021-scratch_assay_using_scikit_image.py

#!/usr/bin/env python
__author__ = "Sreenivas Bhattiprolu"
__license__ = "Feel free to copy, I appreciate if you acknowledge Python for Microscopists"

# https://www.youtube.com/watch?v=jcUx-TQpcM8

#Scratch Assay on time series images

import matplotlib.pyplot as plt
from skimage import io
from skimage.filters.rank import entropy
from skimage.morphology import disk
import numpy as np
from skimage.filters import threshold_otsu


import glob

time = 0
time_list=[]
area_list=[]
path = "images/scratch_assay/*.*"
for file in glob.glob(path):
    dict={}
    img=io.imread(file)
    entropy_img = entropy(img, disk(3))
    thresh = threshold_otsu(entropy_img)
    binary = entropy_img <= thresh
    scratch_area = np.sum(binary == 1)
    print("time=", time, "hr  ", "Scratch area=", scratch_area, "pix\N{SUPERSCRIPT TWO}")
    time_list.append(time)
    area_list.append(scratch_area)
    time += 1

#print(time_list, area_list)
plt.plot(time_list, area_list, 'bo')  #Print blue dots scatter plot

#Print slope, intercept
from scipy.stats import linregress
#print(linregress(time_list, area_list))


slope, intercept, r_value, p_value, std_err = linregress(time_list, area_list)
print("y = ",slope, "x", " + ", intercept  )
print("R\N{SUPERSCRIPT TWO} = ", r_value**2)
#print("r-squared: %f" % r_value**2)