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In this study we present the analysis of in vivo micro-CT scans using a new method based on image registration that accurately evaluates longitudinal micro-CT studies. We tested if detailed changes in the bone architecture could be detected and tracked in individual animals. A prototype in vivo micro-CT scanner (Skyscan 1076) was developed in which tibiae of rats that are lying on a bed under gas anaesthesia were scanned. For this study, three female Wistar rats were used: a sham-operated rat, an ovariectomised (OVX) rat and one rat that served as a reproducibility control. The reproducibility control rat was scanned twice in 1 day. The other animals were scanned at week 0, just before surgery, at week 4 and at week 14 after surgery. Architectural changes over time were detected by overlaying two data sets made at different time points using an algorithm that uses mutual information for optimal registration. The …