I was wandering down the aisle at Staples the other day and saw the different scanners they sell. One of them is the Epson (not 100% sure of the model number) but what intrigued me was the insert that is supposed to be for films and negatives that sits on the glass -- you can sort of see it in this at the bottom http://www.itreviews.co.uk/hardware/h901.htm

There was little letters marked on the item and I am betting the software will scan just the section you have selected. One of them looked about negative size, which is pretty close to chip sized. So slip the chip in the template, and tell the scanner to scan just that area.