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The molecular imaging scanner was located above each transporter pad and was used to scan the object to be transported and converted it to a matter stream.

Because of its crucial function, if the imaging scanner was off by even one thousandth of a percent, the transport would fail. Every transporter pad was equipped with four redundant imaging scanners. This scanner could also be used to program the biofilter. Molecular patterns would be identified with the help of the imaging scanner where upon the biofilter could be programmed to removed those unwanted molecules. (TNG: "Realm of Fear")

In 2369, Chief Miles O'Brien came too late into school, acting as a substitute teacher for his wife Keiko, because the transporter in ops needed a minor adjustment in its upper molecular imaging scanner. (DS9: "The Nagus")

The Star Trek Encyclopedia (4th ed., vol. 2, p. 50) defined the "molecular imaging scanner" as a "Subsystem within a Federation starship's transporter. The molecular imaging scanner is responsible for creating the data matrix that describes every particle of the transport subject. A faulty imaging scanner could result in a transport subject being improperly re-created."

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