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

Abstract

Recent advancements have enabled tissue samples to be profiled at the unprecedented level of detail of a single cell. Analysis of this 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 presents challenges and opportunities. We survey the usage of visualization to interpret single-cell atlas datasets by assessing over 1,800 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.

Citation

MS Keller, E Mörth, TC Smits, S Warchol, G Guo, Q Wang, R Krueger, H Pfister, N Gehlenborg. “The State of Single-Cell Atlas Data Visualization in the Biological Literature”, IEEE Computer Graphics and Applications 1-15 (2025). doi:10.1109/MCG.2025.3583979