Multiplexed embryo profiling links cellular state to zygotic genome activation in single cells

Multicellular self-organization relies on complex interactions across multiple length scales, shaping the transcriptional activity and molecular phenotype of individual cells. Despite advances in spatial omics technologies, mapping protein state composition at high spatial resolution to capture the molecular phenotype across whole-mount structures has remained challenging. Here, we introduce high-throughput 3D iterative indirect immunofluorescence imaging (3D-4i) for the simultaneous detection of multiple proteins and protein states across the entire embryo, and a 3D-dedicated computer vision pipeline for quantifying morphological and molecular properties across subcellular, single-cell, and whole-embryo scales in hundreds of samples. Applying this pipeline to early zebrafish embryos undergoing mid-blastula transition, we determine the cell cycle phase for each cell across the embryo, allowing us to uncover the spatiotemporal dynamics by which global meta-synchronous mitotic waves transition to cell cycle desynchronization. Using statistical analysis, we find that cell cycle phase is the major source of variability in transcription within a division cycle, and combining this with analysis of key transcription factors and chromatin modifier state enables accurate prediction of transcriptional output during zygotic genome activation in individual cells. Collectively, our results demonstrate the strength of 3D-4i in quantifying multimodal effects across spatiotemporal scales and show how it can be utilized to unravel the complex contribution of causal factors that collectively drive multicellular self-organization.