We describe some technical aspects of the application of multi-isotope imaging mass spectrometry (MIMS) to biological research, particularly the use of isotopic tags to localize and measure their incorporation into intracellular compartments. We touch on sample preparation, on image formation, on drift correction and on extraction of quantitative data from isotope ratio imaging. We insist on the wide variety of sample types that can be used, ranging from whole cells prepared directly on Si supports, to thin sections of cells and tissues on Si supports, to ultrathin TEM sections on carbon-coated grid. We attempt to dispel the myth of difficulties in sample preparation, which we view as a needless deterrent to the application of MIMS to the general biological community. We present protocols for the extraction of isotope ratio data from mass images. We illustrate the benefits of using sequential image plane acquisition followed by the application of an autocorrelation algorithm (nanotracking) to remove the effects of specimen drift. We insist on the advantages to display the isotope ratios as hue saturation intensity images. (c) 2006 Elsevier B.V. All rights reserved.