We established a metabolic and functional profile map of the normal rat retina, given the premise that: 1) amino acid neurochemistry reflects metabolic integrity and cellular identity, and 2) the permeation of a cation channel probe, agmatine (1-amino-4-guanidobutane, AGB), reflects cation channel functionality. The purpose was to provide a unique method of simultaneously assessing the metabolic and functional characteristics of the normal retina, upon which a comparison can be made to disease models. Quantitative pattern recognition analysis of overlapping amino acid and AGB expression profiles was used to provide a statistically robust classification of all neural elements according to their metabolic and functional characteristics. This classification was spatially complete and with single-cell resolution. The resulting classification demonstrated 28 statistically separable theme classes dominated by characteristic glutamate, GABA, glycine, and/or taurine profiles, with each of the neuronal theme classes containing further subtypes. The inclusion of a functional parameter (AGB mapping) in the classification process nearly doubled the number of neural elements that could be ascribed a neurochemical/cation profile, compared to when amino acid labeling was used alone. Strong endogenous glutamate gated AGB labeling was observed in horizontal cells, rod bipolar cells, cholinergic amacrine cells, and AII amacrine cells. The resulting amino acid and AGB profile matrix constitutes a nomogram for assessing cellular responses to experimental challenges in models of ocular disease. J. Comp. Neurol. 505:92–113, 2007. © 2007 Wiley-Liss, Inc.