1. A system for extracting information about a sample organism, wherein the sample organism is a small vertebrate that completes embryogenesis within approximately 72 hours following fertilization, the system comprising, an atlas registered to an organism of interest; a storage device for at least temporarily storing an image of the sample organism; an operating device that automatically creates a map of the image of the sample organism and automatically compares the map of the image to the atlas of the organism of interest; and an imaging device, wherein the imaging device takes one or more images of the sample organism, that is used to create the map, at a plurality of levels of resolution using a transmitted light imaging modality; wherein said transmitted light imaging modality is a high-throughput system.