1. A system for obtaining and processing images of a biological material, the system comprising: an optical coherence tomography (OCT) scanner configured to generate a plurality of OCT images; one or more computer readable storage devices configured to store a plurality of computer executable instructions; and one or more hardware computer processors in communication with the one or more computer readable storage devices and configured to execute the plurality of computer executable instructions in order to cause the system to: access, from the OCT scanner, the plurality of OCT images; generate, from the plurality of OCT images, a plurality of enface images of one or more superficial layers of the biological material and a plurality of enface images of one or more deep layers of the biological material; apply one or more image registration techniques to the plurality of enface images of the one or more superficial layers to produce image alignment settings; store the image alignment settings; generate at least one averaged enface image of each of the one or more deep layers by applying one or more image registration techniques, based at least in part on the stored image alignment settings, to the plurality of enface images of the one or more deep layers; and output the one or more averaged enface images.