MATLAB: How to apply Otsu method to a stacked images

Image Processing Toolboxotsu stackedthresholding

Dear all,
I have 21 RGB microscopic images located in one folder. I want to apply the Otsu thresholding to each image in the folder (each image has different Otsu thresholding value).
How to make a "for loop" applied to the 21 images?
I tried this code but it finds the threshold value of the first image and applies it to all 21 images.
Any idea?
Meshoo
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files = dir('*.tif');
for k = 1:(numel(files));
              thresh = [];
              image = imread(files(k).name);
              thresh = graythresh(image);
              newImage = im2bw(image, thresh);
              imwrite(newImage, ['NewImage\', files(k).name,]);
end

Best Answer

Why are you applying monochrome thresholding to RGB images? You need to extract a color channel first, or use rgb2gray().
Assuming they're monochrome, I don't see any reason why this would not work. Take the semicolon off this line:
thresh = graythresh(image)
and see what values get written to the command window.
Also, don't use image as the name of your variable because you'll blow away the built-in image() function.
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