The State of Single-Cell Atlas Data Visualization in the Biological Literature

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Mark S. Keller, Eric Mörth, Thomas C. Smits, Simon Warchol, Grace Guo, Qianwen Wang, Robert Krüger, Hanspeter Pfister, Nils Gehlenborg

Published: 2025, Last Modified: 05 Jan 2026IEEE Computer Graphics and Applications 2025EveryoneRevisionsBibTeXCC BY-SA 4.0
Abstract: Recent advancements have enabled tissue samples to be profiled at the unprecedented level of detail of a single cell. Analysis of these data has enabled discoveries that are relevant to understanding disease and developing therapeutics. Large-scale profiling efforts are underway, which aim to generate “atlas” resources that catalog cellular archetypes, including biomarkers and spatial locations. While the problem of cellular data visualization is not new, the size, resolution, and heterogeneity of single-cell atlas datasets present challenges and opportunities. We survey the usage of visualization to interpret single-cell atlas datasets by assessing over 1800 figure panels from 45 biological publications. We intend for this report to serve as a foundational resource for the visualization community as atlas-scale single-cell datasets are emerging rapidly with aims of advancing our understanding of biological function in health and disease.