Atomic force microscopy is a well-established technique to image all kinds of surfaces at the atomic scale. But the force patterns that emerge can also pin down the chemical identity of individual atoms.
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Shluger, A., Trevethan, T. Atomic fingerprinting. Nature 446, 34–35 (2007). https://doi.org/10.1038/446034b
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DOI: https://doi.org/10.1038/446034b