So3D: a comprehensive three-dimensional spatial omics resource for decoding tissue architecture in physiology and disease

So3D is the first integrative resource dedicated to three-dimensional (3D) spatial omics (http://bio-bigdata.hrbmu.edu.cn/So3D). It currently curates 72 high-quality 3D spatial transcriptomics datasets across four species (human, mouse, drosophila, axolotl), covering 15 tissues and 5 disease types. The database integrates spatial transcriptomics with matched single-cell RNA-seq data to reconstruct tissue-wide 3D molecular landscapes. Key features include: Domain3D: identification and visualization of 3D spatial domains. CellType3D: mapping cell-type deconvolution results in 3D context. SpatialDEG3D: discovery of spatially variable genes in 3D space. Function3D: functional annotation of spatial domains and cell types. Communication3D: inference of intercellular communication in 3D. So3D provides a user-friendly interface for data browsing, visualization, and downloading.