Visualization Multi-Pipeline for Communicating Biology

Mindek, Peter; Kouril, David; Sorger, Johannes; Toloudis, Daniel; Lyons, Blair; Johnson, Graham; Gröller, M. Eduard; Viola, Ivan

doi:10.1109/tvcg.2017.2744518

Cited by 17 publications

(19 citation statements)

References 23 publications

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“…For our proof-of-concept implementation we build on the molecular visualization functionality provided in the Marion framework [40]. We added to this framework the capability to load the previously described GSS data.…”

Section: Realizing Visual Scale Embeddingmentioning

confidence: 99%

Scale Trotter: Illustrative Visual Travels Across Negative Scales

Halladjian

Miao

Kouril

et al. 2020

IEEE Trans. Visual. Comput. Graphics

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NucleusChromosomes Chromosomes with detail Nucleosomes Nucleotides Atoms Fibers Fig. 1. Steps along the voyage into the genomic detail as enabled by ScaleTrotter, showing the semantic scale levels. ScaleTrotter and its visual embedding allow us to seamlessly transition between independent representations and interactively explore them.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.

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Section: Realizing Visual Scale Embeddingmentioning

confidence: 99%

Scale Trotter: Illustrative Visual Travels Across Negative Scales

Halladjian

Miao

Kouril

et al. 2020

IEEE Trans. Visual. Comput. Graphics

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“…With the recipe and a packing algorithm cellPACK generates comprehensive 3D models of cell-scale structures in molecular detail. CellVIEW has also been implemented as a plug-in in the Marion [82] rendering framework.…”

Section: Vmd -Visual Molecular Dynamicsmentioning

confidence: 99%

Multiscale Molecular Visualization

Miao

Klein

Kouril

et al. 2019

Journal of Molecular Biology

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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.

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“…In this paper, we utilize a framework called Marion [30], which incorporates a multi-pipeline approach for communicating biology. We have incorporated many essential effects to enhance the perception of the visualized structures, such as ambient occlusion, halos, depth of field, fog, and a variant of the chameleon coloring approach.…”

Section: Related Workmentioning

confidence: 99%