4D-atlas: a multi-species four-dimensional spatiotemporal transcriptomics database spanning development,...

Four-dimensional (4D) spatial transcriptomics, which captures molecular landscapes across both three-dimensional (3D) tissue architecture and temporal progression, is essential for deciphering dynamic biological processes such as development, regeneration, and disease progression. Here, we present 4D-atlas (https://bio-bigdata.hrbmu.edu.cn/4D-Atlas or https://4d-atlas.bio-database.com/), the first publicly accessible database dedicated to multi-species 4D spatiotemporal transcriptomic atlases. 4D-atlas collects and standardizes 1629 spatial slices spanning 88 distinct time points with 2-41 per dataset and over 22.2 million cells or spatial spots from 15 representative datasets across six species, encompassing embryonic development, tissue regeneration, and disease progression. Beyond data collection, 4D-atlas provides seven interactive analytical modules that enable 4D (3D space + time) exploration of tissue morphogenesis, spatial gene modules, pathway activities, regulatory networks, cell-cell communication, developmental trajectories, and temporal expression patterns. Using a unified analytical pipeline to integrate 3D spatial architecture and molecular information across discrete biological stages, 4D-atlas enables systematic investigation of tissue morphogenesis and dynamic regulatory programs across time and space.