How to retrieve a std::vector of points from cv::Mat?

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You could implement some kind of tree search. Start with a point in your mask and add its neighbours to a stack if they are also in the masked region and remove (set to zero) your starting point. Do the same until your stack is empty. This gives you a running time of O(N) if N is the number of pixels in your mask instead of O(colsrows). This of course only works well if your mask is basically one region. If it consists of many small regions, you will have to look at your whole picture to find each region so that you could again end up in something like O(colsrows).

If I understood it correctly, the task you are looking for is performed by the findCountours function. The findContours method outputs a vector<vector<cv::Point> >. If you apply findCountours in your Mat you will have as many vector<cv::Point> as blobs in your binary image, and each of these vectors contains all the cv::Points that make the blob.