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Abstract In the field of nuclear medicine, single photon emission tomography and positron emission tomography are the two most common techniques in molecular imaging, but the available radioactive tracers have been limited either by energy range or difficulties in production and delivery. Thus, the use of a Compton camera, which features gamma-ray imaging of arbitrary energies from a few hundred keV to more than MeV, is eagerly awaited along with potential new tracers which have never been used in current modalities. In this paper, we developed an ultra-compact Compton camera that weighs only 580 g. The camera consists of fine-pixelized Ce-doped Gd3Al2Ga3O12 scintillators coupled with multi-pixel photon counter arrays. We first investigated the 3-D imaging capability of our camera system for a diffuse source of a planar geometry, and then conducted small animal imaging as pre-clinical evaluation. For the first time, we successfully carried out the 3-D color imaging of a live mouse in just 2 h. By using tri-color gamma-ray fusion images, we confirmed that 131I, 85Sr, and 65Zn can be new tracers that concentrate in each target organ.