Cell3D: a comprehensive database for interactive 3D visualization and crosstalk analysis of single-cell and spatial omics.

Cell3D curates 898 public single-cell and spatial transcriptomic datasets—2 924 646 cells and spots across 105 diseases, 756 cell types, and 83 organs/tissues from 11 species—enabling interactive multi-feature exploration.

• Why it matters: Integrative exploration is limited because most platforms support only one data type and lack interactive visualization for multi-feature analysis across cellular and spatial dimensions.
• What they did: Cell3D integrates twelve functional annotation systems and provides customizable 2D/3D interactive visualization, flexible integration with automatic recognition, and quantitative crosstalk and microenvironment-focused analysis.
• The result: The platform supports exploration from gene expression and clusters to pathway activities and clinical phenotypes, facilitating disease research and biomarker discovery by linking molecular perturbations to tissue architecture.