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A hybrid CMOS/thin-film microsystem for fluorescence contact imaging is presented. The microsystem integrates a high-performance optical interference filter and a 128 ?? 128 pixel active pixel sensor fabricated in a standard 0.35-??m CMOS technology. The thin-film filter has an optical density greater than 6.0 at the wavelength of interest, providing adequate excitation rejection to the 532-nm solid-state laser. Microsystem performance is experimentally validated by imaging spots of Cyanine-3 fluorophore, conventionally used in DNA detection. The emission intensity as a function of fluorophore concentration is measured with an estimated sensitivity of 5000 fluorophore/??m2 . A human DNA microarray has been imaged with the sensor prototype.