I think I found a bug in the most recent ImageJ1.x update. I noticed that in my workflow - I was losing my scaling information at a certain stage. Comparing two different versions of ImageJ1.x: 1.51t versus 1.52m. If you use this little macro - you can see the difference between versions:
run("Blobs (25K)"); run("Set Scale...", "distance=5 known=3 unit=mm"); setAutoThreshold("Default"); //run("Threshold..."); run("Create Mask");
Also took snapshots to show issue:
I’ve got a workaround for the moment… but this needs to be addressed obviously.
Can someone else confirm this? Particularly @Wayne?