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To create a digital copy or entry of something in a computer with an optical scanner. In this usage, a noun or pronoun can be used between "scan" and "in." First, I draw the pictures by hand. Then I scan them in on the computer so they can be turned into frames in our animation software. The bank only sends us bank statements on paper, so I have to scan them all in individually for our year-end audit.
To encode something digitally with an optical scanner: I scanned in all my old photos and saved them on my hard drive. They scanned the text in and then edited it on the computer.