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Summary form only given. Color Doppler optical coherence tomography (CDOCT) is an innovative extension of optical coherence tomography. CDOCT permits spatially localized blood flow velocity mapping simultaneous with microstructural imaging of living tissue. In CDOCT, longitudinal velocity profiles are estimated by measuring Doppler shifts in localized backscattered light spectra. Velocity images are built up from adjacent axial velocity profiles, which are color coded for velocity magnitude and direction as performed in color Doppler ultrasound. CDOCT could potentially be used for retinal perfusion analysis for diagnosing macular diseases and optimizing treatments of vascular disorders. CDOCT uses an optical heterodyne detection technique based on scanning white light interferometry. Therefore the detector current carrier frequency is the same as the resultant Doppler shift in the received light given by the difference of the Doppler shifts due to the reference mirror velocity and moving scatterers in the sample. The width of the detector current power spectrum is proportional to the product of the net Doppler shift and the light source spectrum width. Light backscattered from a turbid specimen generates a speckle pattern consisting of the sum of partial reflections from many randomly distributed scatterers. As a result, the detector current spectrum measured in CDOCT maybe strongly frequency dependent and is modulated by a postulated transfer function, which encodes information regarding scattering sites.