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X-ray micro-CT is widely used for small animal imaging in preclinical studies of cardiopulmonary disease, but further development is needed to improve spatial resolution, temporal resolution, and material contrast. This study presents a set of tools that achieve these improvements. These tools include the mathematical formulation and computational implementation of algorithms for calibration, image reconstruction, and image analysis with our custom micro-CT system. These tools are tested infatcat:wmedh7actrbwjejh5cd4r2pjdq