I have been applying for some time the Otsu threshold to my greyscale 3D stacks (I cannot share a sample image because of non-disclosure agreements).
I usualy use: Image>Adjust>Threshold> Otsu (applied to the stack and using the stack histogram)
I recently tried the Auto Threshold Plugin just to double-check the results (Image>Adjust>Auto threshold>Otsu (applied to the stack and using the stack histogram)
To my surprise, the threshold using the “Adjust>Threshold” provided a value of 141, and the second method, “Auto Threshold”, found the threshold at 140!
I really thought that the algorithm was the same to both cases, and therefore the value would be the same. What could be the reason for such difference?
I just want to add that I wrote the Otsu method in Python and it provided a value of 141, so I guess that the algorithm in “Auto Threshold” either has a bug or I’m not apllying it to the stack correctly?
Thank you for your comments in advance.