Multicellular self-organization depends on interactions across multiple length scales, yet mapping protein states at high spatial resolution in whole-mount embryos remains challenging. Here, we introduce high-throughput 3D in toto iterative immunofluorescence imaging (3D-4i) and a dedicated computer vision pipeline to quantify morphological and molecular features from subcellular to whole-embryo scales across 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, and uncover the spatiotemporal dynamics by which global meta-synchronous mitotic waves transition to cell cycle desynchronization. Using statistical analysis, we find that the cell cycle phase is the major source of variability in transcription within a division cycle, and combining this with the analysis of key transcription factors and chromatin modifier state, included in our multiplexed dataset, enables accurate prediction of transcriptional output during zygotic genome activation in individual cells. Together, these findings establish 3D-4i as a powerful approach for quantifying multimodal, multiscale biological processes underlying multicellular self-organization.