An OCT tracking system, comprising: an imaging unit operable to generate a fundus image of a patient's eye; a tracking unit operable to: either process the fundus image to determine a location of a surgical instrument inserted into the patient's eye or track the motion of the retina and receive a user input for a period of time; and an OCT system comprising: an OCT light source operable to generate an OCT imaging beam; and a beam scanner, wherein the user input is configured to indicate a mode by which cross-sectional OCT scans will track the surgical instrument, and the tracking system is further operable to generate signals to be communicated to the beam scanner, the system being characterized in that the beam scanner is configured to be: operable, based on signals generated by the tracking unit, before or after the period of time, to direct the OCT imaging beam to a set location on the retina; and operable, based at least in part on the determined location of the surgical instrument and only during the period of time, to direct the OCT imaging beam to a particular region within the patient's eye, in which the tip of the surgical instrument is located, such that the relative position between the tip of the surgical instrument inserted into the patient's eye and the scanning area is always maintained. an imaging unit operable to generate a fundus image of a patient's eye; a tracking unit operable to: either process the fundus image to determine a location of a surgical instrument inserted into the patient's eye or track the motion of the retina and receive a user input for a period of time; and an OCT system comprising: an OCT light source operable to generate an OCT imaging beam; and a beam scanner, wherein the user input is configured to indicate a mode by which cross-sectional OCT scans will track the surgical instrument, and the tracking system is further operable to generate signals to be communicated to the beam scanner, the system being characterized in that the beam scanner is configured to be: operable, based on signals generated by the tracking unit, before or after the period of time, to direct the OCT imaging beam to a set location on the retina; and operable, based at least in part on the determined location of the surgical instrument and only during the period of time, to direct the OCT imaging beam to a particular region within the patient's eye, in which the tip of the surgical instrument is located, such that the relative position between the tip of the surgical instrument inserted into the patient's eye and the scanning area is always maintained. either process the fundus image to determine a location of a surgical instrument inserted into the patient's eye or track the motion of the retina and receive a user input for a period of time; and process the fundus image to determine a location of a surgical instrument inserted into the patient's eye or track the motion of the retina and receive a user input for a period of time; and an OCT system comprising: an OCT light source operable to generate an OCT imaging beam; and a beam scanner, wherein the user input is configured to indicate a mode by which cross-sectional OCT scans will track the surgical instrument, and the tracking system is further operable to generate signals to be communicated to the beam scanner, the system being characterized in that the beam scanner is configured to be: operable, based on signals generated by the tracking unit, before or after the period of time, to direct the OCT imaging beam to a set location on the retina; and operable, based at least in part on the determined location of the surgical instrument and only during the period of time, to direct the OCT imaging beam to a particular region within the patient's eye, in which the tip of the surgical instrument is located, such that the relative position between the tip of the surgical instrument inserted into the patient's eye and the scanning area is always maintained. an OCT light source operable to generate an OCT imaging beam; and a beam scanner, wherein the user input is configured to indicate a mode by which cross-sectional OCT scans will track the surgical instrument, and the tracking system is further operable to generate signals to be communicated to the beam scanner, the system being characterized in that the beam scanner is configured to be: operable, based on signals generated by the tracking unit, before or after the period of time, to direct the OCT imaging beam to a set location on the retina; and operable, based at least in part on the determined location of the surgical instrument and only during the period of time, to direct the OCT imaging beam to a particular region within the patient's eye, in which the tip of the surgical instrument is located, such that the relative position between the tip of the surgical instrument inserted into the patient's eye and the scanning area is always maintained. operable, based on signals generated by the tracking unit, before or after the period of time, to direct the OCT imaging beam to a set location on the retina; and operable, based at least in part on the determined location of the surgical instrument and only during the period of time, to direct the OCT imaging beam to a particular region within the patient's eye, in which the tip of the surgical instrument is located, such that the relative position between the tip of the surgical instrument inserted into the patient's eye and the scanning area is always maintained.