Transient changes in the intracellular distribution of calcium ions act as a trigger for a large number of important physiological functions [1,2]. The nature of intracellular Ca changes is complex, however, because Ca is dynamically distributed between several compartments, the most important being the cytosol, mitochondria and the endoplasmic reticulum (ER). Within each compartment, Ca is further partitioned between a large pool bound to buffers (mainly proteins) and a much smaller pool of "free Ca 2+ ." Although small, concentration changes in the latter pools, especially cytosolic free Ca 2+ ([Ca 2+ ] i ), are especially critical for signal transduction. To obtain a general picture of the interactions and spatio-temporal concentration fluctuations that underlie Ca 2+ signaling, correlated measurements of both free and bound Ca pools are highly advantageous [3]. Optical imaging of fluorescent indicators in living cells is the method of choice for measuring [Ca 2+ ] i , while analytical electron microscopy-either electron probe x-ray microanalysis (EPMA) or electron energy loss spectroscopy (EELS)-is the well established approach for determining total Ca (essentially equivalent to bound Ca) within specific subcellular compartments. When these techniques are used in tandem, the combined information provides unique insights into the regulation of Ca 2+ signaling.To illustrate the kinds of information available with this approach, we present here results from recent work aimed at elucidating the role of mitochondrial and ER Ca 2+ transport in the modulation of Ca 2+ signaling in neurons.Our first example explores the role of mitochondrial Ca 2+ uptake in blunting the impact of depolarization-induced Ca 2+ entry on the signaling Ca 2+ pool, i.e., on [Ca 2+ ] i [4,5]. Optical measurements (fura-2) show that sympathetic neurons respond to depolarization with a rise in [Ca 2+ ] i that has several prominent phases (Fig. 1, upper panel). Following a sharp initial rise, [Ca 2+ ] i is clamped at a steady elevated concentration (~750 nM for a depolarization to ~0 mV) for the duration of the stimuli (<2 min), even though Ca 2+ entry continues; upon repolarization (which closes membrane channels and stops Ca 2+ influx), [Ca 2+ ] i recovers only slowly, exhibiting a plateau phase ([Ca 2+ ] ĩ 400 nM) of several minutes duration (arrow). The explanation for this complex behavior is revealed by parallel EMPA measurements of mitochondrial total calcium ([Ca] MT ) ( Fig. 1, lower panel), which show that: 1) continuous Ca 2+ uptake by mitochondria during sustained stimulation targets entering Ca 2+ directly into mitochondria, thereby accounting for the blunted rise and clamped phase of [Ca 2+ ] i ; and 2) subsequent release of the accumulated mitochondrial Ca load, at a rate determined by the responsible transporters and of a length determined by the size of the load, underlies the delayed [Ca 2+ ] i recovery.During the recovery phase, ER Ca 2+ transport also comes into play [6]. EPMA data on total ER Ca concentrations ([Ca] ER ),...