Umm so now that everything has been migrated to scijava pom, I have the same problem to being with which is that ij.op().morphology().fillHoles(fill, mask); does nothing.
Am using this now in the pom:
Do I have to override some inherited pom or is their other way to fill holes in the binary image using ops?
Original and Filled are just the same. Process -> Binary -> FillHoles works though.