A method, device, and system are provided for placing a port (12, 22, 32) for a surgical tool (20, 30) relative to real-time anatomical data. The method comprises: placing an endoscope (10) in a standard port (12); determining real-time anatomical data from an image from the endoscope; using a port localization apparatus (210) to identify an optimal location for an instrument port relative to the image from the endoscope; and creating an instrument port at the identified location.