In this thesis, intravascular imaging techniques such as NIRS-IVUS and OCT were used to research coronary atherosclerosis development and progression in pre-clinical and clinical studies. We explored and described NIRS-detected lipid-rich regions in both calcified and as well as regions with no plaque visible on IVUS-imaging In several chapters, we fused intravascular imaging with spatial information from the CT scan, resulting in a 3D reconstruction of coronary arteries with exact colocalization of atherosclerotic plaque size and composition. Computational fluid dynamics (CFD) were used to research the biomechanical factors such as wall shear stress (WSS) and helical flow in the development of atherosclerotic plaques. Both WSS and plaque composition was used to investigate plaque progression. Furthermore, some methodological chapters described the effect of using different imaging modalities in WSS analysis, the impact of different WSS definitions, and discussed differences between WSS research in pre-clinical and clinical studies.