Anders Ynnerman

• Professor
• Professor (Full) at Linköping University

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...

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...

Common reporting styles of statistical results, such as confidence intervals (CI), are prone to dichotomous interpretations especially on null hypothesis testing frameworks, for example by claiming significant differences between drug treatment and placebo groups due to the non-overlapping CIs of the mean effects, while disregarding the magnitudes...

This paper presents an empirical study on the weights of neural networks, where we interpret each model as a point in a high-dimensional space -- the neural weight space. To explore the complex structure of this space, we sample from a diverse selection of training variations (dataset, optimization procedure, architecture, etc.) of neural network c...

The complexity of today's 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 instance by providing a data flow network editor. Unfortunately, these abstractions result in sever...

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 inj...

The 2018 Visualization Technical Achievement Award goes to Anders Ynnerman for his contributions to medical visualization resulting in the development of virtual autopsies, which have had extraordinary impact in both in medicine and in communication of science to the public. The IEEE Visualization & Graphics Technical Committee (VGTC) is pleased to...

The complexity of today's 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 instance by providing a data flow network editor. Unfortunately, these abstractions result in sever...

We study the effect a guiding magnetic field has on the structure of a pair jet that propagates through a collisionless electron-proton plasma. We model with a PIC simulation a pair cloud with the temperature 400 keV and mean speed 0.9c. The cloud propagates through a spatially uniform, magnetized and cool ambient electron-proton plasma that is at...

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 histolog...

Using the example of interactive exploration of the beating heart, the authors demonstrate how data exploration and analysis can be further improved by adding haptics. This combination of sensory information input leads to the notion of visuo-haptic visualization.

Science communication is facing a paradigm shift, based on the convergence of exploratory and explanatory visualization. In this article, we coin the term exploranation to denote the way in which visualization methods from scientific exploration can be used to communicate results and how methods in explanatory visualization can enrich exploration.

We present the development of an open-source software called OpenSpace that bridges the gap between scientific discoveries and public dissemination and thus paves the way for the next generation of science communication and data exploration. We describe how the platform enables interactive presentations of dynamic and time-varying processes by doma...

A very stable binding site for the interaction between an pentameric oligothiophene and an amyloid-β(1–42) fibril has been identified by means of non-biased molecular dynamics simulations. In this site, the probe is locked in an all-trans conformation with a Coulombic binding energy of 1,200 kJ/mol due to the interactions between the anionic carbox...

Results of planetary mapping are often shared openly for use in scientific research and mission planning. In its raw format, however, the data is not accessible to non-experts due to the difficulty in grasping the context and the intricate acquisition process. We present work on tailoring and integration of multiple data processing and visualizatio...

The expansion of a dense plasma into a dilute plasma across an initially uniform perpendicular magnetic field is followed with a one-dimensional particle-in-cell (PIC) simulation over MHD time scales. The dense plasma expands in the form of a fast rarefaction wave. The accelerated dilute plasma becomes separated from the dense plasma by a tangentia...

The expansion of a dense plasma into a dilute plasma across an initially uniform perpendicular magnetic field is followed with a one-dimensional particle-in-cell (PIC) simulation over MHD time scales. The dense plasma expands in the form of a fast rarefaction wave. The accelerated dilute plasma becomes separated from the dense plasma by a tangentia...

In this work, we address the challenge of seamlessly visualizing astronomical data exhibiting huge scale differences in distance, size, and resolution. One of the difficulties is accurate, fast, and dynamic positioning and navigation to enable scaling over orders of magnitude, far beyond the precision of floating point arithmetic. To this end we pr...

BY COMBINING VISUALIZATION techniques with interactive multi-touch tables and intuitive user interfaces, visitors to museums and science centers can conduct self-guided tours of large volumetric image data. In an interactive learning experience, visitors become the explorers of otherwise invisible interiors of unique artifacts and subjects. Here, w...

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 plasma's expansion direction and binary collisions between particles are absent. The expanding plasma steepens into a quasi-electrostatic shock that is sustained by...

A central topic in scientific visualization is the transfer function (TF) for volume rendering. The TF serves a fundamental role in translating scalar and multivariate data into color and opacity to express and reveal the relevant features present in the data studied. Beyond this core functionality, TFs also serve as a tool for encoding and utilizi...

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-eff...

In this paper, we present a novel visualization approach for the quantitative analysis of knee movement patterns in time-varying data sets. The presented approach has been developed for the analysis of patellofemoral instability, which is a common knee problem, caused by the abnormal movement of the patella (kneecap). Manual kinematic parameter cal...

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...

We present an open-source software development effort called OpenSpace that is tailored for the dissemination of space-related data visualization. In the current stages of the project, we have focussed on the public dissemination of space missions (Rosetta and New Horizons) as well as the support of space weather forecasting. The presented work wil...

We propose a system to analyze and contextualize simulations of coronal mass ejections. As current simulation techniques require manual input, uncertainty is introduced into the simulation pipeline leading to inaccurate predictions that can be mitigated through ensemble simulations. We provide the space weather analyst with a multi-view system prov...

This work presents a visualization system and its application to space missions. The system allows the public to disseminate the scientific findings of space craft and gain a greater understanding thereof. Instruments' field-of-views and their measurements are embedded in an accurate 3 dimensional rendering of the solar system to provide context to...

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 th...

The thin-shell instability has been named as one process, which can generate entangled structures in astrophysical plasma on collisional (fluid) scales. It is driven by a spatially varying imbalance between the ram pressure of the inflowing upstream plasma and the downstream's thermal pressure at a non-planar shock. Here we show by means of a parti...

In this position paper we discuss the usage of various interaction technologies with focus on the presentations of 3D visualizations involving a presenter and an audience. While an interaction technique is commonly evaluated from a user perspective, we want to shift the focus from a sole analysis of the naturalness and the ease-of-use for the user,...

A pair of curved shocks in a collisionless plasma is examined with a two-dimensional particle-in-cell (PIC) simulation. The shocks are created by the collision of two electron-ion clouds at a speed that exceeds everywhere the threshold speed for shock formation. A variation of the collision speed along the initially planar collision boundary, which...

In visualization, the combined role of data reconstruction and its classification plays a crucial role. In this paper we propose a novel approach that improves classification of different materials and their boundaries by combining information from the classifiers at the reconstruction stage. Our approach estimates the targeted materials’ local sup...

TBA

Supporting the growing field of space weather forecasting, we pro- pose a framework to analyze ensemble simulations of coronal mass ejections. As the current simulation technique requires manual in- put, uncertainty is introduced into the simulation pipeline leading to inaccurate predictions. Using our system, the analyst can compare ensemble membe...

In this chapter, we consider the need in multifield visualization to depict information contained in two or more fields in a compositional manner. There are many different visual channels, some of which are more commonly seen in visualization than others. Channel fusion occurs when two or more visual entities have to share the same screen space. By...

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 vol...

The purpose of this work is to investigate, and improve, the feasibility of advanced Region Of Interest (ROI) selection schemes in clinical volume rendering. In particular, this work implements and evaluates an Automated Anatomical ROI (AA-ROI) approach based on the combination of automatic image registration (AIR) and Distance-Based Transfer Funct...

Molecular visualization is often challenged with rendering of large molecular structures in real time. We introduce a novel approach that enables us to show even large protein complexes. Our method is based on the level-of-detail concept, where we exploit three different abstractions combined in one visualization. Firstly, molecular surface abstrac...

We propose an approach for verification of volume rendering correctness based on an analysis of the volume rendering integral, the basis of most DVR algorithms. With respect to the most common discretization of this continuous model (Riemann summation), we make assumptions about the impact of parameter changes on the rendered results and derive con...

Graphical abstract In this paper, we present a novel image based framework capturing and rendering with the lighting found in real world scenes. The framework is based on recent developments in HDR video capture, enabling efficient capture of the full dimensionality of the illumination in large environments exhibiting both complex spatial and angul...

Interactive volume rendering in its standard formulation has become an increasingly important tool in many application domains. In recent years several advanced volumetric illumination techniques to be used in interactive scenarios have been proposed. These techniques claim to have perceptual benefits as well as being capable of producing more real...

One of the most successful approaches to modern high quality HDR-video capture is to use camera setups with multiple sensors imaging the scene through a common optical system. However, such systems pose several challenges for HDR reconstruction algorithms. Previous reconstruction techniques have considered debayering, denoising, resampling (align-...

Diffusion Tensor Imaging (DTI) in combination with fiber tracking algorithms enables visualization and characterization of white matter structures in the brain. However, the low spatial resolution associated with the inherently low signal-to-noise ratio of DTI has raised concerns regarding the reliability of the obtained fiber bundles. Therefore, r...

The study of human activity in space and time is an inherent part of human geography. In order to perform such studies, data on the time use of individuals, in terms of sequence and timing of performed activities, are collected and analysed. A common assumption when analysing individuals' time use is that groups that exhibit similar background and...

We present a new method for sampling the volume rendering integral in volume raycasting where samples are correlated based on transfer function content and data set values. This has two major advantages. First, visual artifacts stemming from structured noise, such as wood grain, can be reduced. Second, we will show that the volume data does no long...

In this paper we present novel algorithms and data structures for capturing, processing and rendering with real world lighting conditions based on high dynamic range video sequences. Based on the captured HDR video data we show how traditional image based lighting can be extended to include illumination variations in both the temporal as well as th...

In this paper, we enable interactive volumetric global illumination by extending photon mapping techniques to handle interactive transfer function (TF) and material editing in the context of volume rendering. We propose novel algorithms and data structures for finding and evaluating parts of a scene affected by these parameter changes, and thus sup...

Protoyping the visualization of heliospheric models using volumetric rendering

In this paper, we first give a high-level overview of medical visualization development over the past 30 years, focusing on key developments and the trends that they represent. During this discussion, we will refer to a number of key papers that we have also arranged on the medical visualization research timeline. Based on the overview and our obse...

Lundström C, Persson A, Ross S, Ljung P, Lindholm S, Gyllensvärd F, Ynnerman A. State-of-the-art of visualization in post-mortem imaging. APMIS 2012; 120: 316–26. Autopsies constitute a valuable feedback to the healthcare chain to achieve improvements in quality of care and cost effectiveness. This review describes post-mortem imaging, which has em...

This article presents two new parametric models of the Bidirectional Reflectance Distribution Function (BRDF), one inspired by the Rayleigh-Rice theory for light scattering from optically smooth surfaces, and one inspired by micro-facet theory. The models represent scattering from a wide range of glossy surface types with high accuracy. In particul...

The expansion of an initially unmagnetized planar rarefaction wave has recently been shown to trigger a thermal anisotropy-driven Weibel instability (TAWI), which can generate magnetic fields from noise levels. It is examined here if the TAWI can also grow in a curved rarefaction wave. The expansion of an initially unmagnetized circular plasma clou...

A major challenge when designing general purpose graphics hardware is to allow efficient access to texture data. Although different rendering paradigms vary with respect to their data access patterns, there is no flexibility when it comes to data caching provided by the graphics architecture. In this paper we focus on volume ray-casting, and show t...

Kinetic modeling is the tool of choice when developing new positron emission tomography (PET) tracers for quantitative functional analysis. Several approaches are widely used to facilitate this process. While all these approaches are inherently different, they are still subject to uncertainty arising from various stages of the modeling process. In...

Kinetic modeling is the tool of choice when developing new positron emission tomography (PET) tracers for quantitative functional analysis. Several approaches are widely used to facilitate this process. While all these approaches are inherently different, they are still subject to uncertainty arising from various stages of the modeling process. In...

Medical imaging plays a central role in a vast range of healthcare practices. The usefulness of 3D visualizations has been demonstrated for many types of treatment planning. Nevertheless, full access to 3D renderings outside of the radiology department is still scarce even for many image-centric specialties. Our work stems from the hypothesis that...

In recent years, many volumetric illumination models have been proposed, which have the potential to simulate advanced lighting effects and thus support improved image comprehension. Although volume ray-casting is widely accepted as the volume rendering technique which achieves the highest image quality, so far no volumetric illumination algorithm...

Understanding and explaining perception of touch is a non-trivial task. Even seemingly trivial differences in exploration may potentially have a significant impact on perception and levels of discrimination. In this study, we explore different aspects of contact related to stiffness perception and their effects on the just noticeable difference (JN...

The expansion of a dense plasma through a more rarefied ionized medium has been studied by means of two-dimensional particle-in-cell simulations. The initial conditions involve a density jump by a factor of 100, located in the middle of an otherwise equally dense electron-proton plasma with uniform proton and electron temperatures of 10 eV and 1 ke...

The parameter estimation variance of the Single Point Active Alignment Method (SPAAM) is studied through an experiment where 11 subjects are instructed to create alignments using an Optical See-Through Head Mounted Display (OSTHMD) such that three separate correspondence point distributions are acquired. Modeling the OSTHMD and the subject's domina...

We present an algorithm that enables real-time dynamic shading in direct volume rendering using general lighting, including directional lights, point lights, and environment maps. Real-time performance is achieved by encoding local and global volumetric visibility using spherical harmonic (SH) basis functions stored in an efficient multiresolution...

In many applications of Direct Volume Rendering (DVR) the importance of a certain material or feature is highly dependent on its relative spatial location. For instance, in the medical diagnostic procedure, the patient's symptoms often lead to specification of features, tissues and organs of particular interest. One such example is pockets of gas w...

A common computer vision task is navigation and mapping. Many indoor navigation tasks require depth knowledge of flat, unstructured surfaces (walls, floor, ceiling). With passive illumination only, this is an ill-posed problem. Inspired by small children using a torchlight, we use a spotlight for active illumination. Using our torchlight approach,...

The correct spatial registration between virtual and real objects in optical see-through augmented reality implies accurate estimates of the user's eyepoint relative to the location and orientation of the display surface. A common approach is to estimate the display parameters through a calibration procedure involving a subjective alignment exercis...

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

We present the first step towards a brain computer interface (BCI) for communication using real-time functional magnetic resonance imaging (fMRI). The subject in the MR scanner sees a virtual keyboard and steers a cursor to select different letters that can be combined to create words. The cursor is moved to the left by activating the left hand, to...

In this paper we study the comprehensive effects on volume rendered images due to numerical errors caused by the use of finite precision for data representation and processing. To estimate actual error behavior we conduct a thorough study using a volume renderer implemented with arbitrary floating-point precision. Based on the experimental data we...

We present a novel approach to interactive and concurrent volume visualization of functional Magnetic Resonance Imaging (fMRI). While the patient is in the scanner, data is extracted in real-time using state-of-the-art signal processing techniques. The fMRI signal is treated as light emission when rendering a patient-specific high resolution refere...

There are numerous advantages described of how imaging technology can support forensic examinations. However, postmortem examinations of bodies are mainly performed to address demands which differ from those of traditional clinical image processing. This needs to be kept in mind when gathering information from image data sets for forensic purposes....

We present a method for controlling a dynamical system using real-time fMRI. The objective for the subject in the MR scanner is to balance an inverted pendulum by activating the left or right hand or resting. The brain activity is classified each second by a neural network and the classification is sent to a pendulum simulator to change the force a...

Multiple-volume visualization is a growing field in medical imaging providing simultaneous exploration of volumes acquired from varying modalities. However, high complexity results in an increased strain on performance compared to single volume rendering as scenes may consist of volumes with arbitrary orientations and rendering is performed with va...

This paper presents a method for resampling a sequence of high dynamic range light probe images into a representation of Incident Light Field (ILF) illumination which enables realtime rendering. The light probe sequences are captured at varying positions in a real world environment using a high dynamic range video camera pointed at a mirror sphere....

This paper introduces Vector Field Perpendicular Surfaces as a means to represent vector data with special focus on variations across the vectors in the field. These surfaces are a perpendicular analogue to streamlines, with the vector data always being parallel to the normals of the surface. In this way the orientation of the data is conveyed to t...

The J = 0 → J' = 0 radiative transitions, usually viewed as allowed through two-photon decay, may also be induced by the hyperfine (HPF) interaction in atoms or ions having a nonzero nuclear spin. We compute new and review existing decay rates for the nsnp3PoJ → ns21SJ'=0 transitions in ions of the Be (n = 2) and Mg (n = 3) isoelectronic sequences....

In this paper we present a history dependent transfer function (HDTF) as a possible approach to enable improved haptic feature detection in high dynamic range (HDR) volume data. The HDTF is a multi-dimensional transfer function that uses the recent force history as a selection criterion to switch between transfer functions, thereby adapting to the...

Despite the enormous complexity of the human mind, fMRI techniques are able to partially observe the state of a brain in action. In this paper we describe an experimental setup for real-time fMRI in a bio-feedback loop. One of the main challenges in the project is to reach a detection speed, accuracy and spatial resolution necessary to attain suffi...

This paper presents methods for photo-realistic rendering using strongly spatially variant illumination captured from real scenes. The illumination is captured along arbitrary paths in space using a high dynamic range, HDR, video camera system with position tracking. Light samples are rearranged into 4-D incident light fields (ILF) suitable for dir...

Work on the construction site is known to be inefficient due to workers spending much time waiting for materials, transporting materials and from frequent interruptions of tasks. Studies on the construction site typically use statistical measures to analyse the sampled data about work and such measures, while very useful, can overlook important fea...

In this paper we present novel means to communicate and present gained knowledge using semi-guided interactive visualizations embedded in standard HTML documents. The goal of the work is to let the analyst (author) explore data and simultaneously save important discoveries and thus enable collaboration and sharing of gained insights over the Intern...

The three papers in this special section are extended versions of three papers from the Ninth Eurographics/IEEE VGTC Symposium on Visualization (EuroVis '07), held in Norrkoping, Sweden, May 23-25, 2007. The papers are summarized here.

Recently the constraint approach to proxy-based volume haptics was introduced which provided a stable and eec- tive means of conveying information about volumetric data through a haptic instrument. In this paper we present a proof that the approach is incapable of handling non- orthogonal constraints and discuss the implications of this restriction...

Within the molecular life sciences extensive use is made of visual representations, ranging from sketches to advanced computer graphics, often used to convey abstract knowledge that is difficult for the student to grasp. This work evaluates a new visual and haptic (tactile/kinetic) tool for protein docking in an in situ learning situation by combin...