Biomedical subjects
Publications and source records attributed to Jarke J van Wijk.
The software package DNAVis offers a fast, interactive and real-time visualization of DNA sequences and their comparative genome annotations. DNAVis implements advanced methods of information visualization such as linked views, perspective walls and semantic zooming, in addition to the display of heterologous data in dot plot-like matrix views.
We present a side-by-side analysis of two recent image space approaches for the visualization of vector fields on surfaces. The two methods, Image Space Advection (ISA) and Image-Based Flow Visualization for Curved Surfaces (IBFVS) generate dense representations of time-dependent vector fields with high spatio-temporal correlation. While the 3D vector fields are associated with arbitrary surfaces represented by triangular meshes, the generation and advection of texture properties is confined to image space. Fast frame rates are achieved by exploiting frame-to-frame coherency and graphics hardware. In our comparison of ISA and IBFVS, we point out the strengths and weaknesses of each approach and give recommendations as to when and where they are best applied.
We present a new approach for the visual analysis of state transition graphs. We deal with multivariate graphs where a number of attributes are associated with every node. Our method provides an interactive attribute-based clustering facility. Clustering results in metric, hierarchical and relational data, represented in a single visualization. To visualize hierarchically structured quantitative data, we introduce a novel technique: the bar tree. We combine this with a node-link diagram to visualize the hierarchy and an arc diagram to visualize relational data. Our method enables the user to gain significant insight into large state transition graphs containing tens of thousands of nodes. We illustrate the effectiveness of our approach by applying it to a real-world use case. The graph we consider models the behavior of an industrial wafer stepper and contains 55 043 nodes and 289 443 edges.
Business data is often presented using simple business graphics. These familiar visualizations are effective for providing overviews, but fall short for the presentation of large amounts of detailed information. Treemaps can provide such detail, but are often not easy to understand. We present how standard treemap algorithms can be adapted such that the results mimic familiar business graphics. Specifically, we present the use of different layout algorithms per level, a number of variations of the squarified algorithm, the use of variable borders, and the use of non-rectangular shapes. The combined use of these leads to histograms, pie charts and a variety of other styles.
The field of visualization is maturing. Many problems have been solved and new directions are sought. In order to make good choices, an understanding of the purpose and meaning of visualization is needed. In this paper, visualization is considered from multiple points of view. First, a technological viewpoint is adopted, where the value of visualization is measured based on effectiveness and efficiency. An economic model of visualization is presented and benefits and costs are established. Next, consequences and limitations of visualization are discussed (including the use of alternative methods, high initial costs, subjectiveness, and the role of interaction). Example uses of the model for the judgment of existing classes of methods are given to understand why they are or are not used in practice. However, such an economic view is too restrictive. Alternative views on visualization are presented and discussed: visualization as an art, visualization as design and, finally, visualization as a scientific discipline.
The genus of a knot or link can be defined via Seifert surfaces. A Seifert surface of a knot or link is an oriented surface whose boundary coincides with that knot or link. Schematic images of these surfaces are shown in every text book on knot theory, but from these it is hard to understand their shape and structure. In this paper, the visualization of such surfaces is discussed. A method is presented to produce different styles of surface for knots and links, starting from the so-called braid representation. Application of Seifert's algorithm leads to depictions that show the structure of the knot and the surface, while successive relaxation via a physically based model gives shapes that are natural and resemble the familiar representations of knots. Also, we present how to generate closed oriented surfaces in which the knot is embedded, such that the knot subdivides the surface into two parts. These closed surfaces provide a direct visualization of the genus of a knot. All methods have been integrated in a freely available tool, called SeifertView, which can be used for educational and presentation purposes.