Methods for improved acquisition and processing of optical coherence tomography (OCT) angiography data are presented. One embodiment involves improving the acquisition of the data by evaluating the quality of different portions of the data to identify sections having non-uniform acquisition parameters or non-uniformities due to opacities in the eye such as floaters. The identified sections can then be brought to the attention of the user or automatically reacquired. In another embodiment, segmentation of layers in the retina includes both structural and flow information derived from motion contrast processing. In a further embodiment, the health of the eye is evaluating by comparing a metric reflecting the density of vessels at a particular location in the eye determined by OCT angiography to a database of values calculated on normal eyes.