Things I did today: Went to class. Received four 3D printers in the mail. Poked a circuit board with metal sticks. Scanned a cookie...
To scan a cookie with autofocus or stacking you can do one of two things. You can either use a low enough magnification/high enough depth of field that everything is (roughly) in focus,
(just use a macro camera, it's much less trouble, sheesh)
...or you can make your intern's intern grind down the cookie until it's mostly flat.
This is exactly as stupid as it sounds. Note that this isn't the same cookie as before --- that one fell on the ground. But hey, after a thousand pictures, you might get a cookie with some parts that are in focus!
...or it could look like a horrifying pustule of a cookie that exemplifies all the bad parts of the scanning technology. full image so you can see just how bad it is: https://www.easyzoom.com/imageaccess/25d4f62f073e4887ace5b873225093b7