Abstract: The present invention provides methods, composition, software and apparatus for in vivo analysis of gene expression and biological function in plants and animals. The invention also provides materials and methods for rapid analysis of data, allowing the methods and compositions of the invention to be used in a high throughput manner. The materials include an optical coherence microscope, the use and identification of detectable OCM substances, and machine readable code that converts OCM signal to binary data and then to a visual image, by which the expression of genes in vivo can be visualized. The present method results in the creation of genomic-scale, computer screenable databases of gene expression that include spatial, temporal, and quantitative data about gene expression in vivo.