Geographic atrophy of the eye can be detected and measured by imaging the eye at a depth greater than the retinal pigment epithelium (RPE) at a plurality of locations of the eye, for example, using optical coherence tomography (OCT); determining a ratio of the intensities of imaging signals of a retinal layer(s) with respect to the intensity of imaging signals of a sub-RPE layer(s) at each location; determining representative values based at least in part on the determined ratios; generating a map of the representative values; and identifying diseased areas from the map. Contours and binary maps may be generated based on the identified diseased areas. The size and shape of the identified areas may be analyzed and monitored over a period of time to phenotype subjects and classify diseases.