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Two of the key challenges in determining the relative merits of porous implants are the objective quantification of their open pore networks and bone growth into the pores. The gold-standard currently employed to quantify bone ingrowth is histomorphometry which can identify different cell types and provide information on bone quality, but it is a 2D measure that samples a very small region. With recent advances in X-ray micro-computed tomography technology (μCT) improving resolution and image quality, μCT offers researchers a new perspective on evaluating bone ingrowth into implants. μCT allows direct 3D imaging and measurements of implants and bone structures that can also be non-destructive, allowing pre- and post-operative comparisons. However, quantification of images from μCT datasets is not fully standardised leading to differing methods between researchers. In particular there is no accepted objective method to identify the region-of-interest positioning and size. In this thesis, a novel approach was developed to address this problem by creating a contralateral limb model as a template for quantification of the operated limb. This model was created by first averaging many normal contralateral limbs. The model was then applied to operated limbs, enabling the automated positioning and size of the volume-of-interest selection for quantification. This in turn allows the objective quantification of bone ingrowth into implants, e.g. a 3D measure of bone ingrowth volume fraction and 3D curvature of partially healed bone, both of which were developed by application of the model. These are used in conjunction with complementary histomorphometric analyses. This new technique was applied to two case studies, looking at the bone ingrowth over time in a Ti implant and in a sol-gel derived bioactive glass scaffold. Early bone ingrowth into porous Ti is an important factor in the successful long-term bone fixation of the implant, while in porous bioactive glasses; it is the first stage of bony defect regeneration. The Ti implants were created by a process called selective laser melting, an exciting additive manufacturing technique that allows precise control of the final structure. The Ti implants were separately studied from a commercial view-point, resulting in the development of a novel non-destructive method of monitoring 3D porous structures during a series of cleaning procedures.