The invention relates to a method for registering intra-operative image data set with pre-operative 3D image data set, including: spatially calibrating an optical 3D sensor system with an intra-operative imaging modality, intra-operatively detecting the surface of an examination area of interest with the 3D sensor system to produce an intra-operative surface mask, intra-operatively recording the area of interest for examination with the intra-operative modality at least partly containing the intra-operative surface mask to obtain an intra-operative image data set, computing the same surface from the pre-operative 3D image data set containing the detected surface to obtain a pre-operative surface mask, registering the intra-operative and pre-operative surface mask with each other, determining a mapping specification between pre-operative 3D image data set and intra-operative image data set based on the calibration and the registration, and overlaying the intra-operative image data set with the pre-operative 3D data set based on the mapping specification.