The past decade has seen major advances in the analytical capability and utility of both fixed beam and scanning beam electron microscopes. In particular, scanning transmission electron microscopy (STEM) and energy-filtering transmission microscopy (EFTEM) have benefited from the development of devices and techniques—including improved electron optics, sensitive solid-state detectors and new software for imaging and electron energy loss spectroscopy (EELS)—that optimize detection of weak spectroscopic signals arising from biological specimens while minimizing specimen damage. Here we discuss and illustrate some of these advances, especially in the context of structural imaging, detection limits and mapping techniques for the biologically important elements phosphorus and calcium. Analytical microscopy of biological tissues is absolutely dependent on cryotechniques. It is generally agreed that rapid freezing and subsequent low-temperature processing, e.g., cryosectioning or direct cryotransfer of frozen-hydrated specimens, is the most reliable way to preserve the native distribution and organization of biological structures. Equally important, however, as an adjunct to spectroscopic analysis is the use of established low-temperature, low-dose techniques for recording optimized images. By limiting beam exposure, low-dose methods greatly improve the quality of images from fragile, freeze-dried preparations. In this case, the quality and information content of, e.g., cryosections are virtually as good as conventional preparations (Fig 1).