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

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.