While digital image processing is widely used for 3-D structure reconstruction from tilt-series recorded in the electron microscopy (EM), a few scanning transmission electron microscopy (STEM) specific procedures have been developed which provide us with useful quantitative information on the structure of biological macromolecules and their assemblies. These include determination of the mass- or elemental distribution within the structure under investigation. Simple procedures evaluate the mass of proteinous particles, the mass-per-length of filaments or the mass-per-area of sheets. Averaging of STEM elastic darkfield (DF) micrographs from regular structures has demonstrated the possibility of obtaining mass maps, which can reveal domains as small as 1,000 daltons. While the elastic DF image defines the (regular) structure at high-resolution, thereby providing a rule for averaging, much weaker signals are simultaneously acquired by detectors positioned at specific energy losses. Since many (approximately 500) identical subunits from a single multichannel micrograph can be averaged, and many such averages can readily be accumulated due to the precise morphological characterization obtained from the elastic DF image, an element map is expected to emerge from thus averaged electron energy loss windows.