Non-radioactive in situ hybridization (ISH) is a powerful technique for revealing gene expression in individual cells, the level of detail necessary for investigating how genes control cell type identity, cell differentiation, and cell-cell signaling. Although the availability of robotic ISH enables the expeditious determination of expression patterns for thousands of genes in serially sectioned tissues, a large collection of ISH images is, per se, of limited benefit. However, via accurate detection of expression strength and spatial normalization of expression location across different specimens, ISH images become a minable resource of annotated gene expression capable of advancing functional genomics in a mode similar to DNA sequence databases. We have developed