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An EM scan was an examination of the electromagnetic spectrum in an attempt to search for some anomalous or characteristic pattern. Starfleet medical personnel typically used this type of scan to diagnose patients. EM scans operated much like an X-ray, using electromagnetic radiation, generally not lethal, to register the internal condition of the body's affected regions. Tricorders and medical scanners were used to implement this type of scan.
In some cases the EM radiation emitted from scanners could aggravate conditions or accelerate a disease, as shown when Doctor Bashir encountered a Dominion virus which was engineered to be excited by EM radiation emitted from Starfleet equipment, subsequently killing all his patients. (DS9: "The Quickening")