I am trying to threshold a signed 16 bit stack, and have distilled my problem down to the following macro:
setAutoThreshold (“Otsu dark stack”);
This is what I get from the macro recorder when I set the threshold interactively (Image>Adjust>Threshold), in which case it seems to work fine (thresholds are [-767,32767] for example). But when I run it as a macro it sets the thresholds to [-32768,-27828]. If I remove “dark” I get [-32768,-33555]. If I remove “stack” it works fine (although it appears to use only the histogram from the current slice). The anomalous results seem to be independent of the thresholding method. In fact it doesn’t seem to matter what I put in for method (“Trump” for instance).
Any advice would be appreciated. Apologies if this is answered elsewhere - I’ve searched.
Fiji, ImageJ 1.52p, Windows 10, x64