How to analyze-particles as beginner?

Question

I am totally new in image analysis and have tried alot with ImageJ or QuPath but unfortunately I can’t find a proper way into it. Here is an image example I would like to quantify:

Has anyone a recommendation which software I should use or how I can quantify those little “dots” also finding out their position?

I tried it with ImageJ, but the image quality is so bad that it does not allow thresholding…

With thresholding it seems impossible to quantify just the “little dots”…

Answer 1

you can solve it in simple way using OpenCV, or you can go further with more sophisticated approach like this one.

import cv2
import numpy as np

img = cv2.imread('img.png')

mask = cv2.cvtColor(img, cv2.COLOR_BGR2GRAY)
th = 35

mask[mask<th] = 0
mask[mask>0] = 255
mask = np.stack([mask, mask, mask], axis=2)

result = np.hstack((img, mask))

cv2.namedWindow("peaks", cv2.WINDOW_NORMAL)
cv2.imshow("peaks", result)
cv2.waitKey(0)
cv2.destroyAllWindows()

Answer 2

I find cv2 complicated and slow. I would do something like this:

from osgeo import gdal


thresh = 100 
raster = gdal.Open(r'image.jpg')
# Extract raster band (each band is a primary colour)
img = raster.GetRasterBand(1).ReadAsArray(x_start,y_start,x_end,y_end) # reading the image on a specific window, keep empty for whole image.

binary_img = img > thresh

Gdal is a great package, but has many dependencies and is a bit harder to install, especially on windows.