I am currently analyzing 8-bit BW TIFF movies in ImageJ and I want to first be able to see the intensity of each pixel as a matrix and then export that matrix so that I can analyze the pixel intensities in Python. Does ImageJ have a way to get the pixel intensity matrix? Thank you all so much!
There is indeed a Save As feature called
Text Image which will let you save an image as a tab separated array of values.
Of note, this will only work for a single image, so you would need to iterate through the stack and save out every image.
I have little experience with Python but presumably it would be easier to just import the TIFF into Python directly then convert it into a numpy array?