Remove spurious small islands of noise in an image - Python OpenCV

Question

I am trying to get rid of background noise from some of my images. This is the unfiltered image.

To filter, I used this code to generate a mask of what should remain in the image:

 element = cv2.getStructuringElement(cv2.MORPH_RECT, (2,2))
 mask = cv2.erode(mask, element, iterations = 1)
 mask = cv2.dilate(mask, element, iterations = 1)
 mask = cv2.erode(mask, element)

With this code and when I mask out the unwanted pixels from the original image, what I get is:

As you can see, all the tiny dots in the middle area are gone, but a lot of those coming from the denser area are also gone. To reduce the filtering, I tried changing the second parameter of getStructuringElement() to be (1,1) but doing this gives me the first image as if nothing has been filtered.

Is there any way where I can apply some filter that is between these 2 extremes?

In addition, can anyone explain to me what exactly does getStructuringElement() do? What is a "structuring element"? What does it do and how does its size (the second parameter) affect the level of filtering?

Answer 1

One can also remove small pixel clusters using the remove_small_objects function in skimage:

import matplotlib.pyplot as plt
from skimage import morphology
import numpy as np
import skimage

# read the image, grayscale it, binarize it, then remove small pixel clusters
im = plt.imread('spots.png')
grayscale = skimage.color.rgb2gray(im)
binarized = np.where(grayscale>0.1, 1, 0)
processed = morphology.remove_small_objects(binarized.astype(bool), min_size=2, connectivity=2).astype(int)

# black out pixels
mask_x, mask_y = np.where(processed == 0)
im[mask_x, mask_y, :3] = 0

# plot the result
plt.figure(figsize=(10,10))
plt.imshow(im)

This displays:

To retain only larger clusters, try increasing min_size (smallest size of retained clusters) and decreasing connectivity (size of pixel neighborhood when forming clusters). Using just those two parameters, one can retain only pixel clusters of an appropriate size.