Synchrotron radiation-based micro computed tomography contributes to the increasing demand for uncovering nondestructively the microscopic morphology of bony tissues and their interface regions with implants using isotropic spatial resolution in three-dimensional space. Using the microscopic ring structure of otoliths, the coherence-related interplay between density resolution and spatial resolution is demonstrated. The monochromatised, highly intense synchrotron radiation allows analysis of the morphology of arthritic joints without significant beam-hardening artefacts in a quantitative manner. It further enables intensity-based segmentation of metallic implants within bone and thereby to quantitatively study the bone morphology around different kinds of middle and inner ear implants. This knowledge permits improving medical interventions and optimising the implant's design with respect to surface modification, mechanical properties, and shape.