sourcecode.txt

from matplotlib import pyplot as plt
from skimage import data
from skimage.feature import blob_dog, blob_log, blob_doh
from math import sqrt
from skimage.color import rgb2gray
import glob
from skimage.io import imread

example_file = glob.glob(r"microbes.jpg")[0]
plt.show(example_file)
cm_gray = plt.get_cmap()
im = imread(example_file, as_grey=True)
plt.imshow(im, cmap=cm_gray)
print("InputImage")

plt.show()

blobs_log = blob_log(im, max_sigma=30, num_sigma=10, threshold=.1)

blobs_log[:, 2] = blobs_log[:, 2] * sqrt(2)
numrows = len(blobs_log)
print("number of objects: " ,numrows)

print("OutputImage")
fig, ax = plt.subplots(1, 1)
plt.imshow(im, cmap=cm_gray)
for blob in blobs_log:
    y, x, r = blob
    c = plt.Circle((x, y), r+5, color='lime', linewidth=2, fill=False)
    ax.add_patch(c)
plt.show()