The interplay between structure and transport is complex, especially when the structure is soft and deformable as is the case in most biological systems. A multidisciplinary approach is a prerequisite to elucidate this complex interplay between structure and external fields. In the past we made use of the toolbox of biological building blocks to study fundamental questions in soft matter, focusing on how flow is affected by structure and vice versa. We applied experimental techniques like in situ ultra-fast confocal microscopy and Small Angle neutron and X-ray scattering in combination with shear flow to access information on a single particle as well as ensemble level, facilitating direct comparison with theory and computer simulations. Presently, we apply these concepts to real life systems, such as the process of fueling up the brain. The brain is supplied with oxygen and nutrients via the microvascular network. To understand the flow through this network the complexity of the fluid, blood, as well as the geometry needs to be taken into account. We study the break up process of blood aggregates in complex flow by tuning the blood aggregation, while we map the brain vasculature into 3D microfluidic channels, using imaging from the Human Brain Project and the novel Scanning Laser Etching technique to produce the channels. This also allows us to program any flaws or locations for oxygen release.