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Cone‐beam microcomputed tomography (microCT) is one of the most popular choices for small animal imaging which is becoming an important tool for studying animal models with transplanted diseases. Region‐of‐interest (ROI) imaging techniques in CT, which can reconstruct an ROI image from the projection data set of the ROI, can be used not only for reducing imaging‐radiation exposure to the subject and scatters to the detector but also for potentially increasing spatial resolution of the reconstructed images. Increasing spatial resolution in microCT images can facilitate improved accuracy in many assessment tasks. A method proposed previously for increasing CT image spatial resolution entails the exploitation of the geometric magnification in cone‐beam CT. Due to finite detector size, however, this method can lead to data truncation for a large geometric magnification. The Feldkamp‐Davis‐Kress (FDK …