How to make a deep copy of a rectangular region of a cv::Mat?
// select a ROI
Mat roi(img, Rect(10,10,100,100));

Mat deepRoiExplorer=roi.clone();

Mat source...;        // your source image
Rect sourceRect(...); // your ROI

// using clone
Mat target = source(sourceRect).clone();

// using copyTo
Mat target(sourceRect.size(), source.type());
source(sourceRect).copyTo(target);