In the "Convert Stack to Binary" dialog the "Calculate threshold for each image" is enabled by default for every session. I always disable this as I always need to convert the whole stack using the same threshold value. But it is quite annoying to have to click this every time, and get the wrong result if I forgot to change it. Can this option perhaps be saved in the IJ_Prefs.txt? Or be turned off by default?
If not, I had a look at the source code at https://imagej.net/ij/source/ij/plugin/Thresholder.java and it appears that the relevant flag is controlled by this line: private static boolean staticUseLocal = true; Can this be made public, so that we can disable this with a script call at startup? Stein -- ImageJ mailing list: http://imagej.nih.gov/ij/list.html
