In fourier domain optical coherence tomography, we can measure the optical thickness ( refractive index n times thickness d), to obtain the retinal layers in order to diagnose many disorders. In this work, we introduce a new method for measurement of refractive index and physical thickness of multiple layers simultaneously by Fourier domain optical coherence tomography, without additional information about the structure of the sample under investigation. The input data to the formulation are the interference spectrum of FD-OCT system and the optical path lengths (OPLs) which obtain from fast fourier transform of interference spectrum. The output of simulation suggest that, the accuracy of the extracted parameters depend on the difference in the refractive index gradient of sample interfaces. Furthermore, we show that the accuracy of the extracted parameters can be affected by uncertainty in obtained OPLs. So, we introduce a method to optimize the accuracy of parameters in spite of uncertainty in measuring OPLs. Simulation results show that, for transparent biological sample merge into an aqueous media, if sample layers has indices less than 1.55 , these parameters can be extracted with the , less than 0.001 .

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