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The features appear to be circular in the fluorescence image, but they are square-like in the AFM image. This may be due to the resolution difference of the two techniques. Scanning confocal microscopy has a lower resolution (- 300 nm, in the case of our equipment), thus the fluorescence image may not represent the real shape of the features.
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The fluorescence was always monitored from the same region on the surface, so the average pixel intensity should be proportional to the number of QDs present in the image if there is no quenching.
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