ScaleTrotter: Illustrative Visual Travels Across Negative Scales

TL;DR

ScaleTrotter tackles visualizing genomic data across a negative-exponent scale-space spanning $4-5$ orders of magnitude, from the nucleus to atoms, where conceptual levels are densely packed and physically connected. The authors introduce visual embedding and a scale-dependent camera to render a context-rich subset of the hierarchy while smoothly traversing scales in integrated 2D/3D visuals. Implementation leverages the Marion framework with GPU instancing and SSAO to realize scale embeddings and controlled data scope, with feedback from illustrators and domain scientists supporting its usefulness. The work illuminates a path toward interactive, illustrative genome depictions suitable for teaching and exploratory research, while outlining data and performance limitations and future directions.

Abstract

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.

Figures (9)

• Figure 1: Multi-scale visualization in astronomy vs. genomics. The size difference between celestial bodies is extremely large (e. g., sun vs. earth---the earth is almost invisible at that scale). The distance between earth and moon is also large, compared to their sizes. In the genome, we have similar relative size differences, yet molecules are densely packed as exemplified by the two base pairs in the DNA double helix.
• Figure 2: https://commons.wikimedia.org/wiki/Gray's_Anatomy_platesGray:1918:AHB, demonstrate layered composition of multi-scale 3D objects by traditional illustrators. The images are in the public domain .
• Figure 3: Visual embedding, schematic principle.
• Figure 4: Two snapshots of scale transition views, \ref{['fig:canvas:a']} between the chromosome and the detailed chromosome scales, as well as \ref{['fig:canvas:b']} between nucleotides and detailed nucleotides scales.
• Figure 5: Sequence of visual scale embeddings, based on the data levels.