Abstract: A system for fluorescence aided surgery stores a 3D data set of a patient, wherein information regarding a spatial position of one or more fluorescence markers within the body of said patient is included in or associated with said 3D patient data set, a visualization tool allowing for augmenting a view or an image of said patient's body with information derived from said 3D patient data set, and an apparatus for detecting fluorescence from said one or more fluorescence markers provided in said patient's body. A computation device derives a spatial relationship between said visualization tool and the patient's body based at least in part on said detected fluorescence, said information regarding said spatial position, and a known spatial relationship between the apparatus for detecting fluorescence and said visualization tool.