I have a plugin that outputs a multipoint overlay on the input stack. What I do then for documenting is duplicating a few slices from the input using “Duplicate”, and it keeps the overlay on the duplicated slices. When I save this duplicated extract manually, the overlay is saved in the tif stack. However, if I do it in a macro, the “Duplicate” command keeps the overlay, but the saveAs(“Tiff”) or the simpler save() functions save the extracted stack without keeping the overlay.
I assume it’s a bug? I’m using IJ 1.51f.