Embodiments of the present invention provide methods and apparatus for imaging a tissue specimen excised during surgery with a combined positron emission tomography (PET) and micro computed tomography (micro CT) scanner. The specimen is scanned with a CT imaging system of the combined PET and micro CT scanner. The specimen is also scanned with a PET imaging system of the combined PET and micro CT scanner. A PET image is constructed based on data acquired by the PET imaging system. A micro CT image is constructed based on data acquired by the micro CT imaging system. The micro CT image includes at least one visualization of a lesion marker.
