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First of all, do you use Java wrapper to OpenCV(in NDK) or you write own function in NDK which use OpenCV? Each calling wrapper from Java to NDK is very expensive, time consuming really big.

So I advice you to write own function in C++, compile it in NDK for Android and write one wrapper to it from Java code.

If you doing it now, you should use multicore process ( 4 image processed in one time)