I<ve created a script to threshold a microscopic image and I would like to know how to fill some white spaces of the image. As you see in the picture my aim is to make a filter to separate only the blue zones. All other white zones (red arrow) should be erased or converted (filled out) to black.

Here is my code:

original = cv2.imread(inputfile + ".jpg")
#cv2.imread(inputfile + ".jpg")
original = cv2.resize(original, (1280, 960)) #resize of original image
img = cv2.cvtColor(original, cv2.COLOR_BGR2GRAY)
median = cv2.medianBlur(img, 3)
ret, th = cv2.threshold(median, 160, 255, cv2.THRESH_BINARY+cv2.THRESH_OTSU)
kernel = np.ones((1,1), np.uint8)
opening = cv2.morphologyEx(th, cv2.MORPH_OPEN, kernel)
edge_touching_removed = clear_border(opening)
contours, hierarchy = cv2.findContours(edge_touching_removed, cv2.RETR_TREE, cv2.CHAIN_APPROX_SIMPLE)

The thing is ... after apply this threshold I will apply contours to the blue zone to caculate area. That is ok... but the thing is I don<t know how to erase the others zones.

Should I export that threshold image and I painted manually? I dont wanna do that... I was thinking that maybe there is a manual fill out code. I used the cv2 morphology but I dont know if I need to do another filter for that.

Thanks