Calculate average pixel intensity for each frame of tif movie

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I imported a tif movie into python which has the dimensions (150,512,512). I would like to calculate the mean pixel intensity for each of the 150 frames and then plot it over time. I could figure out how to calculate the mean intensity over the whole stack (see below), but I am struggling to calculate it for each frame individually.

from skimage import io

im1 = io.imread('movie.tif')


print("The mean of the TIFF stack is:")
print(im1.mean())

How can I get the mean pixel intensities for each frame?

scikit-image pixel tiff video python
1 Answers

You could slice the matrix and obtain the mean for each frame like below

from skimage import io

im1 = io.imread('movie.tif')
for i in range(im1.shape[0]):
    print(im1[i,:,:].mean())

To plot it you can use a library like matplotlib

from skimage import io
import matplotlib.pyplot as plt

im1 = io.imread('movie.tif')
y = []
for i in range(im1.shape[0]):
    y.append(im1[i,:,:].mean())

x = [*range(0, im1.shape[0], 1)]
plt.plot(x,y)
plt.show()
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