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.