In this article we present a detailed discussion of noise sources in Fourier Domain Optical Coherence Tomography (FDOCT) setups. The performance of FDOCT with charge coupled device (CCD) cameras is compared to current standard time domain OCT systems. We describe how to measure sensitivity in the case of FDOCT and confirm the theoretically obtained values. It is shown that FDOCT systems have a large sensitivity advantage and allow for sensitivities well above 80dB, even in situations with low light levels and high speed detection.

We consider the use of single-photon counting detectors in coherence-domain imaging. Detectors operated in this mode exhibit reduced noise, which leads to increased sensitivity for weak light sources and weakly reflecting samples. In particular, we experimentally demonstrate the possibility of using superconducting single-photon detectors (SSPDs) for optical coherence-domain reflectometry (OCDR). These detectors are sensitive over the full spectral range that is useful for carrying out such imaging in biological samples. With counting rates as high as 100 MHz, SSPDs also offer a high rate of data acquisition if the light flux is sufficient.

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We present a new method for identifying and segmenting the retinal pigment epithelium (RPE) in polarization sensitive optical coherence tomography (PS-OCT) images of the human retina. Contrary to previous, intensity based segmentation algorithms, our method uses an intrinsic tissue property of the RPE: its depolarizing, or polarization scrambling effect on backscattered light. Two different segmentation algorithms are presented and discussed: a simpler algorithm based on retardation data, and a more sophisticated algorithm based on local variations of the polarization state calculated from averaged Stokes vector elements. By using a state of the art spectral domain PS-OCT instrument, we demonstrate the method in healthy and diseased eyes.

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