analyse c.elegans movement;you need the image files to run this problem; download zip compressed image files from here and extract at the same directory where the below python programme is saved. https://drive.google.com/file/d/0B5smtso7TwjrZmlRUjhKNlNQbWs/view?usp=sharing

analyse_worm_moving.py

import numpy as np
import matplotlib.pyplot as plt

from skimage.segmentation import boundaries 
from scipy import ndimage

num_image = 4

fig = plt.figure(1)

for idx in range(0,num_image+1):
    print(idx)
    file_name = '2015_1_21(15h 2m 0s){0:04d}.tif'.format(idx)    
    Worm_Image = plt.imread(file_name)
    max_val_img = Worm_Image.max()
    
    plt.clf()
    plt.imshow(Worm_Image)   
    plt.hold(True)
    
    Worm_Image = (0.2989*Worm_Image[:,:,0]/max_val_img 
                + 0.5870*Worm_Image[:,:,1]/max_val_img 
                + 0.1140*Worm_Image[:,:,2]/max_val_img)

    Worm_Image = boundaries.find_boundaries(Worm_Image)
    
    Worm_Image = ndimage.binary_fill_holes(Worm_Image)
    Worm_Image = boundaries.find_boundaries(Worm_Image)
    Worm_Image = Worm_Image.astype('float')
    bd_found   = np.nonzero(Worm_Image)
    
    x_bd = bd_found[0] 
    y_bd = bd_found[1]

    plt.plot(y_bd,x_bd,'.')  
    plt.xlim([1, Worm_Image.shape[1]])
    plt.ylim([1, Worm_Image.shape[0]])     
    plt.pause(0.01)