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Fully automated quantification of the morphologic features of different epithelial cell layers in healthy human corneas.In vivo confocal laser scanning microscopy was performed on the unilateral eyes of 6 healthy volunteers. Stacks of 160 images (400 × 400 μm) with an interslice distance of 0.4 μm were used to generate full thickness volume data sets of the epithelium. Size and shape factors of basal (BC) and intermediate cell (IC) layers were quantified using appropriate image analysis algorithms. Evaluated parameters include mean area, compactness, solidity, major and minor diameter, and maximum boundary distance.Mean area of BC and IC demonstrated a linear increase from 80 to 160 μm². A similar trend was noted with major and minor diameter and maximum boundary distance. Major diameters of BC and IC measured between 13.2 and 17.0 μm, whereas minor diameter of these cells measured between 8.6 and 12.4 μm. The maximum boundary distance of BC and IC ranged from 7.0 to 9.1 μm. Compactness of epithelial cells clustered around 1.45 and 1.5, whereas cell solidity measured between 1.0 and 1.03.Several characteristic morphologic quantities can be calculated using this methodology without manual intervention. Our study demonstrated promising results and suggests that this fully automated morphologic quantification can be successfully applied to assess microstructural changes of the epithelium in normal and various corneal disorders.