A method for calibrating a Fourier domain optical coherence tomography system includes receiving spectral data from an optical detector comprising a linear array of detector elements, each detector element having a position labeled n, wherein detected light was wavelength-dispersed across the linear array of detector elements; determining parameters of a preselected functional relationship between wave number, kn, corresponding to detector element n as a function of optical detector element n based on the spectral data; further receiving subsequent spectral data subsequent to the first-mentioned receiving, wherein detected light was wavelength-dispersed across the linear array of detector elements; converting the subsequent spectral data using the preselected functional relationship between wave number kn and optical detector element n to obtain converted spectral data; and performing an inverse Fourier transform of the converted spectral data to obtain a depth profile.