In the post-genomic era, large-scale efforts have begun to characterize the role of gene products. Several of these efforts aim to systematically discover the activity of all 20,000 genes throughout functionally complex tissue specimens such as embryo and the mature brain. By applying a subdivision-based deformable model of the brain, we rapidly organize spatial gene expression data into a common coordinate system. Doing this enables powerful queries, comparisons, and associations of the data.