A nice thresholding algorithm for bacterial colony isolation Implements Huang's fuzzy thresholding method, recoded from the Java version from ImageJ.
Uses Shannon's entropy function, from Huang L.-K. and Wang M.-J.J. (1995) "Image Thresholding by Minimizing the Measures of Fuzziness" Pattern Recognition, 28(1): 41-51
Copy the python files to your working directory.
python -m unittest test_huang_thresholding.pyThere are bacterial colonies images in 'colonies.npy'
To calculate the Huang Thresholding, you would use the following code to first get the data into numpy and get the histogram values, and then calculate the threshold.
import numpy as np
from huang_thresholding import HuangThresholding
colony_data = np.load("colonies.npy")
histogram_data, _ = np.histogram(colony_data, bins=range(257))
huang_thresholding = HuangThresholding(histogram_data)
threshold = huang_thresholding.find_threshold()