You can do something like this:
// your input binary image
// assuming that blob pixels have positive values, zero otherwise
Mat binary_image;
// threashold specifying minimum area of a blob
double threshold = 100;
vector<vector<Point>> contours;
vector<Vec4i> hierarchy;
vector<int> small_blobs;
double contour_area;
Mat temp_image;
// find all contours in the binary image
binary_image.copyTo(temp_image);
findContours(temp_image, contours, hierarchy, CV_RETR_CCOMP,
CV_CHAIN_APPROX_SIMPLE);
// Find indices of contours whose area is less than `threshold`
if ( !contours_all.empty()) {
for (size_t i=0; i<contours.size(); ++i) {
contour_area = contourArea(contours_all[i]) ;
if ( contour_area < threshold)
small_blobs.push_back(i);
}
}
// fill-in all small contours with zeros
for (size_t i=0; i < small_blobs.size(); ++i) {
drawContours(binary_image, contours, small_blobs[i], cv::Scalar(0),
CV_FILLED, 8);
}
