A key element in the understanding of the rheological behavior of suspensions is their microstructure. Indeed, the spatial distribution of particles is known to depend on flow history in suspensions, which has an impact on their macroscopic properties. These micro-macrocouplings appeal for the development of experimental tools allowing for the rheological characterization of a suspension and the imaging of particles. In this paper, we present the technique we developed to image in three dimensions the microstructure of suspensions of non-Brownian particles, using X-ray computed tomography and subvoxel identification of particle centers. We also give examples of the information we can get in the case of Newtonian and viscoplastic suspensions, referring to Newtonian and viscoplastic suspending fluid. We compute three dimensional pair distribution functions and show that it is possible to get a nearly isotropic microstructure after mixing. Under shear, this microstructure becomes anisotropic in the shear plane (velocity-velocity gradient plane), whereas it is almost isotropic in the two other planes (velocity-vorticity and velocity gradient-vorticity planes). When changing the plane of shear (from a squeeze flow to a rotation flow), the microstructure reorganizes to follow this change of shear plane. It is known that for Newtonian suspensions the anisotropy is independent on the shear rate; we show here that for a viscoplastic suspension it depends on it. Finally, we study the structuration close to boundaries and we evidence some particle alignment along both solid surfaces and, more surprisingly, along free interfaces. (C) 2018 The Society of Rheology.