Implementation of short-scan reconstruction with compensation for geometric alignment for a microCT system

Typical microCT systems for in vivo small animal imaging have a total acquisition time on the order of 10 minutes for a single scan, with the detector read-out time often a major contributor to acquisition length. Reduction of the portion of the scan time spent in read-out can be achieved through short-scan acquisition. Knowledge of and correction for geometric misalignments is another crucial factor in obtaining high quality microCT images. In this work, we have implemented a short-scan Feldkamp algorithm with correction geometric misalignment. Due to our system misalignments, severe ghosting artifacts are present in the reconstruction. We have implemented a reconstruction algorithm with correction for the misalignments which eliminates the ghosting artifacts. Comparisons of full-scan and short-scan reconstructions of both phantom and mouse data show similar image quality. We have also compared short-scan reconstructions to full-scan reconstructions from projection data with roughly the same total acquisition time. In this case, blurring is visible in sagittal slices of the full-scan reconstructions that is not present in the short-scan reconstructions. Short-scan acquisition provides reduction of the total acquisition time resulting in microCT images without the loss in image quality obtained by simply reducing the number of projections for a full-scan acquisition. Axis of rotation horizontal transversal off-center shift and the X-ray source horizontal transversal shift are the most sensitive parameters.