Protocol for 3D digital dynamic histomorphometry of mouse bone via time-lapse registration of serial microCT scans

Serial in vivo microCT enables the quantification of dynamic bone remodeling by capturing formation and resorption over time. Here, we present a protocol to register pre- and post-intervention scans of rodent long bones through an intuitive drag-and-click workflow. We describe steps for rigid registration, enabling spatial mapping and quantification of formed, resorbed, and quiescent cortical and trabecular bone at periosteal and endosteal surfaces across multiple tibial regions. This protocol provides a non-destructive and complementary alternative to classic, fluorochrome-based dynamic histomorphometry.