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I will try to explain what I am trying to do, as it seems to be relevant in order to understand my question.

I am currently trying to do face recognition from a webcam connected to a Raspberry Pi and using the openCV Java wrapper.

Can I use the Raspberry Pi openCV version with the Java wrapper running with Java SE embedded?

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Reading this article (which appears quite well written) it would seem that the answer is yes:

http://bigdinotech.com/tutorials/beaglebone-black-tutorials/building-opencv-on-the-beaglebone-black-or-raspberry-pi/

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