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Recently, small-animal imaging technology has been rapidly developed for longitudinal screening of laboratory animals such as mice and rats. One of newly developed imaging modalities for small animals is an x-ray micro-CT (computed tomography). We have developed two types of x-ray micro-CT systems for small animal imaging. Both systems use flat-panel x-ray detectors and micro-focus x-ray sources to obtain high spatial resolution of 10 μm. In spite of the relatively large field-of-view (FOV) of flat-panel detectors, the spatial resolution in the whole-body imaging of rats should be sacrificed down to the order of 100 μm due to the limited number of x-ray detector pixels. Though the spatial resolution of cone-beam CTs can be improved by moving an object toward an x-ray source, the FOV should be reduced and the object size is also limited. To overcome the limitation of the object size and resolution, we introduce zoom-in micro-tomography for high-resolution imaging of a local region-of-interest (ROI) inside a large object. For zoom-in imaging, we use two kinds of projection data in combination, one from a full FOV scan of the whole object and the other from a limited FOV scan of the ROI. Both of our micro-CT systems have zoom-in micro-tomography capability. One of both is a micro-CT system with a fixed gantry mounted with an x-ray source and a detector. An imaged object is laid on a rotating table between a source and a detector. The other micro-CT system has a rotating gantry with a fixed object table, which makes whole scans without rotating an object. In this paper, we report the results of in vivo small animal study using the developed micro-CTs.