The Large Hadron Collider uses quarks.
They just run the quarks in convinient, stable, color-neutral triplets that we all happen to call protons and more generally, hadrons.
And yes, the experiments thereof show a lot of interesting stuff that happens at quark interaction scale.
What we don't do in the usual sense of microscopy is to get a geometrically accurate image that the usual microscope presents. We don't even try - the objects at this scale simply don't have much of a shape. They are fuzzy and fleeting. Once the object interacts once with our quark beam, it's gone so instead of a single object imaged by multiple particles we get a statistical picture of many of these objects.
The fact that quarks are fermions is not decisive - many modern, as well as historical experiments are done with bosons. Aside from the whole optical microscopy, about a centyry ago, a beam of alpha particles helped us understand that both the mass and the positive electrical charge of an atom are concentrated in the nucleus.