Over the last two decades optical coherence tomography (OCT) has become a clinical gold standard in diagnostic and management of many retinal diseases. Following that success, OCT is now becoming a standard tool in studies of animal models of human retinal diseases allowing longitudinal evaluation of disease progression and responses to therapeutic intervention in the single animal. Recent progress in OCT data acquisition and processing allowed successful cellular resolution detection of outer and inner retina functional response to light stimulation both in humans and experimental animals. In this manuscript, we will describe our latest effort of improving cellular contrast in mouse functional retinal imaging by application of volumetric registration and speckle contrast reduction by temporal averaging of volumetric data sets: i.e., temporal Super Averaging. As an example, the current configuration of our multimodal Scanning Light Ophthalmoscopy / Optical Coherence Tomography (SLO/OCT) mice retinal imaging system, as well as data acquisition and processing schemes, will be presented. Experimental results will be discussed in the context of improved morphological and functional probing of mice retinas at cellular resolution. Finally, current limitations and future directions of instrument development with a focus on improved probing of the retinal function will be discussed as well.