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Jönsson, D., Bergström, A., Forsell, C., Simon, R., Engström, M., Ynnerman, A. & Hotz, I. (2019). A Visual Environment for Hypothesis Formation and Reasoning in Studies with fMRI and Multivariate Clinical Data. In: Eurographics Workshop on Visual Computing for Biology and Medicine: . Paper presented at Eurographics Workshop on Visual Computing for Biology and Medicine.
Open this publication in new window or tab >>A Visual Environment for Hypothesis Formation and Reasoning in Studies with fMRI and Multivariate Clinical Data
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2019 (English)In: Eurographics Workshop on Visual Computing for Biology and Medicine, 2019Conference paper, Published paper (Refereed)
Abstract [en]

We present an interactive visual environment for linked analysis of brain imaging and clinical measurements. The environment is developed in an iterative participatory design process involving neuroscientists investigating the causes of brain-related complex diseases. The hypotheses formation process about correlations between active brain regions and physiological or psychological factors in studies with hundreds of subjects is a central part of the investigation. Observing the reasoning patterns during hypotheses formation, we concluded that while existing tools provide powerful analysis options, they lack effective interactive exploration, thus limiting the scientific scope and preventing extraction of knowledge from available data.Based on these observations, we designed methods that support neuroscientists by integrating their existing statistical analysis of multivariate subject data with interactive visual explorationto enable them to better understand differences between patient groups and the complex bidirectional interplay between clinical measurement and the brain. These exploration concepts enable neuroscientists, for the first time during their investigations, to interactively move between and reason about questions such as ‘which clinical measurements are correlated with a specific brain region?’ or ‘are there differences in brain activity between depressed young and old subjects?’. The environment uses parallel coordinates for effective overview and selection of subject groups, Welch's t-test to filter out brain regions with statistically significant differences, and multiple visualizations of Pearson correlations between brain regions and clinical parameters to facilitate correlation analysis. A qualitative user study was performed with three neuroscientists from different domains. The study shows that the developed environment supports simultaneous analysis of more parameters, provides rapid pathways to insights, and is an effective support tool for hypothesis formation.

National Category
Media and Communication Technology
Identifiers
urn:nbn:se:liu:diva-160856 (URN)10.2312/vcbm.20191232 (DOI)978-3-03868-081-9 (ISBN)
Conference
Eurographics Workshop on Visual Computing for Biology and Medicine
Projects
Seeing Organ Function
Funder
Knut and Alice Wallenberg Foundation, 2013-0076Swedish Research Council, 2015-05462ELLIIT - The Linköping‐Lund Initiative on IT and Mobile CommunicationsSwedish e‐Science Research Center
Available from: 2019-10-10 Created: 2019-10-10 Last updated: 2019-10-10
Falk, M., Ynnerman, A., Treanor, D. & Lundström, C. (2019). Interactive Visualization of 3D Histopathology in Native Resolution. IEEE Transactions on Visualization and Computer Graphics, 25(1), 1008-1017
Open this publication in new window or tab >>Interactive Visualization of 3D Histopathology in Native Resolution
2019 (English)In: IEEE Transactions on Visualization and Computer Graphics, ISSN 1077-2626, E-ISSN 1941-0506, Vol. 25, no 1, p. 1008-1017Article in journal (Refereed) Published
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.

Keywords
Histology, Pathology, Volume Rendering, Expert Evaluation
National Category
Computer Sciences
Identifiers
urn:nbn:se:liu:diva-150420 (URN)10.1109/tvcg.2018.2864816 (DOI)000452640000096 ()
Funder
VINNOVA, 2014-04257
Note

Funding agencies: Excellence Center at Linkoping and Lund in Information Technology (ELLIIT); Swedish e-Science Research Centre (SeRC); DigiPat project by VINNOVA grant [2014-04257]

Available from: 2018-08-22 Created: 2018-08-22 Last updated: 2019-01-07
Jönsson, D., Steneteg, P., Sundén, E., Englund, R., Kottravel, S., Falk, M., . . . Ropinski, T. (2019). Inviwo - A Visualization System with Usage Abstraction Levels. IEEE Transactions on Visualization and Computer Graphics
Open this publication in new window or tab >>Inviwo - A Visualization System with Usage Abstraction Levels
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2019 (English)In: IEEE Transactions on Visualization and Computer Graphics, ISSN 1077-2626Article in journal (Refereed) Published
Place, publisher, year, edition, pages
IEEE, 2019
National Category
Media and Communication Technology
Identifiers
urn:nbn:se:liu:diva-160860 (URN)10.1109/TVCG.2019.2920639 (DOI)
Funder
Swedish e‐Science Research CenterELLIIT - The Linköping‐Lund Initiative on IT and Mobile CommunicationsSwedish Research Council, 2015-05462Knut and Alice Wallenberg Foundation, 2013- 0076
Available from: 2019-10-10 Created: 2019-10-10 Last updated: 2019-10-10
Bock, A., Axelsson, E., Costa, J., Payne, G., Acinapura, M., Trakinski, V., . . . Ynnerman, A. (2019). OpenSpace: A System for Astrographics. IEEE Transactions on Visualization and Computer Graphics, 1-10
Open this publication in new window or tab >>OpenSpace: A System for Astrographics
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2019 (English)In: IEEE Transactions on Visualization and Computer Graphics, ISSN 1077-2626, E-ISSN 1941-0506, p. 1-10Article in journal (Refereed) Epub ahead of print
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.

Place, publisher, year, edition, pages
Institute of Electrical and Electronics Engineers (IEEE), 2019
Keywords
Data visualization;Tools;Rendering (computer graphics);Data models;Astronomy;Space vehicles;Space missions;Astrographics;astronomy;astrophysics;system
National Category
Computer Sciences Computer and Information Sciences Astronomy, Astrophysics and Cosmology
Identifiers
urn:nbn:se:liu:diva-159939 (URN)10.1109/TVCG.2019.2934259 (DOI)
Available from: 2019-08-29 Created: 2019-08-29 Last updated: 2019-09-03Bibliographically approved
Dieckmann, M. E., Folini, D., Hotz, I., Nordman, A., Dell'Acqua, P., Ynnerman, A. & Walder, R. (2019). Structure of a collisionless pair jet in a magnetized electron–proton plasma: flow-aligned magnetic field. Astronomy and Astrophysics, 621, Article ID A142.
Open this publication in new window or tab >>Structure of a collisionless pair jet in a magnetized electron–proton plasma: flow-aligned magnetic field
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2019 (English)In: Astronomy and Astrophysics, ISSN 0004-6361, E-ISSN 1432-0746, Vol. 621, article id A142Article in journal (Refereed) Published
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.

Place, publisher, year, edition, pages
EDP Sciences, 2019
Keywords
PIC simulation, collisionless plasma, relativistic jet
National Category
Astronomy, Astrophysics and Cosmology
Identifiers
urn:nbn:se:liu:diva-154054 (URN)10.1051/0004-6361/201834393 (DOI)000456274900002 ()
Note

Funding agencies; Ecole Nationale Superieure de Lyon, Universite de Lyon; French National Program of High Energy (PNHE); French supercomputing facilities GENCI [EP/P02212X/1, A0030406960]

Available from: 2019-01-24 Created: 2019-01-24 Last updated: 2019-02-06Bibliographically approved
Skånberg, R., Linares, M., König, C., Norman, P., Jönsson, D., Hotz, I. & Ynnerman, A. (2018). VIA-MD: Visual Interactive Analysis of Molecular Dynamics. In: Workshop on Molecular Graphics and Visual Analysis of Molecular Data: . Paper presented at Eurographics Workshop on Visual Computing for Biology and Medicine.
Open this publication in new window or tab >>VIA-MD: Visual Interactive Analysis of Molecular Dynamics
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2018 (English)In: Workshop on Molecular Graphics and Visual Analysis of Molecular Data, 2018Conference paper, Published paper (Refereed)
National Category
Media and Communication Technology
Identifiers
urn:nbn:se:liu:diva-160857 (URN)10.2312/molva.20181102 (DOI)978-3-03868-081-9 (ISBN)
Conference
Eurographics Workshop on Visual Computing for Biology and Medicine
Funder
Swedish Research Council, 2014-4646Swedish National Infrastructure for Computing (SNIC)National Supercomputer Centre (NSC), SwedenEU, European Research Council, 621-2014-4646Swedish e‐Science Research Center
Available from: 2019-10-10 Created: 2019-10-10 Last updated: 2019-10-10
Jönsson, D. & Anders, Y. (2017). Correlated Photon Mapping for Interactive Global Illumination of Time-Varying Volumetric Data. IEEE Transactions on Visualization and Computer Graphics, 23(1), 901-910
Open this publication in new window or tab >>Correlated Photon Mapping for Interactive Global Illumination of Time-Varying Volumetric Data
2017 (English)In: IEEE Transactions on Visualization and Computer Graphics, ISSN 1077-2626, E-ISSN 1941-0506, Vol. 23, no 1, p. 901-910Article in journal (Refereed) Published
Abstract [en]

We present a method for interactive global illumination of both static and time-varying volumetric data based on reduction of the overhead associated with re-computation of photon maps. Our method uses the identification of photon traces invariant to changes of visual parameters such as the transfer function (TF), or data changes between time-steps in a 4D volume. This lets us operate on a variant subset of the entire photon distribution. The amount of computation required in the two stages of the photon mapping process, namely tracing and gathering, can thus be reduced to the subset that are affected by a data or visual parameter change. We rely on two different types of information from the original data to identify the regions that have changed. A low resolution uniform grid containing the minimum and maximum data values of the original data is derived for each time step. Similarly, for two consecutive time-steps, a low resolution grid containing the difference between the overlapping data is used. We show that this compact metadata can be combined with the transfer function to identify the regions that have changed. Each photon traverses the low-resolution grid to identify if it can be directly transferred to the next photon distribution state or if it needs to be recomputed. An efficient representation of the photon distribution is presented leading to an order of magnitude improved performance of the raycasting step. The utility of the method is demonstrated in several examples that show visual fidelity, as well as performance. The examples show that visual quality can be retained when the fraction of retraced photons is as low as 40%-50%.

Place, publisher, year, edition, pages
Institute of Electrical and Electronics Engineers (IEEE), 2017
Keywords
Volume rendering, photon mapping, global illumination, participating media
National Category
Media Engineering
Identifiers
urn:nbn:se:liu:diva-131022 (URN)10.1109/TVCG.2016.2598430 (DOI)000395537600093 ()27514045 (PubMedID)2-s2.0-84999158356 (Scopus ID)
Projects
SERCCMIV
Note

Funding Agencies|Swedish e-Science Research Centre (SeRC)||Swedish Research Council (VR) grant 2016-05462||Knut and Alice Wallenberg Foundation (KAW) grant 2016-0076||

Available from: 2016-09-05 Created: 2016-09-05 Last updated: 2017-04-20Bibliographically approved
Bock, A., Axelsson, E., Bladin, K., Jonathas, C., Gene, P., Matthew, T., . . . Ynnerman, A. (2017). OpenSpace: An open-source astrovisualization framework. The Journal of Open Source Software, 2(15), Article ID 281.
Open this publication in new window or tab >>OpenSpace: An open-source astrovisualization framework
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2017 (English)In: The Journal of Open Source Software, ISSN 2475-9066, Vol. 2, no 15, article id 281Article in journal, Editorial material (Refereed) Published
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.

National Category
Human Computer Interaction
Identifiers
urn:nbn:se:liu:diva-158036 (URN)10.21105/joss.00281 (DOI)
Available from: 2019-06-24 Created: 2019-06-24 Last updated: 2019-08-06Bibliographically approved
Jönsson, D., Falk, M. & Ynnerman, A. (2016). Intuitive Exploration of Volumetric Data Using Dynamic Galleries. IEEE Transactions on Visualization and Computer Graphics, 22(1), 896-905
Open this publication in new window or tab >>Intuitive Exploration of Volumetric Data Using Dynamic Galleries
2016 (English)In: IEEE Transactions on Visualization and Computer Graphics, ISSN 1077-2626, E-ISSN 1941-0506, Vol. 22, no 1, p. 896-905Article in journal (Refereed) Published
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.

Place, publisher, year, edition, pages
IEEE COMPUTER SOC, 2016
Keywords
Transfer function; scalar fields; volume rendering; touch interaction; visualization; user interfaces
National Category
Electrical Engineering, Electronic Engineering, Information Engineering
Identifiers
urn:nbn:se:liu:diva-123054 (URN)10.1109/TVCG.2015.2467294 (DOI)000364043400095 ()26390481 (PubMedID)
Note

Funding Agencies|Swedish Research Council, VR [2011-5816]; Excellence Center at Linkoping and Lund in Information Technology (ELLIIT); Linnaeus Environment CADICS; Swedish e-Science Research Centre (SeRC)

Available from: 2015-12-04 Created: 2015-12-03 Last updated: 2017-12-01
Dieckmann, M. E., Sarri, G., Doria, D., Ynnerman, A. & Borghesi, M. (2016). Particle-in-cell simulation study of a lower-hybrid shock. Physics of Plasmas, 23(6), 062111
Open this publication in new window or tab >>Particle-in-cell simulation study of a lower-hybrid shock
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2016 (English)In: Physics of Plasmas, ISSN 1070-664X, E-ISSN 1089-7674, Vol. 23, no 6, p. 062111-Article in journal (Refereed) Published
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.

Place, publisher, year, edition, pages
AMER INST PHYSICS, 2016
National Category
Fusion, Plasma and Space Physics
Identifiers
urn:nbn:se:liu:diva-130440 (URN)10.1063/1.4953568 (DOI)000379172200017 ()
Note

Funding Agencies|EPSRC [EP/N022696/1]

Available from: 2016-08-15 Created: 2016-08-05 Last updated: 2017-11-28
Organisations
Identifiers
ORCID iD: ORCID iD iconorcid.org/0000-0002-9466-9826

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