A location tracking system maps anatomical structures in a first coordinate system, in a fixed position within a medical imaging system, which captures 3D images in a second coordinate system. The 3D images are converted to and stored in a standardized format in a third coordinate system in accordance with a first coordinate transformation. A first 3D image captured by the imaging system is registered with the first coordinate system so as to produce a second coordinate transformation. The first and second coordinate transformations are combined so as to derive a third coordinate transformation between the first and third coordinate systems. A second 3D image of a body of a subject, captured by the imaging system, is processed in order to extract image features in the third coordinate system. The extracted image features are joined with location data captured by the location tracking system by applying the third coordinate transformation.
