An OCT system and particularly its clock system generates a k-clock signal but also generates an optical frequency reference sweep signal that, for example, indicates the start of the sweep or an absolute frequency reference associated with the sweep at least for the purposes of sampling of the interference signal and/or processing of that interference signal into the OCT images. The clock system is also tunable to allow the control or flexibility over the relationship between the scanning of the swept optical signal and the sampling of the interference signal by the data acquisition system. Specifically, the absolute frequencies of the swept optical signal at which the k-clock signals are generated can be adjusted. Also, the absolute frequency of the swept optical signal at which sampling of the interference signal is initiated can also be changed or stabilized. Moreover, optical frequency sampling interval defined by the k-clock signal can be changed under user control or simply stabilized.