In certain embodiments, a system, a computer-implemented method, and computer-readable medium are disclosed for performing integrated analysis of MSI and OCT images to diagnose eye disorders. MSI and OCT are processed using separate input machine learning models to create input feature maps that are input to an intermediate machine learning model. The intermediate machine learning model processes the input feature maps and outputs a final feature map that is processed by one or more output machine learning models that output one or more estimated representations of a pathology of the eye of the patient.