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.

T

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.