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On page 10 in the this article there is an example of time measurement with AVR. Is the same thing possible to do with this?

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    \$\begingroup\$ Yes is probably the correct answer because they both have timer capture / compare. But rather than expect everyone to sift through long datasheets it'd be better to mention the parts in your question and also mention if after reading both if there's a specific reason you don't think it'd be possible. \$\endgroup\$
    – PeterJ
    Commented Apr 13, 2013 at 11:10

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Yes, the SAM3S M3 Cortex based micro will be able to perform various timer and compare functions, it has quite a sophisticated peripheral with up to 6 16-bit channels, which can also do event counting, frequency measurement, quadrature decoding, etc.
The details are in section 35 (pg.721) of the SAM3S datasheet.

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