When imaging technology meets single-cell omics: new paradigm in developmental biology

Abstract Advanced imaging and single-cell omics technologies are fundamentally transforming developmental biology research, shifting it from static observation to dynamic, spatially resolved systems biology. Super-resolution microscopy breaks the diffraction barrier to visualize nanoscale subcellular dynamics, while light-sheet fluorescence microscopy enables long-term, multi-scale volumetric imaging of living specimens. In parallel, single-cell omics (e.g., transcriptomics and proteomics) decipher molecular heterogeneity and lineage trajectories, and spatially resolved transcriptomics maps gene expression within native tissue contexts at subcellular resolution. However, each approach has inherent limitations: imaging lacks deep molecular profiling, while dissociation-based omics loses spatial context. This review highlights how the integration of these technologies bridges cellular behaviors with molecular mechanisms, providing unprecedented multi-scale perspectives on key developmental processes—including embryogenesis, organogenesis, neural patterning, and disease progression. By synergistically capturing the "when," "where," and "how" of developmental processes, this convergence resolves longstanding questions and establishes a new mechanistic and predictive paradigm in developmental biology. Graphical Abstract