AbstractWe present a simple and robust method to acquire quantitative maps of compositional fluctuations in nanostructures from low magnification high-angle annular dark field (HAADF) micrographs calibrated by energy-dispersive X-ray (EDX) spectroscopy in scanning transmission electron microscopy (STEM) mode. We show that a nonuniform background in HAADF-STEM micrographs can be eliminated, to a first approximation, by use of a suitable analytic function. The uncertainty in probe position when collecting an EDX spectrum renders the calibration of HAADF-STEM micrographs indirect, and a statistical approach has been developed to determine the position with confidence. Our analysis procedure, presented in a flowchart to facilitate the successful implementation of the method by users, was applied to discontinuous InGaN/GaN quantum wells in order to obtain quantitative determinations of compositional fluctuations on the nanoscale.