There is no reason why you could not scan a collagen hydrogen (provided you can fit it in some kind of holder unless its a solid, or semi-solid). However, the protocol you want to set depends highly on the system you have (Bruker, Scanco, Mediso etc), and what you expect to see in the images. The scanners are generally not standardized so protocols are not interchangeable. You will also have to think about what details you want to see in the image (if you want high or low resolution, set by the voxel size), if you want frame averaging and how long you want each projection to last. I imagine there would be little attenuation so beam hardening would be minimal.