Volume EM can be performed using transmission or scanning electron microscopes. Each approach has its own strengths and weaknesses, and the choice is dependant on the required lateral (x, y) and axial (z) resolution, and the size of the structure of interest. Historically, transmission electron microscopy (TEM) was the tool of choice for ultrastructural examination of biomedical specimens at sub-nanometer resolution. However, for many cell biology studies structural resolution is actually limited by the deposition of heavy metals onto membranes during sample preparation. In addition, voxel dimensions may only need to be half that of the smallest expected feature of interest (Briggman and Bock, 2012). Advances in scanning electron microscopy (SEM) technology are now driving a paradigm shift in electron imaging. SEMs with field emission electron sources and high efficiency electron detectors can achieve lateral resolutions in the order of 3nm, allowing visualisation of structures such as synaptic vesicles and membranes (De Winter et al., 2009; Knott et al., 2008; Vihinen et al., 2013; Villinger et al., 2012), though resolving individual leaflets of membrane bilayers remains a challenge (Vihinen et al., 2013). The use of low beam energies also limits the interaction volume, enhancing axial resolution (Hennig and Denk, 2007). In this review, volume imaging in both transmission and scanning EMs will be explored, moving from traditional manual techniques, through to the latest systems where aspects of both sample preparation and imaging have been automated.
