This paper presents a method for automating the evaluation of hemoglobin oxygen saturation in the retina. This method should prove useful for monitoring ischemic retinal diseases and the effect of treatment. In order to obtain saturation values automatically, spectral images must be registered in pairs, the vessels of the retina located and measurement points must be selected. The registration algorithm is based on a data driven approach that circumvents many of the problems that have plagued previous methods. The vessels are extracted using an algorithm based on morphological profiles and supervised classifiers. Measurement points on retinal arterioles and venules as well as reference points on the adjacent fundus are automatically selected. Oxygen saturation values along vessels are averaged to arrive at a more accurate estimate of the retinal vessel oxygen saturation. The system yields reproducible results as well as being sensitive to changes in oxygen saturation.