A method, system and apparatus for image capture and registration are described. The method includes: obtaining a position of an imaging device in a tracking system frame of reference； obtaining a position of a patient in the tracking system frame of reference； determining, based on the position of the imaging device and the position of the patient, a transformation for registering an imaging device frame of reference with a patient frame of reference； receiving an instruction to capture an image, the instruction including coordinates identifying a target area in the patient frame of reference； applying the transformation to convert the coordinates to the imaging device frame of reference； and controlling the imaging device to capture an image based on the converted coordinates.
