Improved indices for the diagnosis and evaluation of conditions affecting the eye. Specifically, the indices include an Enhanced Epithelial Irregularity Factor (eEIF) for the diagnosis and evaluation of conditions such as dry eye syndrome (DES), Bowman's Ectasia Index (BEI), including enhanced BEI (eBEI) and BEI-Max, and Bowman's Relative Thinning (BRT) Index for the diagnosis and evaluation of ectatic conditions such as keratoconus, pellucid marginal degeneration, post-refractive surgery ectasia, and keratoglobus, and Descemet's Membrane Thickening Index (DMT), Descemet's Rejection Index (DRI), and Descemet's Membrane Irregularity Factor (DIF) for the diagnosis and evaluation of conditions such as keratoplasty rejection and failure and Fuchs' dystrophy. These improved indices may be incorporated into optical coherence tomography systems, or any other imaging device capable of capturing high resolution images of the cornea, for more sensitive and specific diagnosis, treatment, and monitoring of certain corneal conditions, in addition to the evaluation of new treatments.