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This paper presents a novel method for automated thickness measurements of nacre from optical coherence tomography (OCT) using polar transform and probability density projection. Our method detects the upper boundary of nacre and the raw boundary is fitted to a circle by a priori. Then polar transform is applied to the image according to the fitted circle. At the following stage, we extract the lower boundary by a transform incorporating unilateral difference and intensity of pixels. Finally, we get the probability distribution of nacre thickness by probability density projection. The proposed approach was evaluated using a large number of pearl optical coherence tomography images and achieved high accuracy, which could meet the requirements of practical applications. Besides, our method is robust to noise, boundary discontinuity, and it is real time. It has potential to be used in processing of some other OCT images with circle-like boundary.