Core Viewpoint - The article discusses a significant advancement in understanding early organogenesis in mouse embryos through the creation of a 3D "digital embryo" using single-cell resolution techniques, which provides insights into organ formation and potential mechanisms of congenital malformations [2][10]. Group 1: Early Organogenesis - Early organogenesis is a critical phase in embryonic development characterized by extensive cell fate determination to initiate organ formation, while also being highly susceptible to developmental defects [4]. - At approximately day 7.5 of embryonic development (E7.5), mouse embryos undergo significant morphological changes, marked by the emergence of key structures such as the heart tube and primitive gut [4]. - The complex process of organ formation relies on precise cell migration, localization, and differentiation, regulated by spatiotemporal gene expression patterns and intricate signaling pathways [4][5]. Group 2: Research Methodology - The research team combined spatial transcriptomics methods (Stereo-seq) with cell segmentation techniques to analyze 285 continuous slices from six embryos at early organogenesis stages (E7.5-E8.0), generating a spatial transcriptomic map at single-cell resolution [6]. - A visualization platform named SEU-3D was developed to reconstruct the 3D "digital embryo," accurately reflecting gene expression patterns and cell states in the native embryonic environment [7]. Group 3: Findings and Implications - The research delineated spatial cell maps of endoderm and mesoderm derivatives, revealing complex signaling networks across germ layers and cell types [8]. - A region known as the progenitor determination zone (PDZ) was identified at the anterior interface of the embryo-extrembryonic region at E7.75, indicating coordinated signaling during heart progenitor formation [8]. - The results collectively establish a comprehensive spatiotemporal embryonic atlas at single-cell resolution, accompanied by a network-based exploration tool for navigating spatial gene expression and signaling networks, paving the way for deeper studies into embryonic development and diseases [10].