Spatiotemporal modeling of molecular holograms by Xiaojie Qiu, Daniel Y. Zhu, Yifan Lu, ..., instant download

Spatiotemporal modeling of molecular holograms by Xiaojie Qiu, Daniel Y. Zhu, Yifan Lu, ..., instant download

SUMMARYQuantifying spatiotemporal dynamics during embryogenesis is crucial for understanding congenital diseases. We developed Spateo ( a 3D spatiotemporal modelingframework, and applied it to a 3D mouse embryogenesis atlas at E9.5 and E11.5, capturing eight million cells.Spateo enables scalable, partial, non-rigid alignment, multi-slice refinement, and mesh correction to createmolecular holograms of whole embryos. It introduces digitization methods to uncover multi-level biologyfrom subcellular to whole organ, identifying expression gradients along orthogonal axes of emergent 3Dstructures, e.g., secondary organizers such as midbrain-hindbrain boundary (MHB). Spateo further jointlymodels intercellular and intracellular interaction to dissect signaling landscapes in 3D structures, includingthe zona limitans intrathalamica (ZLI). Lastly, Spateo introduces ‘‘morphometric vector fields’’ of cell migration and integrates spatial differential geometry to unveil molecular programs underlying asymmetrical murine heart organogenesis and others, bridging macroscopic changes with molecular dynamics. Thus, Spateoenables the study of organ ecology at a molecular level in 3D space over time.