Systems and methods are provided for a microscope-integrated intraoperative scanner system having automated tracking of an instrument tip. A scanning mirror is configured such that a field of view of the OCT system is determined by a position or orientation of the scanning mirror. A drive system is configured to control the scanning mirror. Camera assemblies are configured to determine respective two-dimensional projections of the positions of markers attached to a surgical instrument. A stereo vision system is configured to determine a three-dimensional location of each of the markers from the determined two-dimensional positions. An instrument tracking component is configured to determine a position of a working tip of the surgical instrument according to the determined three-dimensional locations. A drive control is configured to instruct the drive system to adjust the scanner mirror to control the field of view of the OCT system.
