The IVIS Spectrum CT, a preclinical imaging system that integrates an advanced optical imaging and low-dose microCT (micro computed tomography) into a single instrument system, is now available. Spectrum CT enables simultaneous molecular and anatomical longitudinal studies. An array of applications exist for the new instrument with musculoskeletal, vascular, oncology, phenotyping, cardiovascular, and respiratory disease among those areas particularly enabled by the integration of optical and microCT imaging. Features include optical sensitivity capable of detecting a few cells and 3-D reconstructions of optical molecular bioluminescence and fluorescence signals, integrated with 3-D anatomical microCT images.