We describe here how to apply the three-dimensional imaging technique of refractive index matched scanning to hydrogel spheres. Hydrogels are water based materials with a low refractive index, which allows for index matching with water-based solvent mixtures. We discuss here various experimental techniques required to handle specifically hydrogel spheres as opposed to other transparent materials. The deformability of hydrogel spheres makes their identification in three-dimensional images non-trivial. We will also discuss numerical techniques that can be used in general to detect contacting, non-spherical particles in a three-dimensional image. The experimental and numerical techniques presented here give experimental access to the stress tensor of a packing of deformed particles.