Fiji Thresholding Discrepancy

Hello everyone,

I’m interested in thresholding a 12-bit image that is stored in a 16-bit file, using 1 of the 16 thresholding algorithms supplied by Fiji. I’m wondering if my image will be thresholded differently using the applet vs the auto_threshold plugin, while keeping the thresholding algorithm constant.

I understand that the applet’s preview function bins pixel intensities to 8-bit, and that the preview can display results that deviate from the actual threshold pixel value cutoff when thresholding images over 8-bit. I also understand that the auto_threshold plugin does not bin pixel values, and instead calculates the threshold using the full range of pixel intensities of the image.

The website (, Important Notes#2) states that this difference in behavior between the applet and the auto_threshold can yield different thresholding results in an image greater than 8-bit. I have read on this forum however, that the preview function of the applet thresholder only bins pixel values explicitly for preview, and that the real threshold value is calculated based off of the images true bit depth.

I’m wondering if my understanding is at all accurate and if anyone could help clear this apparent discrepancy up for me.

Thanks in advance for any responses, this community has already been a huge help for someone not so technologically inclined!


I don’t have a response to the question, but I wanted to point out that the formatting makes it very difficult (at least on some browsers) to read your question. You might get more responses if you format it for readability, so that all of the text shows up on screen.

Thanks for pointing the odd formatting out to me! I hadn’t realized the previous formatting and agree that it was not conducive for readability. It should be fixed now.