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Twelve-week-old male Wistar rats were subjected to OTM by applying a constant orthodontic force (OF) of 25cN between one of the upper first molars and a mini-screw. In vivo micro-CTs were taken before and after 10, 17, 24 and 31\u00a0days of force application, and superimposed by a novel and rigid voxel-based registration method. Then the tooth and alveolar bone segment at different time points became comparable in the same coordinate system, which facilitated the analysis of their dynamic changes in 3D. By comparison between time points and between OF and no OF sides, this study showed that the OTM rate was not constant through time, but conformed to a \u2018V\u2019 shape changing pattern. Besides, OF induced displacement of both loaded and unloaded teeth, and the latter mirrored the former in a delayed manner. In addition, bone morphometric changes synchronized with OTM rate changes, implying that a higher OTM rate was concomitant with more alveolar bone loss. 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