A medical imaging system generates 3D anatomical images from acquired 2D anatomical images. The system includes a synchronization processor for providing a synchronization signal identifying a particular phase of heart operation of a particular patient. An image acquisition device acquires 2D anatomical images of a patient heart in angularly variable imaging planes over multiple different heart cycles at the particular phase of heart operation in response to the synchronization signal and in response to recorded data indicating imaging previously being performed at particular imaging plane angles. An image processor stores the recorded data to prevent imaging overlap at the particular imaging plane angles and to prevent unnecessary radiation exposure of the patient. The image processor processes 2D images acquired by the image acquisition device of the patient heart in multiple different imaging planes having relative angular separation, to provide a 3D image reconstruction of the patient heart.