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We applied a deep convolutional neural network model for automatic identification of ellipsoid zone (EZ) in spectral domain optical coherence tomography B-scans of retinitis pigmentosa (RP). Midline B-scans having visible EZ from 220 patients with RP and 20 normal subjects were manually segmented for inner limiting membrane, inner nuclear layer, EZ, retinal pigment epithelium, and Bruch's membrane. A total of 2.87 million labeled image patches (33 × 33 pixels) extracted from 480 B-scans were used for training a convolutional neural net