The Microarray Scanner

Fifteen years into the microarray revolution, biochip images – row upon row of red and green spots on a field of black – have become as ubiquitous as DNA gels once were.

But how are those pictures generated? Arrays are imaged using one of two classes of equipment: array imagers and array scanners. Both use lasers to excite the fluorphors on the chip, but where imagers capture a snapshot of the glowing array using a charge-coupled device (CCD camera), scanners read the chip point-by-point using a photomultiplier tube.

The first microarray scanner, built in 1989 by Stephen Fodor and colleagues at Affymax, was a table-sized, home-built affair that included a Zeiss confocal microscope, a laser, and several mirrors. Fodor would go on to head Affymetrix, a Santa Clara, Calif., Affymax spin-off that now holds the lion's share of the microarray market.

Unlike some of its competitors, whose glass microscope...