Genetic variation can alter brain structure and, consequently, function. Comparative statistical analysis of mouse brains across genetic backgrounds requires spatial, single-cell, atlas-scale data, in replicates-a challenge for current technologies. We introduce A tlas-scale T ranscriptome L ocalization using A ggregate S ignatures (ATLAS), a scalable tissue mapping method. ATLAS learns transcriptional signatures from scRNAseq data, encodes them in situ with tens of thousands of oligonucleotide probes, and decodes them to infer cell types and imputed transcriptomes. We validated ATLAS by comparing its cell type inferences with direct MERFISH measurements of marker genes and quantitative comparisons to four other technologies. Using ATLAS, we mapped the central brains of five male and five female C57BL/6J (B6) mice and five male BTBR T+ tf/J (BTBR) mice, an idiopathic model of autism, collectively profiling over 40 million cells across over 400 coronal sections. Our analysis revealed over 40 significant differences in cell type distributions and identified 16 regional composition changes across male-female and B6-BTBR comparisons. ATLAS thus enables systematic comparative studies, facilitating organ-level structure-function analysis of disease models.