Disclosed are methods related to guiding robotic surgery using optical coherence tomography (OCT) and computer-readable media and computer systems executing the methods. They may include receiving a series of cross-sectional slices of 3D space obtained from an OCT probe over biological tissue and processing and filtering the series of slices. The processing and filtering may include spatially smoothing the intensity values of each slice, thresholding each slice after it has been blurred, performing a connected-component analysis to identify blobs on the thresholded slice, filtering the blobs, performing edge detection, and invoking a selective median filter. The processing and filtering can be used to construct a depth map from the received series of cross-sectional slices in order to guide a robotic end effector, based on the depth map.