In bone tissue engineering, mineralisation of extracellular matrix (ECM) can be stimulated using for example a perfusion bioreactor, in which fluid flow is used to apply a shear stress to the cells. Irregular scaffold geometries, however, create an extremely complex mechanical environment (i.e. fluid shear stress). To date, it was not possible to quantitatively determine the influence of mechanical stimulation on mineralized matrix formation within a realistic scaffold geometry. The goal of this project is to quantify the mechanical stimulation within irregular silk fibroin scaffolds under perfusion flow using a combination of longitudinal micro-computed tomography imaging and computational techniques. Moreover, to adapt the loading of the cells during tissue development to an optimum, an adaptive in silico model, which can simulate in vitro bone tissue formation within scaffold will be developed, and validated by comparing to the experimental outcomes.