image processing - Finding number of colored shapes from picture using Python

Question

My problem has to do with recognising colours from pictures. Doing microbiology I need to count the number of cell nuclei present on a picture taken with a microscope camera. I've used GIMP to tag the nuclei with dots of red colour. Now I'd need to make a script in python, which, given an image, would tell me how many red dots are present. There is no red in the picture except in the dots.

I've thought of a rather complicated solution which is probably not the best one: Take a picture and start iterating through pixels checking each one's colour. If that is red, check all 8 nearest pixels, recursively check each red one's neighbours again until no more neighbouring red pixels are found. Then increment nuclei count by one and mark traversed pixels so they won't be iterated through again. Then continue iteration from where it stopped. Seems kind of heavy so I thought I'd ask, maybe someone has already dealt with a similar problem more elegantly.

Regards, Sander

Answer 1

Count nuclei

The code adapted from Python Image Tutorial. Input image with nuclei from the tutorial:

#!/usr/bin/env python
import scipy
from scipy import ndimage

# read image into numpy array
# $ wget http://pythonvision.org/media/files/images/dna.jpeg
dna = scipy.misc.imread('dna.jpeg') # gray-scale image


# smooth the image (to remove small objects); set the threshold
dnaf = ndimage.gaussian_filter(dna, 16)
T = 25 # set threshold by hand to avoid installing `mahotas` or
       # `scipy.stsci.image` dependencies that have threshold() functions

# find connected components
labeled, nr_objects = ndimage.label(dnaf > T) # `dna[:,:,0]>T` for red-dot case
print "Number of objects is %d " % nr_objects

# show labeled image
####scipy.misc.imsave('labeled_dna.png', labeled)
####scipy.misc.imshow(labeled) # black&white image
import matplotlib.pyplot as plt
plt.imsave('labeled_dna.png', labeled)
plt.imshow(labeled)

plt.show()

Output

Number of objects is 17