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Electron energy loss spectrum-imaging (EELSI) in the energy filtering transmission electron microscope (EFTEM) can provide more accurate analysis of elemental distributions than that obtainable by the standard two-window or three-window background subtraction techniques. Spectra containing many channels can be extracted from regions of interest and analyzed using established methods for quantitation. For example, the pre-edge background can be fitted by an inverse power law and subtracted from the post-edge spectrum. EELSI in the EFTEM is often superior to spectrum-imaging in the scanning transmission electron microscope for mapping specimen regions of size greater than 1 μm. This is due the much larger total beam current that is available at the specimen in a fixed-beam microscope relative to a scanned-beam microscope. Our aim here is demonstrate the advantages of such EELSI measurements for analysis of biological specimens. However, we also indicate some potential pitfalls in acquiring elemental maps in the EFTEM, which can be attributed to specimen instabilities during the acquisition.