Electron tomography (ET) is a technique for determining three-dimensional cellular ultrastructure at the nanometer scale from a series of projection images recorded in the electron microscope from a specimen that is tilted through a range of angles. Although the principles of ET have been known for decades, its use has become increasingly widespread in recent years due to technological improvements in instrumentation, specimen preparation techniques, as well as computer acquisition and processing methods. In our laboratory we have been developing unconventional approaches to ET based on scanning transmission electron microscopy (STEM) and energy-filtering electron microscopy (EFTEM). We have shown that these approaches expand the capabilities of ET by enabling analysis of thicker specimens and providing quantitative information about distributions of specific chemical elements as well as heavy atom clusters used to label specific proteins. Until now we have employed standard reconstruction algorithms such as the weighted back-projection and simultaneous iterative reconstruction technique (SIRT). The extent to which these algorithms limit the available information is not yet fully established.