We present ScaleTrotter, a conceptual framework for an interactive, multi-scale visualization of biological mesoscale data and, specifically, genome data. ScaleTrotter allows viewers to smoothly transition from the nucleus of a cell to the atomistic composition of the DNA, while bridging several orders of magnitude in scale. The challenges in creating an interactive visualization of genome data are fundamentally different in several ways from those in other domains like astronomy that require a multi-scale representation as well. First, genome data has intertwined scale levels---the DNA is an extremely long, connected molecule that manifests itself at all scale levels. Second, elements of the DNA do not disappear as one zooms out---instead the scale levels at which they are observed group these elements differently. Third, we have detailed information and thus geometry for the entire dataset and for all scale levels, posing a challenge for interactive visual exploration. Finally, the conceptual scale levels for genome data are close in scale space, requiring us to find ways to visually embed a smaller scale into a coarser one. We address these challenges by creating a new multi-scale visualization concept. We use a scale-dependent camera model that controls the visual embedding of the scales into their respective parents, the rendering of a subset of the scale hierarchy, and the location, size, and scope of the view. In traversing the scales, ScaleTrotter is roaming between 2D and 3D visual representations that are depicted in integrated visuals. We discuss, specifically, how this form of multi-scale visualization follows from the specific characteristics of the genome data and describe its implementation. Finally, we discuss the implications of our work to the general illustrative depiction of multi-scale data.
Also important from Viola and Isenberg's discussion @cite_39 is their concept of , which are traversed in scale space. We also connect the DNA representations at different scales, facilitating a smooth transition between them. In creating this axis of abstraction, we focus primarily on changes of Viola and Isenberg's geometric axis, but without a geometric interpolation of different representations. Instead, we use visual embedding of one scale in another one.
@cite_39
2751478023
Abstract Medial axis as a compact representation of shapes has evolved as an essential geometric structure in a number of applications involving 3D geometric shapes. Since exact computation of the medial axis is difficult in general, efforts continue to approximate them. One line of research considers the point cloud representation of the boundary surface of a solid and then attempts to compute an approximate medial axis from this point sample. It is known that the Voronoi vertices converge to the medial axis for a curve in 2D as the sample density approaches infinity. Unfortunately, the same is not true in 3D. Recently, it is discovered that a subset of Voronoi vertices called poles converge to the medial axis in 3D. However, in practice, a continuous approximation as opposed to a discrete one is sought. Recently few algorithms have been proposed which use the Voronoi diagram and its derivatives to compute this continuous approximation. These algorithms are scale or density dependent. Most of them do not have convergence guarantees, and one of them computes it indirectly from the power diagram of the poles. Recently, we proposed a new algorithm that approximates the medial axis straight from the Voronoi diagram in a scale and density independent manner with convergence guarantees. In this paper, we present several experimental results with this algorithm that support our theoretical claims and also show its effectiveness on practical data sets. Abstract We provide a high-level survey of multiscale molecular visualization techniques, with a focus on application-domain questions, challenges, and tasks. We provide a general introduction to molecular visualization basics and describe a number of domain-specific tasks that drive this work. These tasks, in turn, serve as the general structure of the following survey. First, we discuss methods that support the visual analysis of molecular dynamics simulations. We discuss, in particular, visual abstraction and temporal aggregation. In the second part, we survey multiscale approaches that support the design, analysis, and manipulation of DNA nanostructures and related concepts for abstraction, scale transition, scale-dependent modeling, and navigation of the resulting abstraction spaces. In the third part of the survey, we showcase approaches that support interactive exploration within large structural biology assemblies up to the size of bacterial cells. We describe fundamental rendering techniques as well as approaches for element instantiation, visibility management, visual guidance, camera control, and support of depth perception. We close the survey with a brief listing of important tools that implement many of the discussed approaches and a conclusion that provides some research challenges in the field. We introduce the scale axis transform, a new skelet al shape representation for bounded open sets O ⊂ Rd. The scale axis transform induces a family of skeletons that captures the important features of a shape in a scale-adaptive way and yields a hierarchy of successively simplified skeletons. Its definition is based on the medial axis transform and the simplification of the shape under multiplicative scaling: the s-scaled shape Os is the union of the medial balls of O with radii scaled by a factor of s. The s-scale axis transform of O is the medial axis transform of Os, with radii scaled back by a factor of 1 s. We prove topological properties of the scale axis transform and we describe the evolution s → Os by defining the multiplicative distance function to the shape and studying properties of the corresponding steepest ascent flow. All our theoretical results hold for any dimension. In addition, using a discrete approximation, we present several examples of two-dimensional scale axis transforms that illustrate the practical relevance of our new framework. Three-dimensional geometric data play fundamental roles in many computer vision applications. However, their scale-dependent nature, i.e. the relative variation in the spatial extents of local geometric structures, is often overlooked. In this paper we present a comprehensive framework for exploiting this 3D geometric scale variability. Specifically, we focus on detecting scale-dependent geometric features on triangular mesh models of arbitrary topology. The key idea of our approach is to analyze the geometric scale variability of a given 3D model in the scale-space of a dense and regular 2D representation of its surface geometry encoded by the surface normals. We derive novel corner and edge detectors, as well as an automatic scale selection method, that acts upon this representation to detect salient geometric features and determine their intrinsic scales. We evaluate the effectiveness and robustness of our method on a number of models of different topology. The results show that the resulting scale-dependent geometric feature set provides a reliable basis for constructing a rich but concise representation of the geometric structure at hand.