Extended Data Fig. 10: Spatial mapping of single-cell clusters.

a, Expression of Shh detected by in situ sequencing on all sections, with close up images showing the detection of individual mRNA molecules. Inset shows the expression of Shh by in situ hybridization (Allen Brain Atlas) for reference. b, Manually curated anatomical annotation of all tissue sections (coloured as in the Allen Brain Atlas). c, Illustration of Tangram (mapping single cells to spatial voxels) and our generalized Tangram (mapping clusters to voxels). d, Inferred spatial distribution of roof plate organizers (clusters no. 213, no. 214 and no. 39). e, Inferred spatial distribution of cluster no. 206 on all tissue sections. f, Imputed expression of Prdm12, shown for four informative sections (left) and Allen Brain Atlas ground truth (right). g, Spatial gene expression of Pax6 and imputed gene expression of dorsal (Mitf and Vsx2) and ventral (Vax2 and Pax2) optic vesicle markers in the left and right eye.