This thesis consists of three studies which use atomic-resolution aberration-corrected TEM techniques to investigate the structure and composition of air-sensitive crystals. The first two studies investigate the oxidation of graphene-encapsulated 2D crystals, black phosphorus (BP) and NbSe2. Recent graphene-encapsulation techniques are performed in a glovebox environment, protecting thin (few-layered to monolayer) stacks of these crystals from instantaneously degrading from oxidation. Such protection allows for some of the first detailed structural and compositional studies of these crystals in pristine condition. BP is investigated specifically with a focus on electron beam damage, which can be utilised to sculpt stable features for applications in electronic devices. Intrinsic atomic defects in NbSe2 are identified with atomicresolution imaging, geometric phase analysis (GPA) and compared to density functional theory (DFT) calculations. Point defects such as vacancies and substitutional dopants are identified and play a crucial role in the overall electronic properties of the material. The final study investigates the nucleation and growth of aluminium oxide islands using atomicresolution in-situ environmental TEM (ETEM). Electron beam sputtering is used to remove initial self-healing oxide layers and oxygen is then introduced into the ETEM chamber allowing for the growth of metal oxides at room temperatures to be observed dynamically. Oxidation is studied with respect to oxygen pressure and crystallographic orientation of the aluminium. The study reveals atomic-scale insights into the oxidation mechanism which were previously elusive to bulk spectroscopy and surface science techniques.