Methods are being developed to map the distribution of elements in cellular oganelles and large macromolecular assemblies using the technique of electron-spectroscopic imaging. Experiments are being performed in a scanning transmission electron microscope (STEM) equipped with a cold field-emission gun and a magnetic sector electron spectrometer coupled to a parallel detection array. We have shown that mapping single atoms in biological structures is now becoming within the reach of this instrumentation. Imaging can be performed at low dose using the annular dark-field signal prior to nano-analysis at high dose, so that structure can be correlated with the distribution of specific atoms. Measurements confirm theoretical predictions that single atom detection of phosphorus and other elements can be realized by using a nanometer diameter probe.