A surgical navigation system employs an endoscope (30) and an imaging unit (80). The endoscope (30) include an electromagnetic tracker (40) within a working channel of endoscope (30) for generating electromagnetic sensing signals indicative of one or more poses of the endoscope (30) within an anatomical region, and an endoscopic camera (50) within an imaging channel of the endoscope (30) for generating endoscopic images of the anatomical region. The imaging unit (80) executes an intraoperative calibration of the electromagnetic tracker (40) and the endoscopic camera (50) as a function of an image registration between the preoperative scan image of a calibration site within the anatomical region and one or more endoscopic images of the calibration site within the anatomical region.
