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Single and multiple layers of self-assembled InAs quantum dots (QDs) produced by the indium-flush technique have been studied by transmission electron microscopy (TEM) in an effort to develop techniques to reproducibly grow QDs of uniform size and shape. To monitor the changes in QD dimensions, plan-view samples of capped single layers were studied as well as cross-sectional samples of QDs in multiple layers and stacks. The changes in the observed round- and square-shaped QD images under various plan-view TEM imaging conditions, as well as the contrast reversal in the center of QD images viewed in cross-section are modeled using the many-beam Bloch-wave approach, including strain. The sizes and shapes of the QDs are determined through the interpretation of the observed (primarily strain) contrast in plan-view and the observed (primarily atomic number) contrast in cross-sectional TEM. © 2000 American Institute of Physics.