Biological tissues exhibit significant heterogeneity in chemical composition and three-dimensional microstructure, both of which are crucial for proper function. Diseases often manifest through abnormal microstructures and compositions, which are important to assess using imaging techniques. While the current gold-standard, 2D histology, offers high discriminative power, it sacrifices 3D information and causes tissue damage and alterations. MicroCT, a non-destructive 3D imaging technique, addresses these limitations but struggles with soft tissue contrast due to the low X-ray attenuation of less dense tissues. To overcome this, contrast-enhanced CT (CECT), utilizing contrast-enhancing staining agents (CESAs), has been developed. A variety of CESAs have shown promise for ex vivo, non-destructive soft tissue visualization. However, the selection of CESAs often lacks a systematic understanding of their underlying chemistry and toxicity. Additionally, the slow penetration of CESAs into tissues, which can take days to weeks, further complicates their wider application. Overcoming these challenges is critical for advancing ex vivo 3D X-ray-based histology in biomedical research and clinical applications, particularly for disease diagnosis. Therefore, the current project aims to enhance CECT imaging by investigating CESAs, improving their selection criteria through a more systematic understanding of their binding mechanisms, affinity for different tissue constituents, and toxicity. In a second phase, the project will address the slow penetration issue by exploring diverse engineering solutions to enhance the current passive diffusion of CESAs into tissues.