An outlook into ultra-scale visualization of large-scale biological data

Samatova, Nagiza F.; Breimyer, Paul; Hendrix, William; Schmidt, Matthew C.; Rhyne, Theresa-Marie

doi:10.1109/ultravis.2008.5154061

Cited by 6 publications

(5 citation statements)

References 67 publications

(61 reference statements)

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“…Surveys centered around visualizing processes from omics data from a systems biology and bioinformatics perspective similarly emphasize the challenges of balancing insight with complexity for visualizing these data. The primary focus is often on data analysis, with exploration secondary [SS07; SBH*08; GOB*10; PMP*15; SSHU15]. These works provide an overview of data types, visualization tools, and methods for large‐scale omics data.…”

Section: Molecular Functionmentioning

confidence: 99%

Trends & Opportunities in Visualization for Physiology: A Multiscale Overview

Garrison

Kolesar²,

Viola

et al. 2022

Computer Graphics Forum

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Combining elements of biology, chemistry, physics, and medicine, the science of human physiology is complex and multifaceted. In this report, we offer a broad and multiscale perspective on key developments and challenges in visualization for physiology. Our literature search process combined standard methods with a state-of-the-art visual analysis search tool to identify surveys and representative individual approaches for physiology. Our resulting taxonomy sorts literature on two levels. The first level categorizes literature according to organizational complexity and ranges from molecule to organ. A second level identifies any of three high-level visualization tasks within a given work: exploration, analysis, and communication. The findings of this report may be used by visualization researchers to understand the overarching trends, challenges, and opportunities in visualization for physiology and to provide a foundation for discussion and future research directions in this area. CCS Concepts• Applied computing → Life and medical sciences; • Human-centered computing → Visualization;

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Section: Molecular Functionmentioning

confidence: 99%

Trends & Opportunities in Visualization for Physiology: A Multiscale Overview

Garrison

Kolesar²,

Viola

et al. 2022

Computer Graphics Forum

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“…Specialized server requirements complicate deployments and increase compute infrastructure costs. The lack of sufficient tools for visual analysis of complex and heterogeneous datasets is a problem that has been referred to as the challenge of ultra-scale integrative visualomics 8 . Focusing on individual modalities prevents the achievement of visualization tasks such as comparison and relation for multi-modal datasets, and may limit the utility of current tools in analyses of more complex future assay types.…”

Section: Mainmentioning

confidence: 99%

Vitessce: integrative visualization of multimodal and spatially-resolved single-cell data

Keller¹,

Gold²,

McCallum³

et al. 2021

Preprint

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Vitessce is an open-source interactive visualization framework for exploration of multi-modal and spatially-resolved single-cell data, with a modular architecture compatible with transcriptomic, proteomic, genome-mapped, and imaging data types. Its modular, coordinated multiple view implementation facilitates a wide range of visualization tasks to support all common single-cell assays. Vitessce is a client-side web application designed to be integrated with computational analysis tools and data resources and does not require specialized server infrastructure. The software is available at http://vitessce.io.

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“…In real‐world applications, these strategies for handling and rendering large data often have to be combined to achieve interactive performance and high‐quality images. Furthermore, for future ultra‐scale visualization and exa‐scale computing [ALN*08, SBH*08, MWY*09, AAM*11, Mor12] it is essential that each step of the visualization pipeline is fully scalable.…”

Section: Scalable Processing Strategiesmentioning

confidence: 99%

State‐of‐the‐Art in GPU‐Based Large‐Scale Volume Visualization

Beyer

Hadwiger

Pfister

2015

Computer Graphics Forum

103

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This survey gives an overview of the current state of the art in GPU techniques for interactive large‐scale volume visualization. Modern techniques in this field have brought about a sea change in how interactive visualization and analysis of giga‐, tera‐ and petabytes of volume data can be enabled on GPUs. In addition to combining the parallel processing power of GPUs with out‐of‐core methods and data streaming, a major enabler for interactivity is making both the computational and the visualization effort proportional to the amount and resolution of data that is actually visible on screen, i.e. ‘output‐sensitive’ algorithms and system designs. This leads to recent output‐sensitive approaches that are ‘ray‐guided’, ‘visualization‐driven’ or ‘display‐aware’. In this survey, we focus on these characteristics and propose a new categorization of GPU‐based large‐scale volume visualization techniques based on the notions of actual output‐resolution visibility and the current working set of volume bricks—the current subset of data that is minimally required to produce an output image of the desired display resolution. Furthermore, we discuss the differences and similarities of different rendering and data traversal strategies in volume rendering by putting them into a common context—the notion of address translation. For our purposes here, we view parallel (distributed) visualization using clusters as an orthogonal set of techniques that we do not discuss in detail but that can be used in conjunction with what we present in this survey.

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An outlook into ultra-scale visualization of large-scale biological data

Cited by 6 publications

References 67 publications

Trends & Opportunities in Visualization for Physiology: A Multiscale Overview

Trends & Opportunities in Visualization for Physiology: A Multiscale Overview

Vitessce: integrative visualization of multimodal and spatially-resolved single-cell data

State‐of‐the‐Art in GPU‐Based Large‐Scale Volume Visualization

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