I have just update FIJI with the last version today ImageJ 1.52e and I realized that the calculation of the threshold value done using auto threshold method now depends on the way Bright and Contrast has been set (before to have pressed apply).
It looks not right to me, since the auto adjust has not been applied, so the threshold calculation should have been done on the raw pixel values of the image.
I took a screenshot to demonstrate it:
On the right, the auto Bright and contrast is not set and I then select the threshold method Yen and pressed auto
On the left, the auto Bright and contrast is set and I then select the threshold method Yen and pressed auto
You can download the test image here : http://bioimagingcore.be/A.ome.tif
So is that’s a bug of the interface or a feature?