The discussion will be concerned with new methods we have developed for genome-scale mapping of mammalian brain gene expression patterns in both health and disease. These technologies combine the mathematical concepts of biomedical imaging with the high-throughput tools of genomics. One approach, voxelation, employs analysis from the brain of spatially registered cubes or voxels, while another approach, gene expression tomography, employs analysis of axially rotated sets of slices. In both methods, image reconstruction results in volumetric maps of gene expression analogous to those obtained from biomedical imaging systems. The ultimate goal of our research is to create maps for all relevant biomolecular domains, including the transcriptome and proteome, allowing us to decode the logic by which the wiring diagram of the genome gives rise to the neuronal wiring diagram of the brain.