Fig. 10: Mapping of EMAP ts09 and ts10 mouse embryo atlases (8 × 8 × 8 μm resolution) to cycleHCR whole mouse embryo cells.

a Shows cell centers of measured embryo with prescribed cell type based on UMAP clustering¹⁷. b, k Show ts09 and ts10 atlases with 9 and 14 regions, respectively. d, l Show initial alignment of each atlas to target embryo (black dots) versus e, m Show alignment following estimation of diffeomorphism with xIV-LDDMM. f, g Show vertical cross-section through alignment of ts09 atlas to target before and after deformation, with black arrows indicating area of primitive streak in target embryo and white arrows indicating primitive streak in atlas. h–j Show horizontal cross-section of ts09 atlas h, j before and after deformation and of i target embryo with arrows indicating primitive streak and proamniotic/amniotic cavity. c Shows distance of each embryo cell with primitive streak and parietal endoderm type to corresponding type in ts09 atlas before and after alignment. Full set of computed distances provided in Supplementary Data 2. n–p Show horizontal cross-section of ts10 atlas n, r before and after deformation versus that of p target embryo with arrows indicating area of mesoderm. o–s Show vertical cross-section of ts10 atlas o, s before and after deformation versus q target embryo with solid arrows indicating mesoderm and dotted arrows highlighting area of developing amniotic fold.