Unraveling the underlying mechanisms involved in single and collective cell migration, organization, tissue formation and regeneration are some of the currently spearheading research topics worldwide. To overcome the intrinsic difficulties associated to realistic environments in 3D, a multi-disciplinary framework combining computer simulations and experiments is proposed. The success of this approach relies on result validation (quantita-tive comparison: computational vs. experimental), so we have polished different techniques and computational tools to get as accurate measurements as possible. For that, we take advantage of our own designed microfluidic devices and perform thorough image and statistical analyses.