"Automated Registration of Whole-Body Follow-Up MicroCT Data of Mice"

Martin Baiker, Marius Staring, Clemens W.G.M. Löwik, Johan H.C. Reiber and Boudewijn P.F. Lelieveldt

Abstract

In vivo MicroCT imaging of disease models at multiple time points is of great importance for preclinical oncological research, to monitor disease progression. However, the great postural variability between animals in the imaging device complicates data comparison.
In this paper we propose a method for automated registration of whole-body MicroCT follow-up datasets of mice. First, we register the skeleton, the lungs and the skin of an articulated animal atlas (Segars et al. 2004) to MicroCT datasets, yielding point correspondence of these structures over all time points. This correspondence is then used to regularize an intensity-based B-spline registration. This two step approach combines the robustness of model-based registration with the high accuracy of intensity-based registration.
We demonstrate our approach using challenging whole-body in vivo follow-up MicroCT data and obtain subvoxel accuracy for the skeleton and the skin, based on the Euclidean surface distance. The method is computationally efficient and enables high resolution whole-body registration in ≈17 minutes with unoptimized code, mostly executed single-threaded.

Source code

The source code of the methods described in this paper can be found in the image registration toolkit elastix, available at https://github.com/SuperElastix/elastix.

The metric can be selected through: (Metric <AnyMetric> "CorrespondingPointsEuclideanDistanceMetric").

The exact parameter settings used in this paper can be found at the parameter file database of elastix at entry Par0014.

BibTeX entry