Fig. 5: Transcriptome-scale adult mouse CNS spatial atlas by gene imputation.

a, Schematics of the imputation workflow. Using the STARmap PLUS measurements and a scRNA-seq atlas¹ as inputs, we first performed intermediate mappings using a leave-one-(gene)-out strategy (Methods). The resulting intermediate mappings were used to compute weights between STARmap PLUS cells and scRNA-seq cells for a final imputation to output 11,844 gene-expression profiles in STARmap PLUS cells. b, Representative imputed spatial gene expression maps with corresponding STARmap PLUS and Allen Mouse Brain ISH²³ gene-expression maps. Each dot represents a cell coloured by the expression level of a gene. Scale bar, 0.5 mm. The sample slice number was labelled (top left). c, Examples of imputed spatial expression profile of genes outside the STARmap PLUS 1,022 gene list with the corresponding Allen ISH images²³. Scale bar, 1 mm. The ISH data were obtained from Allen Mouse Brain Atlas²³.