Feature depths can be determined from image sections. In such cases a feature depth is then determined by the placement of a single cursor on the top and bottom of the feature. A more statistically robust method of determining feature depths is the use of the "depth" feature which exploits image bearings or pixel histograms.
This image shows a 10 nm thick film of AuPd for SEM coating on V4 mica. An area has been scratched to allow for a film thickness measurement. A box has been place over a region of the scratch. The right shows a histogram of the pixel heights in that box. The broader portion of the bilobed distribution represents the film-- the narrower portion the substrate. For an ideally plane-fit image, the broadness of these histograms would reflect the Ra. The separation of the two distributions represents the feature depth which is found to be 10.12 nm. For this application that is ideal as a 10-12 nm film of AuPd is ideal for coating for SEM.
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