Semi-automatic misalignment correction for a small animal micro-CT scanner with variable geometry

An enginereed micro-CT scanner for in vivo imaging of small animals (Xalt, which stands for X-ray AnimaL Tomograph) has been recently built at the Institute of Clinical Physiology of the National Research Council (IFC-CNR, Pisa, Italy), in partnership with the University of Pisa. The Xalt scanner is a cone beam micro-CT based on a 2-dimensional flat-panel detector and microfocus x-ray source. The magnification and detector orientation can be manually varied to select the spatial resolution, field of view (FoV) and sensitivity that match the needs of several different imaging protocols for mice, rats and test tubes. Even with high precision mechanical assembly, recalibration for geometric misalignments is necessary after each modification of the scanner geometry. To avoid the burden of geometric recalibration, a semi-automatic cone beam calibration method has been applied and integrated in the reconstruction software. The calibration method does not require measurements on specific phantoms, as it is based on the recovery of redundancies in the projection data of generic objects that are lost when the scanner components are out of alignment. By using this method, our variable geometry micro-CT can be realigned at each scan by analyzing the projection data set (or part of it), without additional phantom measurements. To assess the reliability of our method we have made several acquisitions on a phantom, each carried after mechanical stress of the positioning system. We showed that the semi-automatic calibration method is an effective aid for a fast and reliable scanner realignment, without additional acquisitions.