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The goal of this work was the development of a low-cost micro-CT scanner, which could be used as an add-on in our previously developed PET systems for small-animals. The scanner design consists of a single-processor computer controlling a micro-focus X-ray tube and a flat panel detector, assembled in a common rotating gantry. The geometrical configuration was selected to achieve a spatial resolution of about 12 lp/mm with a field of view appropriate for small animals such as mice and rats. The radiated dose is controlled during the acquisition by two different elements: an aluminium filter and a tungsten shutter, attached to the X-ray source. The shutter is controlled by the computer in synchronism with the gantry rotation and the detector image integration. In order to achieve high performance with regards to per-animal screening time and cost, the acquisition protocol is able to take advantage from the highest frame rate of the detector also performing on-the-fly corrections for the detector raw data. These corrections include geometrical misalignments, sensor non-uniformities and defective elements, as well as conversion to attenuation images. An FDK reconstruction algorithm adapted to the specific cone-beam geometry has been implemented. Symmetries are exploited to accelerate the algorithm and fast back-projection techniques have been developed for those protocols where high resolution is not a requirement.