The paper introduces So3D, the first comprehensive, cross-species online resource dedicated to three-dimensional spatial omics. While previous databases focused on two-dimensional tissue slices, this platform integrates over 70 datasets across four species to reconstruct complex 3D tissue architectures. It features five specialized analysis modules designed to identify spatial domains, map cell type distributions, and identify region-specific biomarkers. Furthermore, the resource enables researchers to investigate cell-cell communication and functional signaling networks within a realistic spatial context. By combining large-scale data integration with interactive visualization, So3D helps scientists decode the intricate microenvironments of both healthy and diseased organs. This breakthrough tool ultimately supports the discovery of new biological insights and therapeutic targets by moving beyond traditional flat imaging.

References:

• Zhao H, Yin X, Wang S, et al. So3D: a comprehensive three-dimensional spatial omics resource for decoding tissue architecture in physiology and disease[J]. Nucleic Acids Research, 2026, 54(D1): D1281-D1290.