thomas
    Linköping University, Department of Electrical Engineering, Automatic Control. Linköping University, The Institute of Technology.
    Gustafsson, Fredrik
    Linköping University, Department of Electrical Engineering, Automatic Control. Linköping University, The Institute of Technology.
    Ynnerman, Anders
    Linköping University, Department of Science and Technology, Media and Information Technology. Linköping University, The Institute of Technology.
    Ellis, Stephen
    NASA Ames Research Center, USA.
    Optical See-Through Head Mounted Display: Direct Linear Transformation Calibration Robustness in the Presence of User Alignment Noise2010In: Proceedings of the 54th Annual Meeting of the Human Factors and Ergonomics Society, 2010Conference paper (Refereed)
    Abstract [en]

    The correct spatial registration between virtual and real objects in optical see-through augmented reality implies accurate estimates of the user’s eyepoint relative to the location and orientation of the display surface. A common approach is to estimate the display parameters through a calibration procedure involving a subjective alignment exercise. Human postural sway and targeting precision contribute to imprecise alignments, which in turn adversely affect the display parameter estimation resulting in registration errors between virtual and real objects. The technique commonly used has its origin incomputer vision, and calibrates stationary cameras using hundreds of correspondence points collected instantaneously in one video frame where precision is limited only by pixel quantization and image blur. Subsequently the input noise level is several order of magnitudes greater when a human operator manually collects correspondence points one by one. This paper investigates the effect of human alignment noise on view parameter estimation in an optical see-through head mounted display to determine how well astandard camera calibration method performs at greater noise levels than documented in computer vision literature. Through Monte-Carlo simulations we show that it is particularly difficult to estimate the user’s eyepoint in depth, but that a greater distribution of correspondence points in depth help mitigate the effects of human alignment noise.

  • 5.
    Bivall Persson, Petter
    et al.
    Linköping University, Department of Science and Technology, Visual Information Technology and Applications (VITA). Linköping University, The Institute of Technology.
    Cooper, Matthew
    Linköping University, Department of Science and Technology, Visual Information Technology and Applications (VITA). Linköping University, The Institute of Technology.
    Tibell, Lena
    Linköping University, Department of Biomedicine and Surgery, Division of cell biology. Linköping University, Faculty of Health Sciences.
    Ainsworth, Shaaron
    Learning Sciences Research Institute, University of Nottingham, Nottingham, UK.
    Ynnerman, Anders
    Linköping University, Department of Science and Technology, Visual Information Technology and Applications (VITA). Linköping University, The Institute of Technology.
    Jonsson, Bengt-Harald
    Linköping University, Department of Physics, Chemistry and Biology, Molecular Biotechnology. Linköping University, The Institute of Technology.
    Designing and Evaluating a Haptic System for Biomolecular Education2007In: IEEE Virtual Reality Conference, 2007. VR '07. / [ed] Sherman, W; Lin, M; Steed, A, Piscataway, NJ, USA: IEEE , 2007, p. 171-178Conference paper (Refereed)
    Abstract [en]

    In this paper we present an in situ evaluation of a haptic system, with a representative test population, we aim to determine what, if any, benefit haptics can have in a biomolecular education context. We have developed a haptic application for conveying concepts of molecular interactions, specifically in protein-ligand docking. Utilizing a semi-immersive environment with stereo graphics, users are able to manipulate the ligand and feel its interactions in the docking process. The evaluation used cognitive knowledge tests and interviews focused on learning gains. Compared with using time efficiency as the single quality measure this gives a better indication of a system's applicability in an educational environment. Surveys were used to gather opinions and suggestions for improvements. Students do gain from using the application in the learning process but the learning appears to be independent of the addition of haptic feedback. However the addition of force feedback did decrease time requirements and improved the students understanding of the docking process in terms of the forces involved, as is apparent from the students' descriptions of the experience. The students also indicated a number of features which could be improved in future development.

  • 6.
    Bivall Persson, Petter
    et al.
    Linköping University, Department of Science and Technology, Visual Information Technology and Applications (VITA). Linköping University, The Institute of Technology.
    Cooper, Matthew
    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, Visual Information Technology and Applications (VITA). Linköping University, The Institute of Technology.
    Jonsson, Bengt-Harald
    Linköping University, The Institute of Technology. Linköping University, Department of Physics, Chemistry and Biology, Molecular Biotechnology.
    Tibell, Lena
    Linköping University, Faculty of Health Sciences. Linköping University, Department of Biomedicine and Surgery, Division of cell biology.
    Use of Chemical Force Feedback for Multisensory Insights into Ligand Docking2007In: VII European Symposium of The Protein Society: From Proteins to Proteome, 2007, p. 151-151Conference paper (Refereed)
  • 7.
    Bivall Persson, Petter
    et al.
    Linköping University, Department of Science and Technology, Visual Information Technology and Applications (VITA). Linköping University, The Institute of Technology.
    Höst, Gunnar E.
    Linköping University, Department of Science and Technology, Visual Information Technology and Applications (VITA). Linköping University, The Institute of Technology.
    Cooper, Matthew D.
    Linköping University, Department of Science and Technology, Visual Information Technology and Applications (VITA). Linköping University, The Institute of Technology.
    Tibell, Lena A. E.
    Linköping University, Department of Clinical and Experimental Medicine. Linköping University, Faculty of Health Sciences.
    Ynnerman, Anders
    Linköping University, Department of Science and Technology, Visual Information Technology and Applications (VITA). Linköping University, The Institute of Technology.
    Improved Feature Detection over Large Force Ranges Using History Dependent Transfer Functions2009In: Third Joint Eurohaptics Conference and Symposium on Haptic Interfaces for Virtual Environments and Teleoperator Systems, WorldHaptics 2009, IEEE , 2009, p. 476-481Conference paper (Refereed)
    Abstract [en]

    In this paper we present a history dependent transfer function (HDTF) as a possible approach to enable improved haptic feature detection in high dynamic range (HDR) volume data. The HDTF is a multi-dimensional transfer function that uses the recent force history as a selection criterion to switch between transfer functions, thereby adapting to the explored force range. The HDTF has been evaluated using artificial test data and in a realistic application example, with the HDTF applied to haptic protein-ligand docking. Biochemistry experts performed docking tests, and expressed that the HDTF delivers the expected feedback across a large force magnitude range, conveying both weak attractive and strong repulsive protein-ligand interaction forces. Feature detection tests have been performed with positive results, indicating that the HDTF improves the ability of feature detection in HDR volume data as compared to a static transfer function covering the same range.

  • 8.
    Bivall Persson, Petter
    et al.
    Linköping University, Department of Science and Technology, Media and Information Technology. Linköping University, Faculty of Science & Engineering.
    Tibell, Lena
    Linköping University, Faculty of Health Sciences. Linköping University, Department of Biomedicine and Surgery, Division of cell biology.
    Cooper, Matthew
    Linköping University, Department of Science and Technology, Visual Information Technology and Applications (VITA). Linköping University, The Institute of Technology.
    Ynnerman, Anders
    Linköping University, Department of Science and Technology, Visual Information Technology and Applications (VITA). Linköping University, The Institute of Technology.
    Jonsson, Bengt-Harald
    Linköping University, The Institute of Technology. Linköping University, Department of Physics, Chemistry and Biology, Molecular Biotechnology.
    Evaluating the Effectiveness of Haptic Visualization in Biomolecular Education - Feeling Molecular Specificity in a Docking Task2006In: 12th IOSTE Symposium, Universiti Science Malaysia , 2006, p. 745-752Conference paper (Refereed)
    Abstract [en]

    Within the molecular life sciences extensive use is made of visual representations, ranging from sketches to advanced computer graphics, often used to convey abstract knowledge that is difficult for the student to grasp. This work evaluates a new visual and haptic (tactile/kinetic) tool for protein docking in an in situ learning situation by combining qualitative and quantitative methods, performing tests and interviews with students; all aiming at a proper inclusion of visualization tools into biomolecular education. Preliminary results indicate time gains, strong positive affective responses and learning gains from the tasks, however the influence of haptics needs further investigation.

  • 9.
    Bock, Alexander
    et al.
    Linköping University, Department of Science and Technology, Media and Information Technology. Linköping University, Faculty of Science & Engineering. New York University, USA.
    Axelsson, Emil
    Linköping University, Department of Science and Technology, Media and Information Technology. Linköping University, Faculty of Science & Engineering.
    Bladin, Karl
    Linköping University, Department of Science and Technology, Media and Information Technology. Linköping University, Faculty of Science & Engineering.
    Jonathas, Costa
    New York University, USA.
    Gene, Payne
    University of Utah, USA.
    Matthew, Territo
    University of Utah, USA.
    Kilby, Joakim
    Linköping University, Department of Science and Technology, Media and Information Technology. Linköping University, Faculty of Science & Engineering.
    Masha, Kuznetsova
    Community Coordinated Modeling Center, NASA, USA.
    Emmart, Carter
    American Museum of Natural History, USA.
    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).
    OpenSpace: An open-source astrovisualization framework2017In: The Journal of Open Source Software, ISSN 2475-9066, Vol. 2, no 15, article id 281Article in journal (Refereed)
    Abstract [en]

    OpenSpace (2017; Bock et al. 2017)is an open source interactive data visualization software designed to visualize the entire known universe and portray our ongoing efforts to investigate the cosmos (Bladin, Karl and Axelsson, Emil and Broberg, Erik and Emmart, Carter and Ljung, Patric and Bock, Alexander and Ynnerman, Anders 2017; Bock, Pembroke, et al. 2015). Bringing the latest techniques from data visualization research to the general public and scientists (Bock, Marcinkowski, et al. 2015), OpenSpace supports interactive presentation of dynamic data from observations, simulations, and space mission planning and operations over a large span of sizes (Axelsson, Emil and Costa, Jonathas and Silva, Cláudio T. and Emmart, Carter and Bock, Alexander and Ynnerman, Anders 2017). The software supports multiple operating systems with an extensible architecture powering high resolution tiled displays, planetarium domes, as well as desktop computers. In addition, OpenSpace enables simultaneous connections across the globe creating opportunity for shared experiences among audiences worldwide.

  • 10.
    Bock, Alexander
    et al.
    Linköping University, Department of Science and Technology, Media and Information Technology. Linköping University, Faculty of Science & Engineering. University of Utah, USA.
    Axelsson, Emil
    Linköping University, Department of Science and Technology, Media and Information Technology. Linköping University, Faculty of Science & Engineering.
    Costa, Jonathas
    New York University, USA.
    Payne, Gene
    University of Utah, USA.
    Acinapura, Micah
    American Museum of Natural History, USA.
    Trakinski, Vivian
    American Museum of Natural History, USA.
    Emmart, Carter
    American Museum of Natural History, USA.
    Silva, Cláudio
    New York University, USA.
    Hansen, Charles
    University of Utah, USA.
    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). University of Utah, USA.
    OpenSpace: A System for Astrographics2019In: IEEE Transactions on Visualization and Computer Graphics, ISSN 1077-2626, E-ISSN 1941-0506, p. 1-10Article in journal (Refereed)
    Abstract [en]

    Human knowledge about the cosmos is rapidly increasing as instruments and simulations are generating new data supporting the formation of theory and understanding of the vastness and complexity of the universe. OpenSpace is a software system that takes on the mission of providing an integrated view of all these sources of data and supports interactive exploration of the known universe from the millimeter scale showing instruments on spacecrafts to billions of light years when visualizing the early universe. The ambition is to support research in astronomy and space exploration, science communication at museums and in planetariums as well as bringing exploratory astrographics to the class room. There is a multitude of challenges that need to be met in reaching this goal such as the data variety, multiple spatio-temporal scales, collaboration capabilities, etc. Furthermore, the system has to be flexible and modular to enable rapid prototyping and inclusion of new research results or space mission data and thereby shorten the time from discovery to dissemination. To support the different use cases the system has to be hardware agnostic and support a range of platforms and interaction paradigms. In this paper we describe how OpenSpace meets these challenges in an open source effort that is paving the path for the next generation of interactive astrographics.

  • 11.
    Bock, Alexander
    et al.
    Linköping University, Department of Science and Technology, Media and Information Technology. Linköping University, Faculty of Science & Engineering.
    Marcinkowski, Michal
    Linköping University, Department of Science and Technology. American Museum of Natural History, New York.
    Kilby, Joakim
    Linköping University, Department of Science and Technology, Media and Information Technology. Linköping University, Faculty of Science & Engineering.
    Emmart, Carter
    American Museum of Natural History, New York.
    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).
    OpenSpace: Public Dissemination of Space Mission Profiles2015Conference paper (Refereed)
  • 12.
    Bock, Alexander
    et al.
    Linköping University, Department of Science and Technology, Media and Information Technology. Linköping University, Faculty of Science & Engineering.
    Mays, M. Leila
    NASA Goddard Space Flight Center, Greenbelt, MD, USA.
    Rastaetter, Lutz
    NASA Goddard Space Flight Center, Greenbelt, MD, USA.
    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).
    Ropinski, Timo
    Linköping University, Department of Science and Technology, Media and Information Technology. Linköping University, Faculty of Science & Engineering.
    VCMass: A Framework for Verification of Coronal Mass Ejection Ensemble Simulations2014Conference paper (Refereed)
    Abstract [en]

    Supporting the growing field of space weather forecasting, we propose a framework to analyze ensemble simulations of coronal mass ejections. As the current simulation technique requires manual input, uncertainty is introduced into the simulation pipeline which leads to inaccurate predictions. Using our system, the analyst can compare ensemble members against ground truth data (arrival time and geo-effectivity) as well as information derived from satellite imagery. The simulations can be compared on a global basis, based on time-resolved quality measures, and as a 3D volumetric rendering with embedded satellite imagery in a multi-view setup. This flexible framework provides the expert with the tools to increase the knowledge about the, as of yet not fully understood, principles behind the formation of coronal mass ejections.

  • 13.
    Bock, Alexander
    et al.
    Linköping University, Department of Science and Technology, Media and Information Technology. Linköping University, Faculty of Science & Engineering.
    Pembroke, Asher
    NASA Goddard Space Flight Center, USA.
    Mays, M. Leila
    NASA Goddard Space Flight Center, USA.
    Rastaetter, Lutz
    NASA Goddard Space Flight Center, USA.
    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).
    Ropinski, Timo
    Ulm University, Germany.
    Visual Verification of Space Weather Ensemble Simulations2015In: 2015 IEEE Scientific Visualization Conference (SciVis), IEEE, 2015, p. 17-24Conference paper (Refereed)
    Abstract [en]

    We propose a system to analyze and contextualize simulations of coronal mass ejections. As current simulation techniques require manual input, uncertainty is introduced into the simulation pipeline leading to inaccurate predictions that can be mitigated through ensemble simulations. We provide the space weather analyst with a multi-view system providing visualizations to: 1. compare ensemble members against ground truth measurements, 2. inspect time-dependent information derived from optical flow analysis of satellite images, and 3. combine satellite images with a volumetric rendering of the simulations. This three-tier workflow provides experts with tools to discover correlations between errors in predictions and simulation parameters, thus increasing knowledge about the evolution and propagation of coronal mass ejections that pose a danger to Earth and interplanetary travel

  • 14.
    Bock, Alexander
    et al.
    Linköping University, Department of Science and Technology, Media and Information Technology. Linköping University, Faculty of Science & Engineering.
    Pembroke, Asher
    NASA Goddard Space Flight Center, Greenbelt, MD, United States.
    Mays, M. Leila
    Catholic University of America, Washington, DC, United States.
    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).
    OpenSpace: An Open-Source Framework for Data Visualization and Contextualization2015Conference paper (Refereed)
    Abstract [en]

    We present an open-source software development effort called OpenSpace that is tailored for the dissemination of space-related data visualization. In the current stages of the project, we have focussed on the public dissemination of space missions (Rosetta and New Horizons) as well as the support of space weather forecasting. The presented work will focus on the latter of these foci and elaborate on the efforts that have gone into developing a system that allows the user to assess the accuracy and validity of ENLIL ensemble simulations. It becomes possible to compare the results of ENLIL CME simulations with STEREO and SOHO images using an optical flow algorithm. This allows the user to compare velocities in the volumetric rendering of ENLIL data with the movement of CMEs through the field-of-views of various instruments onboard the space craft. By allowing the user access to these comparisons, new information about the time evolution of CMEs through the interplanetary medium is possible. Additionally, contextualizing this information in three-dimensional rendering scene, allows the analyst and the public to disseminate this data. This dissemination is further improved by the ability to connect multiple instances of the software and, thus, reach a broader audience. In a second step, we plan to combine the two foci of the project to enable the visualization of the SWAP instrument onboard New Horizons in context with a far-reaching ENLIL simulation, thus providing additional information about the solar wind dynamics of the outer solar system. The initial work regarding this plan will be presented.

  • 15.
    Bourgois, Marc
    et al.
    INO Eurocontrol Experimental Centre.
    Cooper, Matthew
    Linköping University, Department of Science and Technology, Visual Information Technology and Applications (VITA). Linköping University, The Institute of Technology.
    Duong, Vu
    UNO Eurocontrol Experimental Centre.
    Hjalmarsson, Jonas
    Linköping University, Department of Science and Technology.
    Lange, Marcus
    Linköping University, Department of Science and Technology.
    Ynnerman, Anders
    Linköping University, Department of Science and Technology, Visual Information Technology and Applications (VITA). Linköping University, The Institute of Technology.
    Interactive and Immersive 3D Visualization for ATC2005In: USA/Europe Seminar on Air Traffic Management Research and Development,2005, Washinton, DC, USA: FAA , 2005, p. 303-Conference paper (Refereed)
  • 16.
    Chen, Min
    et al.
    University of Oxford, England.
    Ebert, David
    Purdue University, IN 47907 USA.
    Hauser, Helwig
    University of Bergen, Norway.
    Heer, Jeffrey
    University of Washington, WA 98195 USA.
    North, Chris
    Virginia Polytech Institute and State University, VA 24061 USA.
    Qu, Huamin
    Hong Kong University of Science and Technology, Peoples R China.
    Suien, Han-Wei
    Ohio State University, OH 43210 USA.
    Tory, Melanie
    University of Victoria, Canada.
    Ynnerman, Anders
    Linköping University, Department of Science and Technology, Media and Information Technology. Linköping University, The Institute of Technology. Linköping University, Center for Medical Image Science and Visualization (CMIV).
    IEEE VISUAL ANALYTICS SCIENCE & TECHNOLOGY CONFERENCE, IEEE INFORMATION VISUALIZATION CONFERENCE, AND IEEE SCIENTIFIC VISUALIZATION CONFERENCE2014In: IEEE Transactions on Visualization and Computer Graphics, ISSN 1077-2626, E-ISSN 1941-0506, Vol. 20, no 12, p. XI-XIVArticle in journal (Other academic)
    Abstract [en]

    n/a

  • 17.
    Dieckmann, Mark E
    et al.
    Linköping University, Department of Science and Technology, Media and Information Technology. Linköping University, Faculty of Science & Engineering.
    Ahmed, H.
    Queens University of Belfast, North Ireland.
    Doria, D.
    Queens University of Belfast, North Ireland.
    Sarri, G.
    Queens University of Belfast, North Ireland.
    Walder, R.
    University of Lyon, France.
    Folini, D.
    University of Lyon, France.
    Bret, A.
    University of Castilla La Mancha, Spain.
    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).
    Borghesi, M.
    Queens University of Belfast, North Ireland.
    Thin-shell instability in collisionless plasma2015In: Physical Review E. Statistical, Nonlinear, and Soft Matter Physics, ISSN 1539-3755, E-ISSN 1550-2376, Vol. 92, no 3, p. 031101-Article in journal (Refereed)
    Abstract [en]

    Thin-shell instability is one process which can generate entangled structures in astrophysical plasma on collisional (fluid) scales. It is driven by a spatially varying imbalance between the ram pressure of the inflowing upstream plasma and the downstreams thermal pressure at a nonplanar shock. Here we show by means of a particle-in-cell simulation that an analog process can destabilize a thin shell formed by two interpenetrating, unmagnetized, and collisionless plasma clouds. The amplitude of the shells spatial modulation grows and saturates after about ten inverse proton plasma frequencies, when the shell consists of connected piecewise linear patches.

  • 18.
    Dieckmann, Mark E
    et al.
    Linköping University, Department of Science and Technology, Visual Information Technology and Applications (VITA). Linköping University, The Institute of Technology.
    Chapman, SC
    Linkoping Univ, ITN, S-60174 Norrkoping, Sweden Univ Warwick, Dept Phys, Space & Astrophys Grp, Coventry CV4 7AL, W Midlands, England.
    Ynnerman, Anders
    Linköping University, Department of Science and Technology, Visual Information Technology and Applications (VITA). Linköping University, The Institute of Technology.
    Rowlands, G
    Linkoping Univ, ITN, S-60174 Norrkoping, Sweden Univ Warwick, Dept Phys, Space & Astrophys Grp, Coventry CV4 7AL, W Midlands, England.
    Plasma sounding at the upper hybrid frequency2000In: Journal of Geophysical Research, ISSN 0148-0227, E-ISSN 2156-2202, Vol. 105, no A6, p. 13103-13117Article in journal (Refereed)
    Abstract [en]

    A sounder measures the density of plasmas in various parts of the solar system. The sounder emits wave pulses into the ambient plasma and listens to the response. Intensity peaks in the wave response are typically related to two mechanisms. One is provided by waves that are reflected off plasma inhomogeneities and propagate back to the emitting antenna, where they are then detected. The second is provided by waves propagating with the same group velocity as that of the receiving antenna. In the second case the waves stay close to the antenna and thus yield a long-lasting response. Response peaks to sounding at the upper hybrid (UH) frequency have, in most cases, been related to reflected waves. In this work we examine if accompanying waves can give rise to the UH response peak. We examine quantitatively how the plasma response to sounding at the UH frequency depends on the plasma density, on the electron temperature, and on the emission amplitude. For the first two parameters this is done by solving the linear dispersion relation. The well-known property of the UH waves to change from having a zero group velocity to propagating waves, depending on how the electron density compares to the electron cyclotron frequency, is applied to Alouette sounder data. It is discussed how the change in the group velocity may affect the spectral profile of the UH resonance. We present results from numerical particle in cell (PIC) simulations which show that in the case of nonpropagating UH waves, energy can be coupled into the plasma even though the vanishing group velocity of the UH waves should not allow this. The PIC simulations and sounder data from the Alouette mission show that in the case of propagating UH waves the response duration to sounding may be used to determine the electron temperature. Emission amplitudes that are typical for plasma sounders are also shown to suppress the generation of certain electron cyclotron harmonic waves.

  • 19.
    Dieckmann, Mark E
    et al.
    Linköping University, Department of Science and Technology, Visual Information Technology and Applications (VITA). Linköping University, The Institute of Technology.
    Eliasson, B.
    Ruhr-Universität, Bochum, Germany.
    Stathopoulos, A.
    College of William and Mary, Williamsburg, USA.
    Ynnerman, Anders
    Linköping University, Department of Science and Technology, Visual Information Technology and Applications (VITA). Linköping University, The Institute of Technology.
    Connecting shock velocities to electron injection mechanisms2004In: 31st European Physical Society Conference on Plasma Physics,2004, London, UK: European Physical Society , 2004Conference paper (Refereed)
  • 20.
    Dieckmann, Mark E
    et al.
    Linköping University, Department of Science and Technology, Visual Information Technology and Applications (VITA). Linköping University, The Institute of Technology.
    Eliasson, B
    Stathopoulos, A
    Ynnerman, Anders
    Linköping University, Department of Science and Technology, Visual Information Technology and Applications (VITA). Linköping University, The Institute of Technology.
    Connecting shock velocities to electron-injection mechanisms2004In: Physical Review Letters, ISSN 0031-9007, E-ISSN 1079-7114, Vol. 92, no 6Article in journal (Refereed)
    Abstract [en]

    Electrons can be accelerated by their interaction with nonlinearly saturated electrostatic waves up to speeds with which they can undergo diffusive acceleration across supernova remnant shocks. Here, we model this wave-electron interaction by particle-in-cell and Vlasov simulations. We find that the lifetime of the saturated wave is considerably longer in the Vlasov simulation, due to differences in how these simulation methods approximate the plasma. Electron surfing acceleration which requires a stable saturated wave may thus be more important for electron acceleration at shocks than previously thought. For beam speeds above a critical value, which we estimate here, both simulation codes exclude surfing acceleration due to a rapid wave collapse.

  • 21.
    Dieckmann, Mark E
    et al.
    Linköping University, Department of Science and Technology, Visual Information Technology and Applications (VITA). Linköping University, The Institute of Technology.
    Eliasson, B.
    Ruhr-Universität, Bochum, Germany.
    Stathopoulos, A.
    College of William and Mary, Williamsburg, USA.
    Ynnerman, Anders
    Linköping University, Department of Science and Technology, Visual Information Technology and Applications (VITA). Linköping University, The Institute of Technology.
    Kinetic simulation of electron injection by electrostatic waves2004In: Baltic Astronomy, ISSN 1392-0049, Vol. 13, p. 248-288Article in journal (Other academic)
  • 22.
    Dieckmann, Mark E
    et al.
    Linköping University, Department of Science and Technology, Visual Information Technology and Applications (VITA). Linköping University, The Institute of Technology.
    Eliasson, Bengt
    Institute of Theoretical Physics IV Ruhr-University Bochum, Germany.
    Parviainen, Madelene
    Institute of Theoretical Physics IV Ruhr-University Bochum, Germany.
    Shukla, Padma K
    Institute of Theoretical Physics IV Ruhr-University Bochum, Germany.
    Ynnerman, Anders
    Linköping University, Department of Science and Technology, Visual Information Technology and Applications (VITA). Linköping University, The Institute of Technology.
    Electron acceleration by a relativistic two stream instability with oblique B2006In: 33rd European Physical Society Conference on Plasma Physics,2006, Rome: European Physical Society , 2006, p. P4.071-Conference paper (Refereed)
    Abstract [en]

    Electrons that are trapped by a quasi-electrostatic wave move, on average, with the phase speed of the wave. In the presence of a magnetic field B, the trapped electrons could, in principle, be accelerated to cosmic ray energies through cross-field transport. We model this cross-field transport with a particle-in-cell (PIC) simulation for an oblique B. The electron energies at the simulation's end exceed 5 MeV for all pitch angles and they can reach GeV energies along the wavevector. We discuss environments, in which such conditions may exist and for which such an acceleration would be relevant.

  • 23.
    Dieckmann, Mark E
    et al.
    Linköping University, Department of Science and Technology, Visual Information Technology and Applications (VITA). Linköping University, The Institute of Technology.
    Eliasson, Bengt
    Institute of Theoretical Physics IV Ruhr-University Bochum, Germany.
    Parviainen, Madelene
    Institute of Theoretical Physics IV Ruhr-University Bochum, Germany.
    Shukla, Padma K
    Institute of Theoretical Physics IV Ruhr-University Bochum, Germany.
    Ynnerman, Anders
    Linköping University, Department of Science and Technology, Visual Information Technology and Applications (VITA). Linköping University, The Institute of Technology.
    Electron surfing acceleration in oblique magnetic fields2006In: Monthly notices of the Royal Astronomical Society, ISSN 0035-8711, E-ISSN 1365-2966, Vol. 367, no 3, p. 865-872Article in journal (Refereed)
    Abstract [en]

    Initially, inhomogeneous plasma jets, ejected by active galactic nuclei and associated with gamma-ray bursts, are thermalized by the formation of internal shocks. Jet subpopulations can hereby collide at Lorentz factors of a few. As the resulting relativistic shock expands into the upstream plasma, a significant fraction of the upstream ions is reflected. These ions, together with downstream ions that leak through the shock, form relativistic beams of ions that outrun the shock. The thermalization of these beams via the two-stream instability is thought to contribute significantly to plasma heating and particle acceleration by the shock. Here, the capability of a two-stream instability to generate relativistic field-aligned and cross-field electron flow, is examined for a magnetized plasma by means of a particle-in-cell (PIC) simulation. The electrons interact with the developing quasi-electrostatic waves and oblique magnetic fields. The simulation results bring forward evidence that such waves, by their non-linear interactions with the plasma, produce a highly relativistic field-aligned electron flow and electron energies, which could contribute to the radio synchrotron emissions from astrophysical jets, to ultrarelativistic leptonic subpopulations propagating with the jet and to the halo particles surrounding the accretion disc of the black hole.

  • 24.
    Dieckmann, Mark E
    et al.
    Linköping University, Department of Science and Technology, Visual Information Technology and Applications (VITA). Linköping University, The Institute of Technology.
    Eliasson, Bengt
    Institute of Theoretical Physics IV Ruhr-University Bochum, Germany.
    Ynnerman, Anders
    Linköping University, Department of Science and Technology, Visual Information Technology and Applications (VITA). Linköping University, The Institute of Technology.
    Shukla, Padma K
    Institute of Theoretical Physics IV Ruhr-University Bochum, Germany.
    Numerical Modeling of Gamma Ray Bursts2006Report (Other academic)
  • 25.
    Dieckmann, Mark E
    et al.
    Linköping University, Department of Science and Technology, Media and Information Technology. Linköping University, Faculty of Science & Engineering.
    Folini, Doris
    École Normale Supérieure, Lyon, CRAL, UMR CNRS 5574, Université de Lyon, Lyon, France .
    Hotz, Ingrid
    Linköping University, Department of Science and Technology, Media and Information Technology. Linköping University, Faculty of Science & Engineering.
    Nordman, Aida
    Linköping University, Department of Science and Technology, Media and Information Technology. Linköping University, Faculty of Science & Engineering.
    Dell'Acqua, Pierangelo
    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.
    Walder, Rolf
    École Normale Supérieure, Lyon, CRAL, UMR CNRS 5574, Université de Lyon, Lyon, France .
    Structure of a collisionless pair jet in a magnetized electron–proton plasma: flow-aligned magnetic field2019In: Astronomy and Astrophysics, ISSN 0004-6361, E-ISSN 1432-0746, Vol. 621, article id A142Article in journal (Refereed)
    Abstract [en]

    Aims. We study the effect a guiding magnetic field has on the formation and structure of a pair jet that propagates through a collisionless electron–proton plasma at rest.

    Methods. We model with a particle-in-cell (PIC) simulation a pair cloud with a temperature of 400 keV and a mean speed of 0.9c (c - light speed). Pair particles are continuously injected at the boundary. The cloud propagates through a spatially uniform, magnetized, and cool ambient electron–proton plasma at rest. The mean velocity vector of the pair cloud is aligned with the uniform background magnetic field. The pair cloud has a lateral extent of a few ion skin depths.

    Results. A jet forms in time. Its outer cocoon consists of jet-accelerated ambient plasma and is separated from the inner cocoon by an electromagnetic piston with a thickness that is comparable to the local thermal gyroradius of jet particles. The inner cocoon consists of pair plasma, which lost its directed flow energy while it swept out the background magnetic field and compressed it into the electromagnetic piston. A beam of electrons and positrons moves along the jet spine at its initial speed. Its electrons are slowed down and some positrons are accelerated as they cross the head of the jet. The latter escape upstream along the magnetic field, which yields an excess of megaelectronvolt positrons ahead of the jet. A filamentation instability between positrons and protons accelerates some of the protons, which were located behind the electromagnetic piston at the time it formed, to megaelectronvolt energies.

    Conclusions. A microscopic pair jet in collisionless plasma has a structure that is similar to that predicted by a hydrodynamic model of relativistic astrophysical pair jets. It is a source of megaelectronvolt positrons. An electromagnetic piston acts as the contact discontinuity between the inner and outer cocoons. It would form on subsecond timescales in a plasma with a density that is comparable to that of the interstellar medium in the rest frame of the latter. A supercritical fast magnetosonic shock will form between the pristine ambient plasma and the jet-accelerated plasma on a timescale that exceeds our simulation time by an order of magnitude.

  • 26.
    Dieckmann, Mark E
    et al.
    Linköping University, Department of Science and Technology, Visual Information Technology and Applications (VITA). Linköping University, The Institute of Technology.
    Ljung, Patric
    Linköping University, Department of Science and Technology, Visual Information Technology and Applications (VITA). Linköping University, The Institute of Technology.
    Ynnerman, Anders
    Linköping University, Department of Science and Technology, Visual Information Technology and Applications (VITA). Linköping University, The Institute of Technology.
    McClements, KG
    Linkoping Univ, Inst Technol & Nat Sci, S-60174 Norrkoping, Sweden UKAEA Euratom Fus Assoc, Culham Sci Ctr, Abingdon OX14 3DB, Oxon, England.
    Large-scale numerical simulations of ion beam instabilities in unmagnetized astrophysical plasmas2000In: Physics of Plasmas, ISSN 1070-664X, E-ISSN 1089-7674, Vol. 7, no 12, p. 5171-5181Article in journal (Refereed)
    Abstract [en]

    Collisionless quasiperpendicular shocks with magnetoacoustic Mach numbers exceeding a certain threshold are known to reflect a fraction of the upstream ion population. These reflected ions drive instabilities which, in a magnetized plasma, can give rise to electron acceleration. In the case of shocks associated with supernova remnants (SNRs), electrons energized in this way may provide a seed population for subsequent acceleration to highly relativistic energies. If the plasma is weakly magnetized, in the sense that the electron cyclotron frequency is much smaller than the electron plasma frequency omega (p), a Buneman instability occurs at omega (p). The nonlinear evolution of this instability is examined using particle-in-cell simulations, with initial parameters which are representative of SNR shocks. For simplicity, the magnetic field is taken to be strictly zero. It is shown that the instability saturates as a result of electrons being trapped by the wave potential. Subsequent evolution of the waves depends on the temperature of the background protons T-i and the size of the simulation box L. If T-i is comparable to the initial electron temperature T-e, and L is equal to one Buneman wavelength lambda (0), the wave partially collapses into low frequency waves and backscattered waves at around omega (p). If, on the other hand, T-i much greater thanT(e) and L = lambda (0), two high frequency waves remain in the plasma. One of these waves, excited at a frequency slightly lower than omega (p), may be a Bernstein-Greene-Kruskal mode. The other wave, excited at a frequency well above omega (p), is driven by the relative streaming of trapped and untrapped electrons. In a simulation with L = 4 lambda (0), the Buneman wave collapses on a time scale consistent with the excitation of sideband instabilities. Highly energetic electrons were not observed in any of these simulations, suggesting that the Buneman instability can only produce strong electron acceleration in a magnetized plasma. [S1070-664X(00)02712-9].

  • 27.
    Dieckmann, Mark E
    et al.
    Linköping University, Department of Science and Technology, Visual Information Technology and Applications (VITA). Linköping University, The Institute of Technology.
    Ljung, Patric
    Linköping University, Department of Science and Technology, Visual Information Technology and Applications (VITA). Linköping University, The Institute of Technology.
    Ynnerman, Anders
    Linköping University, Department of Science and Technology, Visual Information Technology and Applications (VITA). Linköping University, The Institute of Technology.
    McClements, K.G.
    EURATOM/UKAEA Fusion Association, Culham Science Center, Abingdom, Oxfordshire OX 14 3DB, United Kingdom.
    Three-dimensional visualization of electron acceleration in a magnetized plasma2002In: IEEE Transactions on Plasma Science, ISSN 0093-3813, E-ISSN 1939-9375, Vol. 30, no 1 I, p. 20-21Article in journal (Refereed)
    Abstract [en]

    We examine wave-particle interactions in a magnetized plasma. We present snapshots of an animation of the three-dimensional electron phase space distribution produced by an electrostatic wave propagating across a magnetic field. The distribution function has been evolved by a particle in cell simulation. The electron phase space has been visualized by distributing the simulation electrons over an array representing phase space density and by volume rendering this array. The results are, due to the choice of initial plasma and wave parameters, of relevance for electron acceleration at astrophysical shocks.

  • 28.
    Dieckmann, Mark E
    et al.
    Linköping University, Department of Science and Technology, Media and Information Technology. Linköping University, Faculty of Science & Engineering.
    Sarri, G.
    Queens University of Belfast, North Ireland.
    Doria, D.
    Queens University of Belfast, North Ireland.
    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).
    Borghesi, M.
    Queens University of Belfast, North Ireland.
    Particle-in-cell simulation study of a lower-hybrid shock2016In: Physics of Plasmas, ISSN 1070-664X, E-ISSN 1089-7674, Vol. 23, no 6, p. 062111-Article in journal (Refereed)
    Abstract [en]

    The expansion of a magnetized high-pressure plasma into a low-pressure ambient medium is examined with particle-in-cell simulations. The magnetic field points perpendicular to the plasmas expansion direction and binary collisions between particles are absent. The expanding plasma steepens into a quasi-electrostatic shock that is sustained by the lower-hybrid (LH) wave. The ambipolar electric field points in the expansion direction and it induces together with the background magnetic field a fast E cross B drift of electrons. The drifting electrons modify the background magnetic field, resulting in its pile-up by the LH shock. The magnetic pressure gradient force accelerates the ambient ions ahead of the LH shock, reducing the relative velocity between the ambient plasma and the LH shock to about the phase speed of the shocked LH wave, transforming the LH shock into a nonlinear LH wave. The oscillations of the electrostatic potential have a larger amplitude and wavelength in the magnetized plasma than in an unmagnetized one with otherwise identical conditions. The energy loss to the drifting electrons leads to a noticeable slowdown of the LH shock compared to that in an unmagnetized plasma. Published by AIP Publishing.

  • 29.
    Dieckmann, Mark E
    et al.
    Linköping University, Department of Science and Technology, Visual Information Technology and Applications (VITA). Linköping University, The Institute of Technology.
    Shukla, P. K.
    Theoretische Physik IV, Ruhr-University Bochum.
    Parviainen, M.
    Theoretische Physik IV Ruhr-University Bochum.
    Ynnerman, Anders
    Linköping University, Department of Science and Technology, Visual Information Technology and Applications (VITA). Linköping University, The Institute of Technology.
    Numerical simulation and visualization of stochastic and ordered electron motion forced by electrostatic waves in a magnetized plasma2005In: Physics of Plasmas, ISSN 1070-664X, E-ISSN 1089-7674, Vol. 12, no 9, p. 92902-Article in journal (Refereed)
    Abstract [en]

    The interaction of electrons with strong electrostatic waves and an external magnetic field, which is oriented obliquely to the wave vector, leads to stochastic acceleration and acceleration by the cross-field transport of trapped electrons. This wave-particle interaction involves three velocity components of the electrons and, for a plane wave, one spatial position. The phase-space evolution is also affected by nonlinear oscillations in the amplitude of the saturated wave, and the system becomes explicitly time dependent. Here, the wave-particle interactions are investigated with a particle-in-cell simulation, and the results are visualized by examining orbits of individual electrons and also time-evolving phase-space structures. Two clearly distinct electron populations are identified, one due to cross-field transport and the other due to stochastic interactions, which are robust against growing secondary modes. © 2005 American Institute of Physics.

  • 30.
    Dieckmann, Mark E
    et al.
    Linköping University, Department of Science and Technology, Visual Information Technology and Applications (VITA). Linköping University, The Institute of Technology.
    Ynnerman, Anders
    Linköping University, Department of Science and Technology, Visual Information Technology and Applications (VITA). Linköping University, The Institute of Technology.
    Chapman, S.C.
    Rowlands, G.
    Andersson, N.
    National Supercomputer Centre (NSC), University of Linköping, Valla Campus, SE-58183 Linköping, Sweden.
    Simulating thermal noise2004In: Physica Scripta, ISSN 0031-8949, E-ISSN 1402-4896, Vol. 69, no 6, p. 456-460Article in journal (Refereed)
    Abstract [en]

    Thermal noise measurements by space-borne antennas are commonly used to determine plasma parameters like the electron density and the plasma temperature from the noise spectra. It would be desirable to have a controlled experiment in which noise from a plasma with known properties is sampled in space and in time and which results can then be used to reproduce the satellite measurements. Here we examine the possibility to use particle-in-cell (PIC) simulations as such an experiment. In this work we present a statistically averaged noise spectrum computed with a PIC code for a simple single-Maxwellian and unmagnetized electron plasma and we compare it to both, the thermal noise spectrum for the corresponding real plasma and the noise spectrum we would anticipate from our numerical scheme. We find that we can produce noise fields with sufficiently low amplitudes to keep the plasma in a linear regime. We show that the simulation noise at low and at large wave numbers differs not only from thermal noise of a physical plasma but also from the numerical noise we would expect from our numerical scheme. We explain the drop of the noise power at low wave numbers by our initial conditions. We find experimentally the relation that connects the theoretical noise spectrum for our simulation code with that we actually measure, provided that the phase velocity of the noise is less than the maximum velocity of the computational particles.

  • 31.
    Dieckmann, Mark Eric
    et al.
    Linköping University, Department of Science and Technology, Media and Information Technology. Linköping University, Faculty of Science & Engineering.
    Bock, Alexander
    Linköping University, Department of Science and Technology, Media and Information Technology. Linköping University, Faculty of Science & Engineering.
    Ahmed, Hamad
    Centre for Plasma Physics (CPP), Queen's University Belfast, BT7 1NN, Belfast, UK.
    Doria, Domenico
    Centre for Plasma Physics (CPP), Queen's University Belfast, BT7 1NN, Belfast, UK.
    Sarri, Gianluca
    Centre for Plasma Physics (CPP), Queen's University Belfast, BT7 1NN, Belfast, UK.
    Ynnerman, Anders
    Linköping University, Department of Science and Technology, Media and Information Technology. Linköping University, Faculty of Science & Engineering.
    Borghesi, Marco
    Centre for Plasma Physics (CPP), Queen's University Belfast, BT7 1NN, Belfast, UK.
    Shocks in unmagnetized plasma with a shear flow: Stability and magnetic field generation2015In: Physics of Plasmas, ISSN 1070-664X, E-ISSN 1089-7674, Vol. 22, no 7, p. 1-9, article id 072104Article in journal (Refereed)
    Abstract [en]

    A pair of curved shocks in a collisionless plasma is examined with a two-dimensional particle-in-cell simulation. The shocks are created by the collision of two electron-ion clouds at a speed that exceeds everywhere the threshold speed for shock formation. A variation of the collision speed along the initially planar collision boundary, which is comparable to the ion acoustic speed, yields a curvature of the shock that increases with time. The spatially varying Mach number of the shocks results in a variation of the downstream density in the direction along the shock boundary. This variation is eventually equilibrated by the thermal diffusion of ions. The pair of shocks is stable for tens of inverse ion plasma frequencies. The angle between the mean flow velocity vector of the inflowing upstream plasma and the shock's electrostatic field increases steadily during this time. The disalignment of both vectors gives rise to a rotational electron flow, which yields the growth of magnetic field patches that are coherent over tens of electron skin depths.

  • 32.
    Dieckmann, Mark Eric
    et al.
    Linköping University, Department of Science and Technology, Media and Information Technology. Linköping University, The Institute of Technology.
    Sarri, Gianluca
    Centre for Plasma Physics, Queen's University Belfast, UK.
    Murphy, Gareth
    Dublin Institute for Advanced Studies, Dublin, Ireland.
    Bret, Antoine
    Harvard-Smithsonian Center for Astrophysics.
    Romagnani, Lorenzo
    LULI, Ecole Polytechnique, CNRS, CEA, UPMC, Palaiseau, France .
    Kourakis, Ioannis
    Centre for Plasma Physics, Queen's University Belfast, UK.
    Borghesi, Marco
    Centre for Plasma Physics, Queen's University Belfast, UK.
    Ynnerman, Anders
    Linköping University, Department of Science and Technology, Media and Information Technology. Linköping University, The Institute of Technology.
    Drury, Luke o'c
    Dublin Institute for Advanced Studies, Dublin, Ireland.
    PIC simulation of a thermal anisotropy-driven Weibel instability in a circular rarefaction wave2012In: New Journal of Physics, ISSN 1367-2630, E-ISSN 1367-2630, Vol. 14, no 023007Article in journal (Refereed)
    Abstract [en]

    The expansion of an initially unmagnetized planar rarefaction wave has recently been shown to trigger a thermal anisotropy-driven Weibel instability (TAWI), which can generate magnetic fields from noise levels. It is examined here whether the TAWI can also grow in a curved rarefaction wave. The expansion of an initially unmagnetized circular plasma cloud, which consists of protons and hot electrons, into a vacuum is modelled for this purpose with a two-dimensional particle-in-cell (PIC) simulation. It is shown that the momentum transfer from the electrons to the radially accelerating protons can indeed trigger a TAWI. Radial current channels form and the aperiodic growth of a magnetowave is observed, which has a magnetic field that is oriented orthogonal to the simulation plane. The induced electric field implies that the electron density gradient is no longer parallel to the electric field. Evidence is presented here that this electric field modification triggers a second magnetic instability, which results in a rotational low-frequency magnetowave. The relevance of the TAWI is discussed for the growth of small-scale magnetic fields in astrophysical environments, which are needed to explain the electromagnetic emissions by astrophysical jets. It is outlined how this instability could be examined experimentally.

  • 33.
    Eklund, Anders
    et al.
    Linköping University, Center for Medical Image Science and Visualization (CMIV). Linköping University, Department of Biomedical Engineering, Medical Informatics. Linköping University, The Institute of Technology.
    Andersson, Mats
    Linköping University, Center for Medical Image Science and Visualization (CMIV). Linköping University, Department of Biomedical Engineering, Medical Informatics. Linköping University, The Institute of Technology.
    Ohlsson, Henrik
    Linköping University, Department of Electrical Engineering, Automatic Control. Linköping University, The Institute of Technology.
    Ynnerman, Anders
    Linköping University, Center for Medical Image Science and Visualization (CMIV). Linköping University, Department of Science and Technology, Visual Information Technology and Applications (VITA). Linköping University, The Institute of Technology.
    Knutsson, Hans
    Linköping University, Center for Medical Image Science and Visualization (CMIV). Linköping University, Department of Biomedical Engineering, Medical Informatics. Linköping University, The Institute of Technology.
    A Brain Computer Interface for Communication Using Real-Time fMRI2010In: Proceedings of the 20th International Conference on Pattern Recognition, Los Alamitos, CA, USA: IEEE Computer Society, 2010, p. 3665-3669Conference paper (Refereed)
    Abstract [en]

    We present the first step towards a brain computer interface (BCI) for communication using real-time functional magnetic resonance imaging (fMRI). The subject in the MR scanner sees a virtual keyboard and steers a cursor to select different letters that can be combined to create words. The cursor is moved to the left by activating the left hand, to the right by activating the right hand, down by activating the left toes and up by activating the right toes. To select a letter, the subject simply rests for a number of seconds. We can thus communicate with the subject in the scanner by for example showing questions that the subject can answer. Similar BCI for communication have been made with electroencephalography (EEG). The subject then focuses on a letter while different rows and columns of the virtual keyboard are flashing and the system tries to detect if the correct letter is flashing or not. In our setup we instead classify the brain activity. Our system is neither limited to a communication interface, but can be used for any interface where five degrees of freedom is necessary.

  • 34.
    Eklund, Anders
    et al.
    Linköping University, Department of Biomedical Engineering, Medical Informatics. Linköping University, Center for Medical Image Science and Visualization, CMIV. Linköping University, The Institute of Technology.
    Ohlsson, Henrik
    Linköping University, Department of Electrical Engineering, Electronics System. Linköping University, Center for Medical Image Science and Visualization, CMIV. Linköping University, The Institute of Technology.
    Andersson, Mats
    Linköping University, Department of Biomedical Engineering, Medical Informatics. Linköping University, Center for Medical Image Science and Visualization, CMIV. Linköping University, The Institute of Technology.
    Rydell, Joakim
    Linköping University, Department of Biomedical Engineering, Medical Informatics. Linköping University, Center for Medical Image Science and Visualization, CMIV. 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.
    Knutsson, Hans
    Linköping University, Department of Biomedical Engineering, Medical Informatics. Linköping University, Center for Medical Image Science and Visualization, CMIV. Linköping University, The Institute of Technology.
    Balancing an Inverted Pendulum by Thinking A Real-Time fMRI Approach2009Conference paper (Other academic)
    Abstract [en]

    We present a method for controlling a dynamical system using real-time fMRI. The objective for the subject in the MR scanner is to balance an inverse pendulum by activating the left or right hand or resting. The brain activity is classified each second by a neural network and the classification is sent to a pendulum simulator to change the force applied to the pendulum. The state of the inverse pendulum is shown to the subject in a pair of VR goggles. The subject was able to balance the inverse pendulum both with real activity and imagined activity. The developments here have a potential to aid people with communication disabilities e.g., locked in people. It might also be a tool for stroke patients to be ableto train the damaged brain area and get real-time feedback of when they do it right.

  • 35.
    Eklund, Anders
    et al.
    Linköping University, Center for Medical Image Science and Visualization (CMIV). Linköping University, Department of Biomedical Engineering, Medical Informatics. Linköping University, The Institute of Technology.
    Ohlsson, Henrik
    Linköping University, Department of Electrical Engineering, Automatic Control. Linköping University, The Institute of Technology.
    Andersson, Mats
    Linköping University, Center for Medical Image Science and Visualization (CMIV). Linköping University, Department of Biomedical Engineering, Medical Informatics. Linköping University, The Institute of Technology.
    Rydell, Joakim
    Linköping University, Center for Medical Image Science and Visualization (CMIV). Linköping University, Department of Biomedical Engineering, Medical Informatics. Linköping University, The Institute of Technology.
    Ynnerman, Anders
    Linköping University, Center for Medical Image Science and Visualization (CMIV). Linköping University, Department of Science and Technology, Visual Information Technology and Applications (VITA). Linköping University, The Institute of Technology.
    Knutsson, Hans
    Linköping University, Center for Medical Image Science and Visualization (CMIV). Linköping University, Department of Biomedical Engineering, Medical Informatics. Linköping University, The Institute of Technology.
    Using Real-Time fMRI to Control a Dynamical System2009In: ISMRM 17th Scientific Meeting & Exhibition, 2009Conference paper (Refereed)
    Abstract [en]

    We present e method for controlling a dynamical system using real-time fMRI. The objective for the subject in the MR scanner is to balance an inverse pendulum by activating the left or right hand or resting. The brain activity is clasified each second by a neural network and the classification is sent to a pendulum simulator to change the state of the pendulum. The state of the inverse pendulum is shown to the subject in a pair of VR goggles. The subject was able to balance the inverse pendulum during a 7 minute test run.

  • 36.
    Eklund, Anders
    et al.
    Linköping University, Center for Medical Image Science and Visualization (CMIV). Linköping University, Department of Biomedical Engineering, Medical Informatics. Linköping University, The Institute of Technology.
    Ohlsson, Henrik
    Linköping University, Department of Electrical Engineering, Automatic Control. Linköping University, The Institute of Technology.
    Andersson, Mats
    Linköping University, Center for Medical Image Science and Visualization (CMIV). Linköping University, Department of Biomedical Engineering, Medical Informatics. Linköping University, The Institute of Technology.
    Rydell, Joakim
    Linköping University, Center for Medical Image Science and Visualization (CMIV). Linköping University, Department of Biomedical Engineering, Medical Informatics. Linköping University, The Institute of Technology.
    Ynnerman, Anders
    Linköping University, Center for Medical Image Science and Visualization (CMIV). Linköping University, Department of Science and Technology, Visual Information Technology and Applications (VITA). Linköping University, The Institute of Technology.
    Knutsson, Hans
    Linköping University, Center for Medical Image Science and Visualization (CMIV). Linköping University, Department of Biomedical Engineering, Medical Informatics. Linköping University, The Institute of Technology.
    Using Real-Time fMRI to Control a Dynamical System2009Report (Other academic)
    Abstract [en]

    We present e method for controlling a dynamical system using real-time fMRI. The objective for the subject in the MR scanner is to balance an inverse pendulum by activating the left or right hand or resting. The brain activity is clasified each second by a neural network and the classification is sent to a pendulum simulator to change the state of the pendulum. The state of the inverse pendulum is shown to the subject in a pair of VR goggles. The subject was able to balance the inverse pendulum during a 7 minute test run.

  • 37.
    Eklund, Anders
    et al.
    Linköping University, Department of Biomedical Engineering, Medical Informatics. Linköping University, The Institute of Technology. Linköping University, Center for Medical Image Science and Visualization (CMIV).
    Ohlsson, Henrik
    Linköping University, Department of Electrical Engineering, Automatic Control. Linköping University, The Institute of Technology.
    Andersson, Mats
    Linköping University, Department of Biomedical Engineering, Medical Informatics. Linköping University, The Institute of Technology. Linköping University, Center for Medical Image Science and Visualization (CMIV).
    Rydell, Joakim
    Linköping University, Department of Biomedical Engineering, Medical Informatics. Linköping University, The Institute of Technology. Linköping University, Center for Medical Image Science and Visualization (CMIV).
    Ynnerman, Anders
    Linköping University, Center for Medical Image Science and Visualization (CMIV). Linköping University, Department of Science and Technology, Visual Information Technology and Applications (VITA). Linköping University, The Institute of Technology.
    Knutsson, Hans
    Linköping University, Department of Biomedical Engineering, Medical Informatics. Linköping University, The Institute of Technology. Linköping University, Center for Medical Image Science and Visualization (CMIV).
    Using Real-Time fMRI to Control a Dynamical System by Brain Activity Classification2009In: Medical Image Computing and Computer-Assisted Intervention – MICCAI 2009: 12th International Conference, London, UK, September 20-24, 2009, Proceedings, Part I / [ed] Gerhard Goos, Juris Hartmanis and Jan van Leeuwen, Springer Berlin/Heidelberg, 2009, 1, p. 1000-1008Conference paper (Refereed)
    Abstract [en]

    We present a method for controlling a dynamical system using real-time fMRI. The objective for the subject in the MR scanner is to balance an inverted pendulum by activating the left or right hand or resting. The brain activity is classified each second by a neural network and the classification is sent to a pendulum simulator to change the force applied to the pendulum. The state of the inverted pendulum is shown to the subject in a pair of VR goggles. The subject was able to balance the inverted pendulum during several minutes, both with real activity and imagined activity. In each classification 9000 brain voxels were used and the response time for the system to detect a change of activity was on average 2-4 seconds. The developments here have a potential to aid people with communication disabilities, such as locked in people. Another future potential application can be to serve as a tool for stroke and Parkinson patients to be able to train the damaged brain area and get real-time feedback for more efficient training.

  • 38. Ernvik, Aron
    et al.
    Bergström, Staffan
    Lundström, Claes
    Linköping University, Department of Science and Technology, Media and Information Technology.
    Ljung, Patric
    Linköping University, Department of Science and Technology, Media and Information Technology.
    Ynnerman, Anders
    Linköping University.
    Image data set compression based on viewing parameters for storing medical image data from multidimensional data sets, related systems, methods and computer products2012Patent (Other (popular science, discussion, etc.))
  • 39.
    Etiene, Tiago
    et al.
    University of Utah, UT 84112 USA .
    Jönsson, Daniel
    Linköping University, Department of Science and Technology, Media and Information Technology. 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.
    Scheidegger, Carlos
    ATandT Labs Research, NJ 07932 USA .
    Comba, Joao L. D.
    University of Federal Rio Grande do Sul, Brazil .
    Gustavo Nonato, Luis
    University of Sao Paulo, Brazil .
    Kirby, Robert M.
    University of Utah, UT 84112 USA .
    Ynnerman, Anders
    Linköping University, Department of Science and Technology, Media and Information Technology. Linköping University, The Institute of Technology.
    Silva, Claudio T.
    NYU, NY 11201 USA .
    Verifying Volume Rendering Using Discretization Error Analysis2014In: IEEE Transactions on Visualization and Computer Graphics, ISSN 1077-2626, E-ISSN 1941-0506, Vol. 20, no 1, p. 140-154Article in journal (Refereed)
    Abstract [en]

    We propose an approach for verification of volume rendering correctness based on an analysis of the volume rendering integral, the basis of most DVR algorithms. With respect to the most common discretization of this continuous model (Riemann summation), we make assumptions about the impact of parameter changes on the rendered results and derive convergence curves describing the expected behavior. Specifically, we progressively refine the number of samples along the ray, the grid size, and the pixel size, and evaluate how the errors observed during refinement compare against the expected approximation errors. We derive the theoretical foundations of our verification approach, explain how to realize it in practice, and discuss its limitations. We also report the errors identified by our approach when applied to two publicly available volume rendering packages.

  • 40.
    Falk, Martin
    et al.
    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.
    Treanor, Darren
    Linköping University, Center for Medical Image Science and Visualization (CMIV). Leeds Teaching Hospitals NHS Trust, United Kingdom.
    Lundström, Claes
    Linköping University, Center for Medical Image Science and Visualization (CMIV). Sectra, Linköping, Sweden.
    Interactive Visualization of 3D Histopathology in Native Resolution2019In: IEEE Transactions on Visualization and Computer Graphics, ISSN 1077-2626, E-ISSN 1941-0506, Vol. 25, no 1, p. 1008-1017Article in journal (Refereed)
    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.

  • 41.
    Felsberg, Michael
    et al.
    Linköping University, Department of Electrical Engineering, Computer Vision. Linköping University, The Institute of Technology.
    Larsson, Fredrik
    Linköping University, Department of Electrical Engineering, Computer Vision. Linköping University, The Institute of Technology.
    Han, Wang
    Nanyang Technological University, China.
    Ynnerman, Anders
    Linköping University, Department of Science and Technology, Media and Information Technology. Linköping University, The Institute of Technology.
    Schön, Thomas
    Linköping University, Department of Electrical Engineering, Automatic Control. Linköping University, The Institute of Technology.
    Torch Guided Navigation2010In: Proceedings of the 2010 SSBA Symposium, 2010, p. 8-9Conference paper (Other academic)
    Abstract [en]

    A common computer vision task is navigation and mapping. Many indoor navigation tasks require depth knowledge of at, unstructured surfaces (walls, oor, ceiling). With passive illumination only, this is an ill-posed problem. Inspired by small children using a torchlight, we use a spotlight for active illumination. Using our torchlight approach, depth and orientation estimation of unstructured, at surfaces boils down to estimation of ellipse parameters. The extraction of ellipses is very robust and requires little computational effort.

  • 42.
    Felsberg, Michael
    et al.
    Linköping University, Department of Electrical Engineering, Computer Vision. Linköping University, The Institute of Technology.
    Larsson, Fredrik
    Linköping University, Department of Electrical Engineering, Computer Vision. Linköping University, The Institute of Technology.
    Wang, Han
    National University Singapore.
    Ynnerman, Anders
    Linköping University, Center for Medical Image Science and Visualization (CMIV). Linköping University, Department of Science and Technology, Media and Information Technology. Linköping University, The Institute of Technology.
    Schön, Thomas
    Linköping University, Department of Electrical Engineering, Automatic Control. Linköping University, The Institute of Technology.
    Torchlight Navigation2010In: Proceedings of the 20th International Conferenceon Pattern Recognition, 2010, p. 302-306Conference paper (Refereed)
    Abstract [en]

    A common computer vision task is navigation and mapping. Many indoor navigation tasks require depth knowledge of flat, unstructured surfaces (walls, floor, ceiling). With passive illumination only, this is an ill-posed problem. Inspired by small children using a torchlight, we use a spotlight for active illumination. Using our torchlight approach, depth and orientation estimation of unstructured, flat surfaces boils down to estimation of ellipse parameters. The extraction of ellipses is very robust and requires little computational effort.

  • 43. Gunnarsson, Ann-Sofie
    et al.
    Rauhala, Malinda
    Henrysson, Anders
    Linköping University, Department of Science and Technology, Visual Information Technology and Applications (VITA). Linköping University, The Institute of Technology.
    Ynnerman, Anders
    Linköping University, Department of Science and Technology, Visual Information Technology and Applications (VITA). Linköping University, The Institute of Technology.
    Visualization of Sensor Data Using Mobile Phone Augmented Reality2006In: ISMAR 2006,2006, Los Alamitos, CA, USA: IEEE Computer Society , 2006, p. 233-Conference paper (Refereed)
  • 44.
    Hernell, Frida
    et al.
    Linköping University, Department of Science and Technology, Visual Information Technology and Applications (VITA). Linköping University, The Institute of Technology.
    Ljung, Patric
    Linköping University, Department of Science and Technology, Visual Information Technology and Applications (VITA). Linköping University, The Institute of Technology.
    Ynnerman, Anders
    Linköping University, Department of Science and Technology, Visual Information Technology and Applications (VITA). Linköping University, The Institute of Technology.
    Efficient Ambient and Emissive Tissue Illumination using Local Occlusion in Multiresolution Volume Rendering2007In: Volume Graphics 2007 Eurographics / IEEE VGTC Symposium Proceedings Sixth International Symposium on Volume Graphics, IEEE , 2007, p. 1-8Conference paper (Refereed)
    Abstract [en]

    This paper introduces a novel technique to compute illumination for Direct Volume Rendering. By adding shadow effects to volume rendered images, the perception of shapes and tissue properties can be significantly improved and it has the potential to increase the diagnostic value of medical volume rendering. The integrated intensity of incident light for a voxel is computed using a local approximation of the ambient occlusion, thus avoiding the rendering of tissues with very low illumination. Luminous tissue effects are also introduced to enhance the illumination model, controlled through an emissive component in the transfer function. This effect allows the user to highlight specific structures and can give a better understanding of tissue density. Multiresolution volume management and GPU-based computation is used to significantly speed-up the calculations and to support large data sets. The scheme yields interactive frame rates for incrementally refined ambient and emissive illumination for arbitrary transfer function changes.

  • 45.
    Hernell, Frida
    et al.
    Linköping University, Department of Science and Technology, Visual Information Technology and Applications (VITA). Linköping University, The Institute of Technology.
    Ljung, Patric
    Linköping University, Department of Science and Technology, Visual Information Technology and Applications (VITA). Linköping University, The Institute of Technology.
    Ynnerman, Anders
    Linköping University, Department of Science and Technology, Visual Information Technology and Applications (VITA). Linköping University, The Institute of Technology.
    Interactive Global Light Propagation in Direct Volume Rendering using Local Piecewise Integration2008In: Volume and Point-Based Graphics 2008, Eurographics / IEEE VGTC Symposium Proceedings Seventh International Symposium on Volume Graphics, Eurographics Association , 2008, p. 105-112Conference paper (Refereed)
    Abstract [en]

    A novel technique for efficient computation of global light propagation in interactive DVR is presented in this paper. The approach is based on a combination of local shadows from the vicinity of each voxel with global shadows calculated at high resolution but stored in a sparser grid. The resulting intensities are then used as the initial illumination for an additional pass that computes first order scattering effects. The method captures global shadowing effects with enhanced shadows of near structures. A GPU framework is used to evaluate the illumination updates at interactive frame rates, using incremental refinements of the in-scattered light. 

  • 46.
    Hernell, Frida
    et al.
    Linköping University, Department of Science and Technology, Media and Information Technology. Linköping University, The Institute of Technology.
    Ljung, Patric
    Siemens Corporation Research.
    Ynnerman, Anders
    Linköping University, Department of Science and Technology, Media and Information Technology. Linköping University, The Institute of Technology.
    Local Ambient Occlusion in Direct Volume Rendering2010In: IEEE Transactions on Visualization and Computer Graphics, ISSN 1077-2626, E-ISSN 1941-0506, Vol. 16, no 4, p. 548-559Article in journal (Refereed)
    Abstract [en]

    This paper presents a novel technique to efficiently compute illumination for Direct Volume Rendering using a local approximation of ambient occlusion to integrate the intensity of incident light for each voxel. An advantage with this local approach is that fully shadowed regions are avoided, a desirable feature in many applications of volume rendering such as medical visualization. Additional transfer function interactions are also presented, for instance, to highlight specific structures with luminous tissue effects and create an improved context for semitransparent tissues with a separate absorption control for the illumination settings. Multiresolution volume management and GPU-based computation are used to accelerate the calculations and support large data sets. The scheme yields interactive frame rates with an adaptive sampling approach for incrementally refined illumination under arbitrary transfer function changes. The illumination effects can give a better understanding of the shape and density of tissues and so has the potential to increase the diagnostic value of medical volume rendering. Since the proposed method is gradient-free, it is especially beneficial at the borders of clip planes, where gradients are undefined, and for noisy data sets.

  • 47.
    Hernell, Frida
    et al.
    Linköping University, Department of Science and Technology, Media and Information Technology.
    Ljung, Patric
    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).
    Local ambient occlusion in direct volume rendering2010In: Visualization and Computer Graphics, IEEE Transactions on, ISSN 1077-2626, Vol. 16, no 4, p. 548-559Article in journal (Refereed)
    Abstract [en]

    This paper presents a novel technique to efficiently compute illumination for Direct Volume Rendering using a local approximation of ambient occlusion to integrate the intensity of incident light for each voxel. An advantage with this local approach is that fully shadowed regions are avoided, a desirable feature in many applications of volume rendering such as medical visualization.

    Additional transfer function interactions are also presented, for instance, to highlight specific structures with luminous tissue effects and create an improved context for semitransparent tissues with a separate absorption control for the illumination settings. Multiresolution volume management and GPU-based computation are used to accelerate the calculations and support large data sets. The scheme yields interactive frame rates with an adaptive sampling approach for incrementally refined illumination under arbitrary transfer function changes. The illumination effects can give a better understanding of the shape and density of tissues and so has the potential to increase the diagnostic value of medical volume rendering. Since the proposed method is gradient-free, it is especially beneficial at the borders of clip planes, where gradients are undefined, and for noisy data sets.

  • 48.
    Hernell, Frida
    et al.
    Linköping University, Department of Science and Technology, Visual Information Technology and Applications (VITA). Linköping University, Center for Medical Image Science and Visualization (CMIV). Linköping University, The Institute of Technology.
    Ynnerman, Anders
    Linköping University, Department of Science and Technology, Visual Information Technology and Applications (VITA). Linköping University, The Institute of Technology. Linköping University, Center for Medical Image Science and Visualization (CMIV).
    Smedby, Örjan
    Linköping University, Faculty of Health Sciences. Linköping University, Department of Medicine and Care, Medical Radiology. Östergötlands Läns Landsting, Centre for Medical Imaging, Department of Radiology UHL. Linköping University, Center for Medical Image Science and Visualization (CMIV).
    A blending technique for enhanced depth perception in medical x-ray vision applications2007In: Medicine Meets Virtual Reality 15 / [ed] James D. Westwood, Randy S. Haluck, Helene M. Hoffman, Greg T. Mogel, Roger Phillips, Richard A. Robb, Kirby G. Vosburgh, IOS Press, 2007, Vol. 125, p. 176-178Conference paper (Refereed)
    Abstract [en]

    Depth perception is a common problem for x-ray vision in augmented reality applications since the goal is to visualize occluded and embedded objects. In this paper we present an x-ray vision blending method for neurosurgical applications that intensifies the interposition depth cue in order to achieve enhanced depth perception. The proposed technique emphasizes important structures, which provides the user with an improved depth context.

  • 49.
    Holmgren, S.
    et al.
    Department of Scientific Computing, Uppsala University, Box 337, SE-75105 Uppsala, Sweden.
    Ynnerman, Anders
    Linköping University, Department of Science and Technology, Visual Information Technology and Applications (VITA). Linköping University, The Institute of Technology.
    The Swedish National Graduate School in Scientific Computing (NGSSC)2003Conference paper (Other academic)
    Abstract [en]

    The Swedish National Graduate School in Scientific Computing (NGSSC) was founded in 1996, and has so far admitted 75 graduate students in five nationally announced admission rounds. The aim of NGSSC is to produce PhDs with skills in strategically important disciplines together with a broad knowledge of numerical and computational techniques, and to spread the use of computations into new areas of research. NGSSC consists of both a geographical and a disciplinary network and focuses on providing core knowledge on advanced computational techniques to graduate students in application fields. This presents some special challenges to the program, such as developing its own identity and dealing with the very different backgrounds of the students. The NGSSC activities focus on a package of specially developed courses, tailored for student groups with very mixed backgrounds. The courses are given in intensive format, and are compulsory for the students participating in the program. © 2003 Elsevier B.V. All rights reserved.

  • 50.
    Jern, Mikael
    et al.
    Linköping University, Department of Science and Technology, Visual Information Technology and Applications (VITA). Linköping University, The Institute of Technology.
    Rogstadius, Jakob
    Linköping University, Department of Science and Technology, Visual Information Technology and Applications (VITA). Linköping University, The Institute of Technology.
    Åström, Tobias
    Linköping University, Department of Science and Technology, Visual Information Technology and Applications (VITA). Linköping University, The Institute of Technology.
    Ynnerman, Anders
    Linköping University, Department of Science and Technology, Visual Information Technology and Applications (VITA). Linköping University, The Institute of Technology.
    Visual Analytics Presentation Tools applied in HTML Documents2008In: Information Visualisation, 2008. IV '08. 12th International Conference, Los Alamitos, CA, USA: IEEE Computer Society, 2008, p. 200-207Conference paper (Refereed)
    Abstract [en]

    In this paper we present novel means to communicate and present gained knowledge using semi-guided interactive visualizations embedded in standard HTML documents. The goal of the work is to let the analyst (author) explore data and simultaneously save important discoveries and thus enable collaboration and sharing of gained insights over the Internet. The readers of the document will benefit from receiving an integrated and interactive document that can "coach" them in the understanding and testing of hypotheses leading to faster understanding and a higher confidence level in the presented visual information. The approach is based on the visual analytics (VA) toolkit (GAV), which also provides a mechanism that supports the storage of interactive events in an analytical reasoning process through "memorized interactive visualization views" or snapshots that can be saved at any time during an explorative data analysis process. In a typical scenario an application, comprised of GAV VA components, is embedded in the HTML document together with target data and the snapshots of discoveries. Any standard HTML event, such as the user clicking a textual link or an image can be used to instantiate a snapshot, creating a link between a descriptive text and an interactive visualization presentation. As the GAV application and corresponding data are integrated with the HTML code, residing on the client machine, hardware accelerated graphics can be used to provide interactive performance of demanding visualizations. We demonstrate the potential of the developed methods in the context of geoanalytics and molecular visualization scenarios.

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