Elucidating the developmental processes of organisms requires a comprehensive understanding of cell lineages across spatial, temporal, and molecular dimensions. Advances in imaging and omics technologies allow us to generate technically challenging multidimensional datasets that capture developmental dynamics at unprecedented resolution and across scales (from molecule to organism). In this talk, I will describe how we integrate light-sheet microscopy with scRNAseq, yielding a time-resolved multimodal atlas of zebrafish development named Zebrahub (zebrahub.org). I will showcase its application in elucidating the differentiation of complex late pluripotent progenitors. Finally, I will show our recent effort leveraging Multiomic assays and tracking data to perform in silico experiments and gain mechanistic insights into development and differentiation.

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