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Hotz, Ingrid, ProfessorORCID iD iconorcid.org/0000-0001-7285-0483
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Publications (10 of 67) Show all publications
Jankowai, J. & Hotz, I. (2020). Feature Level-Sets: Generalizing Iso-surfaces to Multi-variate Data. IEEE Transactions on Visualization and Computer Graphics, 26(2), 1308-1319
Open this publication in new window or tab >>Feature Level-Sets: Generalizing Iso-surfaces to Multi-variate Data
2020 (English)In: IEEE Transactions on Visualization and Computer Graphics, ISSN 1077-2626, E-ISSN 1941-0506, Vol. 26, no 2, p. 1308-1319Article in journal (Refereed) Published
Abstract [en]

Iso-surfaces or level-sets provide an effective and frequently used means for feature visualization. However, they are restricted to simple features for uni-variate data. The approach does not scale when moving to multi-variate data or when considering more complex feature definitions. In this paper, we introduce the concept of traits and feature level-sets, which can be understood as a generalization of level-sets as it includes iso-surfaces, and fiber surfaces as special cases. The concept is applicable to a large class of traits defined as subsets in attribute space, which can be arbitrary combinations of points, lines, surfaces and volumes.  It is implemented into a system that provides an interface to define traits in an interactive way and multiple rendering options. We demonstrate the effectiveness of the approach using multi-variate data sets of different nature, including vector and tensor data, from different application domains.

Place, publisher, year, edition, pages
Institute of Electrical and Electronics Engineers (IEEE), 2020
National Category
Other Computer and Information Science
Identifiers
urn:nbn:se:liu:diva-151231 (URN)10.1109/TVCG.2018.2867488 (DOI)000506637400003 ()30183637 (PubMedID)2-s2.0-85052841941 (Scopus ID)
Funder
ELLIIT - The Linköping‐Lund Initiative on IT and Mobile Communications
Note

Funding agencies: ELLIIT program; Swedish eScience Research Centre (SeRC)

Available from: 2018-09-13 Created: 2018-09-13 Last updated: 2020-02-03Bibliographically approved
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: 2019-10-29
Engelke, W., Lawonn, K., Preim, B. & Hotz, I. (2019). Autonomous Particles for Interactive Flow Visualization. Paper presented at EuroVis 2018, Conference on Visualization 4-8 June, Czech Republic. Computer graphics forum (Print) (1), 248-259
Open this publication in new window or tab >>Autonomous Particles for Interactive Flow Visualization
2019 (English)In: Computer graphics forum (Print), ISSN 0167-7055, E-ISSN 1467-8659, no 1, p. 248-259Article in journal (Refereed) Published
Abstract [en]

We present an interactive approach to analyse flow fields using a new type of particle system, which is composed of autonomous particles exploring the flow. While particles provide a very intuitive way to visualize flows, it is a challenge to capture the important features with such systems. Particles tend to cluster in regions of low velocity and regions of interest are often sparsely populated. To overcome these disadvantages, we propose an automatic adaption of the particle density with respect to local importance measures. These measures are user defined and the systems sensitivity to them can be adjusted interactively. Together with the particle history, these measures define a probability for particles to multiply or die, respectively. There is no communication between the particles and no neighbourhood information has to be maintained. Thus, the particles can be handled in parallel and support a real‐time investigation of flow fields. To enhance the visualization, the particles' properties and selected field measures are also used to specify the systems rendering parameters, such as colour and size. We demonstrate the effectiveness of our approach on different simulated vector fields from technical and medical applications.

Place, publisher, year, edition, pages
John Wiley & Sons, 2019
Keywords
flow visualization, scientific visualization, visualization, real-time rendering, Visualization Human-centered computing: Visualization application domains–Scientific Visualization
National Category
Computer Sciences
Identifiers
urn:nbn:se:liu:diva-151724 (URN)10.1111/cgf.13528 (DOI)000462660600016 ()
Conference
EuroVis 2018, Conference on Visualization 4-8 June, Czech Republic
Note

Funding agencies: Stiftelsen for Strategisk Forskning Sweden (SSF) [BD15-0082]; Excellence Center at Linkoping and Lund in Information Technology (ELLIIT); Swedish e-Science Research Centre (SeRC)

Available from: 2018-10-03 Created: 2018-10-03 Last updated: 2019-04-18Bibliographically approved
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: 2020-01-03
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
Dieckmann, M. E., Falk, M., Steneteg, P., Folini, D., Hotz, I., Nordman, A., . . . Walder, R. (2019). Structure of a collisionless pair jet in a magnetizedelectron-proton plasma: Flow-aligned magnetic field. In: High Energy Phenomena in Relativistic Outflows VII (HEPRO VII): Formation and propagation of relativistic outflows. Paper presented at High Energy Phenomena in Relativistic Outflows VII (HEPRO VII). Sissa Medialab srl, Article ID 006.
Open this publication in new window or tab >>Structure of a collisionless pair jet in a magnetizedelectron-proton plasma: Flow-aligned magnetic field
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2019 (English)In: High Energy Phenomena in Relativistic Outflows VII (HEPRO VII): Formation and propagation of relativistic outflows, Sissa Medialab srl, 2019, article id 006Conference paper, Published 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.

Place, publisher, year, edition, pages
Sissa Medialab srl: , 2019
Keywords
PIC simulation, collisionless plasma, relativistic jet
National Category
Fusion, Plasma and Space Physics
Identifiers
urn:nbn:se:liu:diva-164075 (URN)10.22323/1.354.0006 (DOI)
Conference
High Energy Phenomena in Relativistic Outflows VII (HEPRO VII)
Available from: 2020-03-04 Created: 2020-03-04 Last updated: 2020-03-11
Jönsson, D., Bergström, A., Algström, I., Simon, R., Engström, M., Walter, S. & Hotz, I. (2019). Visual Analysis for Understanding Irritable Bowel Syndrome. In: Paul Rea (Ed.), Biomedical Visualisation: (pp. 111-122). Cham: Springer
Open this publication in new window or tab >>Visual Analysis for Understanding Irritable Bowel Syndrome
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2019 (English)In: Biomedical Visualisation / [ed] Paul Rea, Cham: Springer, 2019, p. 111-122Chapter in book (Refereed)
Abstract [en]

The cause of irritable bowel syndrome (IBS), a chronic disorder characterized by abdominal pain and disturbed bowel habits, is largely unknown. It is believed to be related to physical properties in the gut, central mechanisms in the brain, psychological factors, or a combination of these. To understand the relationships within the gut-brain axis with respect to IBS, large numbers of measurements ranging from stool samples to functional magnetic resonance imaging are collected from patients with IBS and healthy controls. As such, IBS is a typical example in medical research where research turns into a big data analysis challenge. In this chapter we demonstrate the power of interactive visual data analysis and exploration to generate an environment for scientific reasoning and hypothesis formulation for data from multiple sources with different character. Three case studies are presented to show the utility of the presented work.

Place, publisher, year, edition, pages
Cham: Springer, 2019
Series
Advances in Experimental Medicine and Biology ; 1156
Keywords
Explorative data analytics, Visualization in medicine, Irritable bowel syndrome
National Category
Media and Communication Technology
Identifiers
urn:nbn:se:liu:diva-160859 (URN)10.1007/978-3-030-19385-0_8 (DOI)000514372000009 ()31338781 (PubMedID)9783030193843 (ISBN)9783030193850 (ISBN)
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
Note

Funding agencies:  Knut and Alice Wallenberg Foundation (KAW)Knut & Alice Wallenberg Foundation [2013-0076]; Swedish research councilSwedish Research Council [2015-05462]; SeRC (Swedish e-Science Research Center); ELLIIT environment for strategic research in Sweden

Available from: 2019-10-10 Created: 2019-10-10 Last updated: 2020-03-19Bibliographically approved
Engelke, W. & Hotz, I. (2018). Evolutionary Lines for Flow Visualization. In: Jimmy Johansson and Filip Sadlo and Tobias Schreck (Ed.), EuroVis 2018, 20th EG/VGTC Conference on Visualization, 4-8 June, Brno, Czech Republic: . Paper presented at EuroVis 2018, 20th EG/VGTC Conference on Visualization, 4-8 June, Brno, Czech Republic (pp. 7-11). The Eurographics Association
Open this publication in new window or tab >>Evolutionary Lines for Flow Visualization
2018 (English)In: EuroVis 2018, 20th EG/VGTC Conference on Visualization, 4-8 June, Brno, Czech Republic / [ed] Jimmy Johansson and Filip Sadlo and Tobias Schreck, The Eurographics Association , 2018, p. 7-11Conference paper, Published paper (Refereed)
Abstract [en]

In this work we explore evolutionary algorithms for selected a visualization application. We demonstrate its potential using an example from flow visualization showing promising first results. Evolutionary algorithms, as guided search approach, find close-to-optimal solutions with respect to some fitness function in an iterative process using biologically motivated mechanisms like selection, mutation and recombination. As such, they provide a powerful alternative to filtering methods commonly used in visualization where the space of possible candidates is densely sampled in a pre-processing step from which the best candidates are selected and visualized. This approach however tends to be increasingly inefficient with growing data size or expensive candidate computations resulting in large pre-processing times. We present an evolutionary algorithm for the problem of streamline selection to highlight features of interest in flow data. Our approach directly optimizes the solution candidates with respect to a user selected fitness function requiring significantly less computations. At the same time the problem of possible under-sampling is solved since we are not tied to a preset resolution. We demonstrate our approach on the well-known flow around an obstacle as case with a two-dimensional search space. The blood flow in an aneurysm serves as an example with a three-dimensional search space. For both, the achieved results are comparable to line filtering approaches with much less line computations.

Place, publisher, year, edition, pages
The Eurographics Association, 2018
National Category
Computer Sciences
Identifiers
urn:nbn:se:liu:diva-151725 (URN)10.2312/eurovisshort.20181070 (DOI)9783038680604 (ISBN)
Conference
EuroVis 2018, 20th EG/VGTC Conference on Visualization, 4-8 June, Brno, Czech Republic
Available from: 2018-10-03 Created: 2018-10-03 Last updated: 2018-10-23
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
Gustafsson, T., Engelke, W., Englund, R. & Hotz, I. (2017). Concepts of Hybrid Data Rendering. In: Ingrid Hotz and Martin Falk (Ed.), Proceedings of SIGRAD 2017, August 17-18, 2017 Norrköping, Sweden: . Paper presented at SIGRAD 2017, August 17-18, 2017 Norrköping, Sweden (pp. 32-39). Linköping: Linköping University Electronic Press, 143
Open this publication in new window or tab >>Concepts of Hybrid Data Rendering
2017 (English)In: Proceedings of SIGRAD 2017, August 17-18, 2017 Norrköping, Sweden / [ed] Ingrid Hotz and Martin Falk, Linköping: Linköping University Electronic Press, 2017, Vol. 143, p. 32-39Conference paper, Published paper (Refereed)
Abstract [en]

We present a concept for interactive rendering of multiple data sets of varying type, including geometry and volumetric data, in one scene with correct transparency. Typical visualization applications involve multiple data fields from various sources. A thorough understanding of such data often requires combined rendering of theses fields. The choice of the visualization concepts, and thus the rendering techniques, depends on the context and type of the individual fields. Efficiently combining different techniques in one scene, however, is not always a straightforward task. We tackle this problem by using an A-buffer based approach to gather color and transparency information from different sources, combine them and generate the final output image. Thereby we put special emphasis on efficiency and low memory consumption to allow a smooth exploration of the data. Therefore, we compare different A-buffer implementations with respect to memory consumption and memory access pattern. Additionally we introduce an early-fragment-discarding heuristic using inter-frame information to speed up the rendering..

Place, publisher, year, edition, pages
Linköping: Linköping University Electronic Press, 2017
Series
Linköping Electronic Conference Proceedings, ISSN 1650-3686, E-ISSN 1650-3740 ; 143
Keywords
Hybrid Rendering, A-Buffer, Volume Rendering
National Category
Computer and Information Sciences
Identifiers
urn:nbn:se:liu:diva-143256 (URN)9789176853849 (ISBN)
Conference
SIGRAD 2017, August 17-18, 2017 Norrköping, Sweden
Available from: 2017-11-27 Created: 2017-11-27 Last updated: 2018-04-03Bibliographically approved
Organisations
Identifiers
ORCID iD: ORCID iD iconorcid.org/0000-0001-7285-0483

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