liu.seSearch for publications in DiVA
Change search
Refine search result
1 - 20 of 20
CiteExportLink to result list
Permanent link
Cite
Citation style
  • apa
  • ieee
  • modern-language-association-8th-edition
  • vancouver
  • oxford
  • Other style
More styles
Language
  • de-DE
  • en-GB
  • en-US
  • fi-FI
  • nn-NO
  • nn-NB
  • sv-SE
  • Other locale
More languages
Output format
  • html
  • text
  • asciidoc
  • rtf
Rows per page
  • 5
  • 10
  • 20
  • 50
  • 100
  • 250
Sort
  • Standard (Relevance)
  • Author A-Ö
  • Author Ö-A
  • Title A-Ö
  • Title Ö-A
  • Publication type A-Ö
  • Publication type Ö-A
  • Issued (Oldest first)
  • Issued (Newest first)
  • Created (Oldest first)
  • Created (Newest first)
  • Last updated (Oldest first)
  • Last updated (Newest first)
  • Disputation date (earliest first)
  • Disputation date (latest first)
  • Standard (Relevance)
  • Author A-Ö
  • Author Ö-A
  • Title A-Ö
  • Title Ö-A
  • Publication type A-Ö
  • Publication type Ö-A
  • Issued (Oldest first)
  • Issued (Newest first)
  • Created (Oldest first)
  • Created (Newest first)
  • Last updated (Oldest first)
  • Last updated (Newest first)
  • Disputation date (earliest first)
  • Disputation date (latest first)
Select
The maximal number of hits you can export is 250. When you want to export more records please use the Create feeds function.
  • 1.
    Abrikosov, Alexei I.
    et al.
    Linköping University, Department of Science and Technology, Media and Information Technology. Linköping University, Faculty of Science & Engineering.
    Masood, Talha Bin
    Linköping University, Department of Science and Technology, Media and Information Technology. Linköping University, Faculty of Science & Engineering.
    Falk, Martin
    Linköping University, Department of Science and Technology, Media and Information Technology. Linköping University, Faculty of Science & Engineering.
    Hotz, Ingrid
    Linköping University, Department of Science and Technology, Media and Information Technology. Linköping University, Faculty of Science & Engineering.
    Topological analysis of density fields: An evaluation of segmentation methods2021In: Computers & graphics, ISSN 0097-8493, E-ISSN 1873-7684, Vol. 98, p. 231-241Article in journal (Refereed)
    Abstract [en]

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

    Download full text (pdf)
    fulltext
  • 2.
    Dieckmann, Mark E
    et al.
    Linköping University, Department of Science and Technology, Media and Information Technology. Linköping University, Faculty of Science & Engineering.
    Falk, Martin
    Linköping University, Department of Science and Technology, Media and Information Technology. Linköping University, Faculty of Science & Engineering.
    Folini, Doris
    Ecole Normale Supérieure, Lyon, CRAL, UMR CNRS 5574, Université de Lyon, 69622 Lyon, France.
    Walder, Rolf
    Ecole Normale Supérieure, Lyon, CRAL, UMR CNRS 5574, Université de Lyon, 69622 Lyon, France.
    Steneteg, Peter
    Linköping University, Department of Science and Technology, Media and Information Technology. Linköping University, Faculty of Science & Engineering.
    Hotz, Ingrid
    Linköping University, Department of Science and Technology, Media and Information Technology. Linköping University, Faculty of Science & Engineering.
    Ynnerman, Anders
    Linköping University, Department of Science and Technology, Media and Information Technology. Linköping University, Faculty of Science & Engineering.
    Collisionless Rayleigh–Taylor-like instability of the boundary between a hot pair plasma and an electron–proton plasma: The undular mode2020In: Physics of Plasmas, ISSN 1070-664X, E-ISSN 1089-7674, Vol. 27, no 11, p. 1-14, article id 112106Article in journal (Refereed)
    Abstract [en]

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

    Download full text (pdf)
    fulltext
  • 3.
    Dieckmann, Mark E
    et al.
    Linköping University, Department of Science and Technology, Media and Information Technology. Linköping University, Faculty of Science & Engineering.
    Falk, Martin
    Linköping University, Department of Science and Technology, Media and Information Technology. Linköping University, Faculty of Science & Engineering.
    Steneteg, Peter
    Linköping University, Department of Science and Technology, Media and Information Technology. Linköping University, Faculty of Science & Engineering.
    Folini, Doris
    CRAL, École Normale Supérieure, 69622 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
    CRAL, École Normale Supérieure, 69622 Lyon, France.
    Structure of a collisionless pair jet in a magnetized electron-proton plasma: Flow-aligned magnetic field2019In: High Energy Phenomena in Relativistic Outflows VII (HEPRO VII): Formation and propagation of relativistic outflows, 2019, article id 006Conference paper (Refereed)
    Abstract [en]

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

  • 4.
    Dieckmann, Mark E
    et al.
    Linköping University, Department of Science and Technology, Media and Information Technology. Linköping University, Faculty of Science & Engineering.
    Spencer, Selina-Jane
    Centre for Fusion, Space and Astrophysics, University of Warwick, Coventry, CV4 7AL, UK.
    Falk, Martin
    Linköping University, Department of Science and Technology, Media and Information Technology. Linköping University, Faculty of Science & Engineering.
    Rowlands, George
    Centre for Fusion, Space and Astrophysics, University of Warwick, Coventry, CV4 7AL, UK.
    Preferential acceleration of positrons by a filamentation instability between an electron–proton beam and a pair plasma beam2020In: Physics of Plasmas, ISSN 1070-664X, E-ISSN 1089-7674, Vol. 27, no 12, article id 122102Article in journal (Refereed)
    Abstract [en]

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

    Download full text (pdf)
    fulltext
  • 5.
    Falk, Martin
    et al.
    Linköping University, Department of Science and Technology, Media and Information Technology. Linköping University, Faculty of Science & Engineering.
    Ljung, Patric
    Linköping University, Department of Science and Technology, Media and Information Technology. Linköping University, Faculty of Science & Engineering.
    Lundström, Claes
    Linköping University, Department of Science and Technology, Media and Information Technology. Linköping University, Faculty of Science & Engineering. Linköping University, Center for Medical Image Science and Visualization (CMIV).
    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).
    Hotz, Ingrid
    Linköping University, Department of Science and Technology, Media and Information Technology. Linköping University, Faculty of Science & Engineering.
    Feature Exploration in Medical Volume Data using Local Frequency Distributions2020In: / [ed] B. Kozlíková, M. Krone, and N. N. Smit, 2020Conference paper (Refereed)
    Abstract [en]

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

  • 6.
    Falk, Martin
    et al.
    Linköping University, Department of Science and Technology, Media and Information Technology. Linköping University, Faculty of Science & Engineering. Swedish e-Science Research Centre (SeRC), Sweden.
    Tobiasson, Victor
    Science for Life Laboratory, Department of Biochemistry and Biophysics, Stockholm University, Solna, Sweden.
    Bock, Alexander
    Linköping University, Department of Science and Technology, Media and Information Technology. Linköping University, Faculty of Science & Engineering. Swedish e-Science Research Centre (SeRC), Sweden.
    Hansen, Charles
    Linköping University, Department of Science and Technology, Media and Information Technology. Linköping University, Faculty of Science & Engineering. Kahlert School of Computing, University of Utah.
    Ynnerman, Anders
    Linköping University, Department of Science and Technology, Media and Information Technology. Linköping University, Faculty of Science & Engineering. Swedish e-Science Research Centre (SeRC), Sweden.
    A Visual Environment for Data Driven Protein Modeling and Validation2023In: IEEE Transactions on Visualization and Computer Graphics, ISSN 1077-2626, E-ISSN 1941-0506Article in journal (Refereed)
    Abstract [en]

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

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

    Download full text (pdf)
    fulltext
  • 7.
    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.

    Download full text (pdf)
    fulltext
  • 8.
    Friederici, Anke
    et al.
    Otto-von-Guericke-University Magdeburg, Magdeburg, Germany.
    Falk, Martin
    Linköping University, Department of Science and Technology, Media and Information Technology. Linköping University, Faculty of Science & Engineering.
    Hotz, Ingrid
    Linköping University, Department of Science and Technology, Media and Information Technology. Linköping University, Faculty of Science & Engineering.
    A Winding Angle Framework for Tracking and Exploring Eddy Transport in Oceanic Ensemble Simulations2021In: Workshop on Visualisation in Environmental Sciences (EnvirVis), The Eurographics Association , 2021Conference paper (Refereed)
    Abstract [en]

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

  • 9.
    Hotz, Ingrid
    et al.
    Linköping University, Department of Science and Technology, Media and Information Technology. Linköping University, Faculty of Science & Engineering.
    Falk, MartinLinköping University, Department of Science and Technology, Media and Information Technology. Linköping University, Faculty of Science & Engineering.
    Proceedings of SIGRAD 2017, August 17-18, 2017 Norrköping, Sweden2017Conference proceedings (editor) (Refereed)
    Abstract [en]

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

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

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

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

    The SIGRAD 2017 organizers

    Martin Falk, Daniel Jönsson, Ingrid Hotz

    Download full text (pdf)
    Proceedings of SIGRAD 2017, August 17-18, 2017 Norrköping, Sweden
  • 10.
    Jönsson, Daniel
    et al.
    Linköping University, Department of Science and Technology, Media and Information Technology. Linköping University, Faculty of Science & Engineering.
    Falk, Martin
    Linköping University, Department of Science and Technology, Media and Information Technology. Linköping University, Faculty of Science & Engineering.
    Ynnerman, Anders
    Linköping University, Department of Science and Technology, Media and Information Technology. Linköping University, Faculty of Science & Engineering. Linköping University, Center for Medical Image Science and Visualization (CMIV).
    Intuitive Exploration of Volumetric Data Using Dynamic Galleries2016In: IEEE Transactions on Visualization and Computer Graphics, ISSN 1077-2626, E-ISSN 1941-0506, Vol. 22, no 1, p. 896-905Article in journal (Refereed)
    Abstract [en]

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

    Download full text (pdf)
    fulltext
  • 11.
    Jönsson, Daniel
    et al.
    Linköping University, Department of Science and Technology, Media and Information Technology. Linköping University, Faculty of Science & Engineering.
    Steneteg, Peter
    Linköping University, Department of Science and Technology, Media and Information Technology. Linköping University, Faculty of Science & Engineering.
    Sundén, Erik
    Linköping University, Department of Science and Technology, Media and Information Technology. Linköping University, Faculty of Science & Engineering.
    Englund, Rickard
    Linköping University, Department of Science and Technology, Media and Information Technology. Linköping University, Faculty of Science & Engineering.
    Kottravel, Sathish
    Linköping University, Department of Science and Technology, Media and Information Technology. Linköping University, Faculty of Science & Engineering.
    Falk, Martin
    Linköping University, Department of Science and Technology, Media and Information Technology. Linköping University, Faculty of Science & Engineering.
    Ynnerman, Anders
    Linköping University, Department of Science and Technology, Media and Information Technology. Linköping University, Faculty of Science & Engineering.
    Hotz, Ingrid
    Linköping University, Department of Science and Technology, Media and Information Technology. Linköping University, Faculty of Science & Engineering.
    Ropinski, Timo
    Linköping University, Department of Science and Technology, Media and Information Technology. Linköping University, Faculty of Science & Engineering.
    Inviwo - A Visualization System with Usage Abstraction Levels2020In: IEEE Transactions on Visualization and Computer Graphics, ISSN 1077-2626, Vol. 26, no 11, p. 3241-3254Article in journal (Refereed)
    Abstract [en]

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

    Download full text (pdf)
    fulltext
  • 12.
    Kauker, Daniel
    et al.
    VISUS, University of Stuttgart.
    Falk, Martin
    Linköping University, Department of Science and Technology, Media and Information Technology. Linköping University, Faculty of Science & Engineering.
    Reina, Guido
    VISUS, University of Stuttgart.
    Ynnerman, Anders
    Linköping University, Department of Science and Technology, Media and Information Technology. Linköping University, Faculty of Science & Engineering. Linköping University, Center for Medical Image Science and Visualization (CMIV).
    Ertl, Thomas
    VISUS, University of Stuttgart.
    VoxLink—Combining sparse volumetric data and geometry for efficient rendering2016In: Computational Visual Media, ISSN 2096-0662, Vol. 2, no 1, p. 45-56Article in journal (Refereed)
    Abstract [en]

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

    Download full text (pdf)
    fulltext
  • 13.
    Kottravel, Sathish
    et al.
    Linköping University, Department of Science and Technology, Media and Information Technology. Linköping University, Faculty of Science & Engineering.
    Falk, Martin
    Linköping University, Department of Science and Technology, Media and Information Technology. Linköping University, Faculty of Science & Engineering.
    Sundén, Erik
    Linköping University, Department of Science and Technology, Media and Information Technology. Linköping University, Faculty of Science & Engineering.
    Ropinski, Timo
    Visual Computing Research Group, Ulm University, Germany.
    Coverage-Based Opacity Estimation for Interactive Depth of Field in Molecular Visualization2015In: IEEE Pacific Visualization Symposium (PacificVis 2015), IEEE Computer Society, 2015, p. 255-262Conference paper (Refereed)
    Abstract [en]

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

    Download full text (pdf)
    fulltext
  • 14.
    Kozlíková, Barbora
    et al.
    Masaryk University, Czech Republic.
    Krone, Michael
    VISUS, University of Stuttgart, Germany.
    Lindow, Norbert
    Zuse Institute Berlin, Germany.
    Falk, Martin
    Linköping University, Department of Science and Technology, Media and Information Technology. Linköping University, Faculty of Science & Engineering.
    Baaden, Marc
    Laboratoire de Biochimie Théorique, France.
    Baum, Daniel
    Zuse Institute Berlin, Germany.
    Viola, Ivan
    Institute of Computer Graphics and Algorithms, Vienna University of Technology, Austria.
    Parulek, Julius
    Department of Informatics, University of Bergen, Norway.
    Hege, Hans-Christian
    Zuse Institute Berlin, Germany.
    Visualization of Molecular Structure: The State of the Art2015In: Eurographics Conference on Visualization (EuroVis) - STARs / [ed] R. Borgo and F. Ganovelli and I. Viola, Eurographics - European Association for Computer Graphics, 2015Conference paper (Refereed)
    Abstract [en]

    Structural properties of molecules are of primary concern in many fields. This report provides a comprehensive overview on techniques that have been developed in the fields of molecular graphics and visualization with a focus on applications in structural biology. The field heavily relies on computerized geometric and visual representations of three-dimensional, complex, large, and time-varying molecular structures. The report presents a taxonomy that demonstrates which areas of molecular visualization have already been extensively investigated and where the field is currently heading. It discusses visualizations for molecular structures, strategies for efficient display regarding image quality and frame rate, covers different aspects of level of detail, and reviews visualizations illustrating the dynamic aspects of molecular simulation data. The report concludes with an outlook on promising and important research topics to enable further success in advancing the knowledge about interaction of molecular structures.

  • 15.
    Lindholm, Stefan
    et al.
    Linköping University, Department of Science and Technology, Media and Information Technology. Linköping University, The Institute of Technology.
    Falk, Martin
    Linköping University, Department of Science and Technology, Media and Information Technology. Linköping University, The Institute of Technology.
    Sundén, Erik
    Linköping University, Department of Science and Technology, Media and Information Technology. Linköping University, The Institute of Technology.
    Bock, Alexander
    Linköping University, Department of Science and Technology, Media and Information Technology. Linköping University, The Institute of Technology.
    Ynnerman, Anders
    Linköping University, Department of Science and Technology, Media and Information Technology. Linköping University, Center for Medical Image Science and Visualization (CMIV). Linköping University, The Institute of Technology.
    Ropinski, Timo
    Linköping University, Department of Science and Technology, Media and Information Technology. Linköping University, The Institute of Technology.
    Hybrid Data Visualization Based On Depth Complexity Histogram Analysis2015In: Computer graphics forum (Print), ISSN 0167-7055, E-ISSN 1467-8659, Vol. 34, no 1, p. 74-85Article in journal (Refereed)
    Abstract [en]

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

    Download full text (pdf)
    fulltext
  • 16.
    Lukasczyk, Jonas
    et al.
    Technische Universität Kaiserslautern, Kaiserslautern, Germany.
    Beran, Jakob
    Stockholm University, Stockholm, Sweden.
    Engelke, Wito
    Linköping University, Department of Science and Technology, Media and Information Technology. Linköping University, Faculty of Science & Engineering.
    Falk, Martin
    Linköping University, Department of Science and Technology, Media and Information Technology. Linköping University, Faculty of Science & Engineering.
    Friederici, Anke
    KTH Royal Institute of Technology, Stockholm, Sweden.
    Garth, Christoph
    Technische Universität Kaiserslautern, Kaiserslautern, Germany.
    Hofmann, Lutz
    Heidelberg University, Heidelberg, Germany.
    Hotz, Ingrid
    Linköping University, Department of Science and Technology, Media and Information Technology. Linköping University, Faculty of Science & Engineering.
    Hristov, Petar
    University of Leeds, Leeds, UK.
    Köpp, Wiebke
    KTH Royal Institute of Technology, Stockholm, Sweden.
    Masood, Talha Bin
    Linköping University, Department of Science and Technology, Media and Information Technology. Linköping University, Faculty of Science & Engineering.
    Olejniczak, Małgorzata
    University of Warsaw, Warsaw, Poland.
    Rosen, Paul
    University of South Florida, Tampa, USA.
    Sohns, Jan-Tobias
    Technische Universität Kaiserslautern, Kaiserslautern, Germany.
    Weinkauf, Tino
    KTH Royal Institute of Technology, Stockholm, Sweden.
    Werner, Kilian
    Technische Universität Kaiserslautern, Kaiserslautern, Germany.
    Tierny, Julien
    CNRS, Sorbonne Universite, Paris, France.
    Report of the TopoInVis TTK Hackathon: Experiences, Lessons Learned, and Perspectives2021In: Topological Methods in Data Analysis and Visualization VI: Theory, Applications, and Software / [ed] Ingrid Hotz, Talha Bin Masood, Filip Sadlo and Julien Tierny, Springer, 2021, p. 359-373Chapter in book (Refereed)
    Abstract [en]

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

    Download full text (pdf)
    fulltext
  • 17.
    Masood, Talha Bin
    et al.
    Linköping University, Department of Science and Technology, Media and Information Technology. Linköping University, Faculty of Science & Engineering.
    Budin, Joseph
    Sorbonne Université, Paris, France.
    Falk, Martin
    Linköping University, Department of Science and Technology, Media and Information Technology. Linköping University, Faculty of Science & Engineering.
    Favelier, Guillaume
    INRIA Saclay - Île-de-France, Palaiseau, France.
    Garth, Christoph
    TU Kaiserslautern, Kaiserslautern, Germany.
    Gueunet, Charles
    Kitware, New York, USA.
    Guillou, Pierre
    Sorbonne Université, Paris, France.
    Hofmann, Lutz
    Heidelberg University, Heidelberg, Germany.
    Hristov, Petar
    University of Leeds, Leeds, UK.
    Kamakshidasan, Adhitya
    INRIA Saclay - Île-de-France, Palaiseau, France.
    Kappe, Christopher
    TU Kaiserslautern, Kaiserslautern, Germany.
    Klacansky, Pavol
    SCI Institute, University of Utah, Salt Lake City, USA.
    Laurin, Patrick
    ShapeShift3D, Montreal, Canada.
    Levine, Joshua A.
    University of Arizona, Tucson, USA.
    Lukasczyk, Jonas
    Arizona State University, Phoenix, USA.
    Sakurai, Daisuke
    Kyushu University, Fukuoka, Japan.
    Soler, Maxime
    Total / Sorbonne Université, Paris, France.
    Steneteg, Peter
    Linköping University, Department of Science and Technology, Media and Information Technology. Linköping University, Faculty of Science & Engineering.
    Tierny, Julien
    CNRS / Sorbonne Université, Paris, France.
    Usher, Will
    SCI Institute, University of Utah, Salt Lake City, USA.
    Vidal, Jules
    Sorbonne Université, Paris, France.
    Wozniak, Michal
    ShapeShift3D, Montreal, Canada.
    An Overview of the Topology ToolKit2021In: Topological Methods in Data Analysis and Visualization VI: Theory, Applications, and Software / [ed] Ingrid Hotz, Talha Bin Masood, Filip Sadlo and Julien Tierny, Springer, 2021, p. 327-342Chapter in book (Refereed)
    Abstract [en]

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

    Download full text (pdf)
    fulltext
  • 18.
    Menges, Anna-Leonie
    et al.
    Univ Hosp Zurich, Switzerland.
    Nackenhorst, Maja
    Med Univ Vienna, Austria.
    Müller, Johannes R.
    Tech Univ Dresden, Germany.
    Engl, Marie-Luise
    Tech Univ Munich, Germany.
    Hegenloh, Renate
    Tech Univ Munich, Germany.
    Pelisek, Jaroslav
    Univ Hosp Zurich, Switzerland.
    Geibelt, Ellen
    Tech Univ Dresden, Germany.
    Hofmann, Anja
    Tech Univ Dresden, Germany.
    Reeps, Christian
    Tech Univ Dresden, Germany.
    Biro, Gabor
    Tech Univ Munich, Germany.
    Eckstein, Hans-Henning
    Tech Univ Munich, Germany; German Ctr Cardiovasc Res DZHK, Germany.
    Zimmermann, Alexander
    Univ Hosp Zurich, Switzerland.
    Magee, Derek
    HeteroGenius Ltd, England; Univ Leeds, England.
    Falk, Martin
    Linköping University, Department of Science and Technology, Media and Information Technology. Linköping University, Faculty of Science & Engineering.
    Sachs, Nadja
    Tech Univ Munich, Germany; German Ctr Cardiovasc Res DZHK, Germany.
    Busch, Albert
    Tech Univ Munich, Germany; Tech Univ Dresden, Germany.
    Completing the view – histologic insights from circular AAA specimen including 3D imaging2023In: Diagnostic Pathology, E-ISSN 1746-1596, Vol. 18, no 1, article id 73Article in journal (Refereed)
    Abstract [en]

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

    Download full text (pdf)
    fulltext
  • 19.
    Skånberg, Robin
    et al.
    Linköping University, Department of Science and Technology, Media and Information Technology. Linköping University, Faculty of Science & Engineering. Swedish e-Science Research Centre (SeRC), Stockholm, Sweden.
    Falk, Martin
    Linköping University, Department of Science and Technology, Media and Information Technology. Linköping University, Faculty of Science & Engineering. Swedish e-Science Research Centre (SeRC), Stockholm, Sweden.
    Linares, Mathieu
    Linköping University, Department of Science and Technology, Laboratory of Organic Electronics. Linköping University, Faculty of Science & Engineering. Swedish e-Science Research Centre (SeRC), Stockholm, Sweden.
    Ynnerman, Anders
    Linköping University, Department of Science and Technology, Media and Information Technology. Linköping University, Faculty of Science & Engineering. Swedish e-Science Research Centre (SeRC), Stockholm, Sweden.
    Hotz, Ingrid
    Linköping University, Department of Science and Technology, Media and Information Technology. Linköping University, Faculty of Science & Engineering. Swedish e-Science Research Centre (SeRC), Stockholm, Sweden.
    Tracking Internal Frames of Reference for Consistent Molecular Distribution Functions2022In: IEEE Transactions on Visualization and Computer Graphics, ISSN 1077-2626, E-ISSN 1941-0506, Vol. 28, no 9, p. 3126-3137Article in journal (Refereed)
    Abstract [en]

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

    Download full text (pdf)
    fulltext
  • 20.
    Steneteg, Peter
    et al.
    Linköping University, Department of Science and Technology, Media and Information Technology. Linköping University, Faculty of Science & Engineering.
    Jönsson, Daniel
    Linköping University, Department of Science and Technology, Media and Information Technology. Linköping University, Faculty of Science & Engineering. Linköping University, Center for Medical Image Science and Visualization (CMIV).
    Falk, Martin
    Linköping University, Department of Science and Technology, Media and Information Technology. Linköping University, Faculty of Science & Engineering.
    Hotz, Ingrid
    Linköping University, Department of Science and Technology, Media and Information Technology. Linköping University, Faculty of Science & Engineering.
    Volume Raycasting Sampling Revisited2019Conference paper (Refereed)
    Abstract [en]

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

1 - 20 of 20
CiteExportLink to result list
Permanent link
Cite
Citation style
  • apa
  • ieee
  • modern-language-association-8th-edition
  • vancouver
  • oxford
  • Other style
More styles
Language
  • de-DE
  • en-GB
  • en-US
  • fi-FI
  • nn-NO
  • nn-NB
  • sv-SE
  • Other locale
More languages
Output format
  • html
  • text
  • asciidoc
  • rtf