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OpenCV 2 has many things that wasn't in OpenCV 1. Mat instead of IplImage is just one them. But format of OpenCV 1 is still part of the interface for competability reasons, so you will need to make minimal changes (if any) in your code when you move to newer version of OpenCV. Of course if you want to use some of new features of OpenCV 2 you will have to use new interface, but those changes can be made gradually in the future.
