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.