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Our group has previously reported on performing single photon emission tomography (SPECT) studies on rats, using a GE Hawkeye millennium SPECT-CT scanner with pinhole collimators. The main challenge to obtaining quantitative physiological information from such data is the lack of X-ray attenuation data for the small animals. In this paper we present an experimental design in which a nonspecific clinical SPECT-CT scanner is used to collect both transmission and emission scan data for small animals. Necessary hardware enhancements include construction of a new animal bed and construction of a modified emission-transmission calibration object. An emission scan of this calibration object is used to determine the study-specific geometrical parameters of the gantry. In the past, we have shown that 25 adjustable parameters are needed to describe the angle-dependent positions of the detectors and pinhole collimators in order to obtain sufficient spatial precision. A CT scan of the calibration object is used to achieve three-dimensional image registration by aligning the transmission and emission fields of view. The emission system matrix is calculated by ray tracing. The algorithm corrects for X-ray attenuation and for the system geometric response that results from the finite sizes of the pinhole aperture and the detector pixels. The system matrix was applied to the reconstruction of static and dynamic SPECT images using the ML-EM algorithm with a total-variation regularization term. In future studies, time-varying data from the first minute of acquisition will be used to extract kinetic information about how radiopharmaceuticals interact with different tissue types.