Design and implementation of CCD image-based DNA chip scanner with automatic focus calibration

Abstract

To address the slow scanning speed of the laser confocal method for scanning DNA chips, we designed and built a CCD image-based DNA chip scanner. A high-powered LED was selected as excitation light source. To avoid stray light in the optical path, we designed a light entrance, an extinction dark room, a diaphragm, and an extinctor that eliminated 99.95% of the stray light. A focal automatic calibration scheme is proposed; the only addition to the hardware was the focusing motor and the connection device between the motor and the lens. Furthermore, variance was used as the image sharpness evaluation function, with the combination of rough and fine calibration to increase real-time performance. An experiment showed that the accuracy of automatic focal calibration is higher than that of the manual method with repeatability error of 2.1%, and the time required is between 18.72 and 55.78 s. The sensitivity can reach 1.12 flour/μm 2 with a resolution of 10.04 μm. Using the proposed scanner and a commercial Boao scanner on a fluorescence dot on the same genetic defect chip found a consistency coefficient of 0.95. The scanner has the advantage of simple hardware structure, quick detection, and favourite performance.