van Robert Liere

GraphSplatting: visualizing graphs as continuous fields

This paper introduces GraphSplatting, a technique which transforms a graph into a two-dimensional scalar field. The scalar field can be rendered as a color coded map, a height field, or a set of contours. Splat fields allow for the visualization of arbitrarily large graphs without cluttering. They provide density information which can be used to determine the structure of the graph. The construction, visualization, and interaction with splat fields is discussed. Two applications illustrate the usage of GraphSplatting.

Four-dimensional imaging of chromatin dynamics during the assembly of the interphase nucleus.

Large-scale chromatin organization is likely to play an important role in epigenetic control of gene expression. This implies that after mitosis the correct chromatin organization must be re-established in the nuclei of the two daughter cells. Here we analyze the dynamic behavior of chromatin during the transition from late anaphase to G1 in dividing HeLa cells, which express green fluorescent protein-tagged histone H2B. Time-lapse confocal microscopy was used to image the movement and the decondensation of chromatin as cell division progresses. Typically, time series of over 100 three-dimensional images (4D images) were collected, spanning a time period of up to three hours. Special care was taken to avoid photodamage, since cell cycle progression is exquisitely sensitive to photochemical damage. Quantitative analysis of the 4D images revealed that during the anaphase to G1 transition the movement of chromatin domains relative to other chromatin is remarkably limited. Chromatin dynamics can best be described as a radial expansion of the cluster of chromosomes that is present in late anaphase. We find that decondensation occurs in two phases. First a rapid decondensation by about a factor of two, followed by a slower phase in which part of the chromatin does not decondense any further, whereas the remaining chromatin decondenses further about two fold.

Optical tracking using projective invariant marker pattern properties

We describe a novel optical tracker algorithm for the tracking of interaction devices in virtual and augmented reality. The tracker uses invariant properties of marker patterns to efficiently identify and reconstruct the pose of these interaction devices. Since invariant properties are sensitive to noise in the 2D marker positions, an offline training session is used to determine deviations in these properties. These deviations are taken into account when searching for the patterns once the tracker is used.

An analysis of orientation prediction and filtering methods for VR/AR

To enable a user to perform virtual reality tasks as efficiently as possible, reducing tracking inaccuracies from noise and latency is crucial. Much work has been done to improve tracking performance by using predictive filtering methods. However, it is unclear what the benefits of each of these methods are in practice, which parameters influence their performance, and what the extent of this influence is. We present an analysis of various orientation prediction and filtering methods using various hand tasks and synthetic signals, and evaluate their performance in relation to each other. We identify critical parameters and analyse their influence on accuracy. Our results show that for the tested datasets, the use of an EKF is sufficient for orientation prediction in VR/AR.

Enhancing fish tank VR

Fish tank VR systems provide head coupled perspective projected stereo images on a display device of limited dimensions that resides at a fixed location. Therefore, fish tank VR systems provide only a limited virtual workspace. As a result, such systems are less suited for displaying virtual worlds that extend beyond the available workspace and depth perception problems arise when displaying objects (virtually) located on the edge of the workspace in between the viewer and the display screen. In this paper we present two techniques to reduce this disadvantage: cadre viewing and amplified head rotations. The first aims to eliminate the problems in depth perception for objects with negative parallax touching the screen surround. Subjective observations from an informal user study indicate a reduction of confusion in depth perception. The second provides a transparent navigation technique to allow users to view larger portions of the virtual world without the need for an additional input device to navigate. A user study shows it performs equally well when compared to a technique based on the use of an additional spatial input device.

Co-location and tactile feedback for 2D widget manipulation

This study investigated the effect of co-location and tactile feedback on 2D widget manipulation tasks in virtual environments. Task completion time and positioning accuracy during each task were measured for subjects under 4 situations (co-located vs no co-located and tactile feedback vs no tactile feedback). Performance results indicate that co-location and tactile feedback both significantly improve the performance of 2D widget manipulation in 3D virtual environments. Subjective results support these findings.

Three extensions to subtractive crosstalk reduction

Stereo displays suffer from crosstalk, an effect that reduces or even inhibits the viewers ability to correctly fuse stereoscopic images. In this paper, three extensions for improved software crosstalk reduction are introduced. First, we propose a reduction method operating in CIELAB color space to find a perceptually better color match for crosstalk corrected pixels. Second, we introduce a geometry-based reduction method that operates on fused 3D pixels. Finally, a run-time optimization is introduced that avoids the need to process each pixel. We evaluated our CIELAB-based method using the Visible Differences Predictor (VDP). Our results show that we are able to significantly improve crosstalk reduction compared to previously used methods that operate in RGB color space. The combination of our methods provides an improved, real-time software crosstalk reduction framework, applicable to a wider range of scenes, delivering better quality, higher performance, and more flexibility.

Interacting with molecular structures: user performance versus system complexity

Effective interaction in a virtual environment requires that the user can adequately judge the spatial relationships between the objects in a 3D scene. In order to accomplish adequate depth perception, existing virtual environments create useful perceptual cues through stereoscopy, motion parallax and (active or passive) haptic feedback. Specific hardware, such as high-end monitors with stereoscopic glasses, head-mounted tracking and mirrors are required to accomplish this. Many potential VR users however refuse to wear cumbersome devices and to adjust to an imposed work environment, especially for longer periods of time. It is therefore important to quantify the repercussions of dropping one or more of the above technologies. These repercussions are likely to depend on the application area, so that comparisons should be performed on tasks that are important and/or occur frequently in the application field of interest. In this paper, we report on a formal experiment in which the effects of different hardware components on the speed and accuracy of three-dimensional (3D) interaction tasks are established. The tasks that have been selected for the experiment are inspired by interactions and complexities, as they typically occur when exploring molecular structures. From the experimental data, we develop linear regression models to predict the speed and accuracy of the interaction tasks. Our findings show that hardware supported depth cues have a significant positive effect on task speed and accuracy, while software supported depth cues, such as shadows and perspective cues, have a negative effect on trial time. The task trial times are smaller in a simple fish-tank like desktop environment than in a more complex co-location enabled environment, sometimes at the cost of reduced accuracy.

The design and implementation of a VR-architecture for smooth motion

We introduce an architecture for smooth motion in virtual environments. The system performs forward depth image warping to produce images at video refresh rates. In addition to color and depth, our 3D warping approach records per-pixel motion information during rendering of the three-dimensional scene. These enhanced depth images are used to perform per-pixel advection, which considers object motion and view changes. Our dual graphics card architecture is able to render the 3D scene at the highest possible frame rate on one graphics card, while doing the depth image warping on a second graphics engine at video refresh rate. This architecture allows us to compensate for visual artifacts, also called motion judder, arising when the rendering frame rate is lower than the video refresh rate. The evaluation of our method shows motion judder can be effectively removed.

Chromatin decondensation: a case study of tracking features in confocal data

In this case study we discuss an interactive feature tracking system and its use for the analysis of chromatin decondensation. Features are described as points in a multidimensional attribute space. Distances between points are used as a measure for feature correspondence. Users can interactively experiment with the correspondence measure in order to gain insight in chromatin movement. In addition, by defining time as an attribute, tracking problems related to noisy confocal data can be circumvented.In this case study we discuss an interactive feature tracking system and its use for the analysis of chromatin decondensation. Features are described as points in a multidimensional attribute space. Distances between points are used as a measure for feature correspondence. Users can interactively experiment with the correspondence measure in order to gain insight in chromatin movement. In addition, by defining time as an attribute, tracking problems related to noisy confocal data can be circumvented.