I am trying to extract and count the number of buds in of a flower in an x-ray image. in the example images it is so obvious where the buds are and how many buds there are, but I can not get the buts seperated enough for proper counting. It is no problem if I get some false hits on the stem, because we plan to feed the cropped buds into a NN for classification
the result I get is
The perfect result would be the below image, this is impossible i know, but it should be better than the above result
You can tweak this image by changing the threshold but then for the other images the result gets far worse.
16 bit original detector images
used code to get to current result.
// read first sample image
cv::Mat img8 = cv::imread("img8/006-img8bit.tif", cv::IMREAD_UNCHANGED);
// do some blur to remove most of the noise
cv::Mat imBlur;
cv::blur(img8, imBlur, cv::Size(5, 5));
// do close on grey image
cv::Mat imClose;
cv::Mat element = cv::getStructuringElement(cv::MORPH_ELLIPSE, cv::Size(15, 15));
cv::morphologyEx(imBlur, imClose, cv::MORPH_CLOSE, element);
// threshold image met auto threshold t.o.v. achtergrond kleur.
cv::Mat imgThresh;
//cv::adaptiveThreshold(imClose, imgThresh, 255, cv::ADAPTIVE_THRESH_MEAN_C, cv::THRESH_BINARY, 71, 15.0);
cv::threshold(imClose, imgThresh, 29, 255, cv::THRESH_BINARY); // automatic thresholding
// fillup small holes in threshold image
element = cv::getStructuringElement(cv::MORPH_ELLIPSE, cv::Size(5, 5));
cv::Mat imThClosed;
cv::morphologyEx(imgThresh, imThClosed, cv::MORPH_CLOSE, element, cv::Point(-1, -1), 2);
// try to remove most stems from image
cv::Mat imgThClean;
element = cv::getStructuringElement(cv::MORPH_ELLIPSE, cv::Size(23, 23));
//cv::erode(imThClosed, imgThClean, element);
cv::morphologyEx(imThClosed, imgThClean, cv::MORPH_OPEN, element, cv::Point(-1, -1), 2);
// make contours
std::vector<std::vector<cv::Point> > contours;
cv::findContours(imgThClean.clone(), contours, cv::RETR_EXTERNAL, cv::CHAIN_APPROX_SIMPLE);
// draw the contours
cv::drawContours(img8, contours, -1, cv::Scalar(255));
