Organ approximation in μCT data with low soft tissue contrast using an articulated whole-body atlas

In this article, we present an approach for organ approximation in low contrast mu CT data of mice using a whole-body mouse atlas (Segars et al. [1]). Starting from a set of landmarks on bone and joint locations, further correspondences are derived on surface representations of the lung by atlas-based registration and on the skin by employing a local geodesic shape context. Subsequently, landmarks on the skeleton, the lung and the skin are used to constrain a Thin-Plate-Spline (TPS) based mapping of major organs from the atlas to the subject domain. The feasibility of the method has been tested by means of 26 CT mouse datasets and a different whole-body mouse atlas (Digimouse [2]). Proper mapping of the lung and the skin as well as major organs could be achieved in all cases yielding a mean Euclidean distance between surface nodes of 0.42 +/- 0.068 mm for the lung and 0.34 +/- 0.036 mm for the skin. The performance of the organ interpolation has been assessed on basis of manual segmentations of two CT datasets of mice with injected contrast agent and the Digimouse. The calculated dice indices of volume overlap show significant improvement compared to earlier studies.