This thesis reports a novel method to prepare liquid specimens for atom probe tomography (APT) by graphene encapsulation, and demonstrates direct imaging of nanoparticles and biomolecules in their hydrated state with APT, as well as extends the graphene encapsulation method to achieve high-throughput APT imaging. The proposed graphene encapsulation method lays the foundation for a new route to analyze materials atom-by-atom in a controlled liquid environment.