This thesis considers the theory and calculations of image formation mechanisms for various modes of three-dimensional imaging in aberration-corrected scanning transmission electron microscopy. Discrete tomography is used to determine and refine the three-dimensional structure of molecular nanowire bundles. The structure determination is expedited by the use of annular dark-field imaging, an incoherent imaging mode which provides directly interpretable images. The development of spherical aberration correctors and the subsequent reduction in probe sizes, including the depth of field, has made optical depth sectioning a feasible technique. The localisation in three dimensions of substitutional impurity atoms in zone-axis imaging is discussed. Both the channelling of the probe and the pre-focussing effect of the atomic column play an important role in determining the depth response of the impurity atom. Interband scattering within a sample is shown to be influential in imaging crystals containing dislocations and optical depth sectioning is explored as a possible option for overcoming surface relaxation effects in the imaging of screw dislocations end-on. The possibility of extending the optical depth sectioning approach using aberration-corrected scanning confocal electron microscopy is discussed. The coherent and incoherent imaging modes, involving elastically and inelastically scattered electrons respectively, are investigated.