An optical coherence analysis system, comprising: an interferometer configured to divide a swept optical signal between a reference arm and a sample arm and to combine optical signals returning from the reference arm and the sample arm to generate an interference signal; an optical swept source system configured to generate the swept optical signal; a clock system configured to generate k-clock signals in response to frequency sweeping of the swept optical signal and to generate an optical frequency reference sweep signal indicating that the frequency of the swept optical signal is at a particular sweep frequency, wherein the clock system comprises a clock/trigger optical module configured to generate the k-clock signals and an optical trigger signal to indicate the sweep frequency by spectrally filtering the swept optical signal; a trigger logic module configured to generate the optical frequency reference sweep signal to indicate a start of the sweep; and a detection system configured to detect the interference signal in response to the k-clock signals to generate evenly spaced samples of the interference signal and to use the optical frequency reference sweep signal to stabilize sampling across sweeps of the swept optical signal, wherein the optical frequency reference sweep signal is based on the optical trigger signal and an electronic trigger signal generated by a controller of the optical swept source system; and the controller is configured to receive temperature information from the clock/trigger optical module and to generate a drive signal to change a temperature of the clock/trigger optical module to change the timings of the optical trigger signal and the k-clock signals relative to each other for the same electronic trigger timing. an interferometer configured to divide a swept optical signal between a reference arm and a sample arm and to combine optical signals returning from the reference arm and the sample arm to generate an interference signal; an optical swept source system configured to generate the swept optical signal; a clock system configured to generate k-clock signals in response to frequency sweeping of the swept optical signal and to generate an optical frequency reference sweep signal indicating that the frequency of the swept optical signal is at a particular sweep frequency, wherein the clock system comprises a clock/trigger optical module configured to generate the k-clock signals and an optical trigger signal to indicate the sweep frequency by spectrally filtering the swept optical signal; a trigger logic module configured to generate the optical frequency reference sweep signal to indicate a start of the sweep; and a detection system configured to detect the interference signal in response to the k-clock signals to generate evenly spaced samples of the interference signal and to use the optical frequency reference sweep signal to stabilize sampling across sweeps of the swept optical signal, wherein the optical frequency reference sweep signal is based on the optical trigger signal and an electronic trigger signal generated by a controller of the optical swept source system; and the controller is configured to receive temperature information from the clock/trigger optical module and to generate a drive signal to change a temperature of the clock/trigger optical module to change the timings of the optical trigger signal and the k-clock signals relative to each other for the same electronic trigger timing.