The systems and methods described herein provide improved techniques for OCT guided robotic ophthalmic procedures. A method includes receiving, during OCT scanning of an eye, position data of a plurality of galvanometer scanners from a plurality of absolute and incremental encoders coupled to the corresponding galvanometer scanners. The method further includes receiving scan data related to one or more tissues of the eye. The method further includes determining, a set of first positions of the one or more tissues of the eye in a first 3D coordinate system. The method further includes determining, based on the set of first positions and a mapping between the first and a second 3D coordinate systems, a position in the second 3D coordinate system for a surgical instrument coupled to a robotic device. The method includes causing the robotic device to move the surgical instrument to the position in the second 3D coordinate system.