Performance characterization of a low-cost dual-channel camera-based microarray scanner

In this paper, we have proposed, designed, implemented, and characterized a low-cost camera-based microarray scanner which is capable of imaging fluorescently-labeled DNA or Protein microarrays. The proposed system is designed to simultaneously measure two different fluorescent dyes using two parallel channels which increase the overall scan speed. We have shown that the wide dynamic range of system makes it able to detect fluorophore densities from 100-10
⁶
molecule/μm
²
. In each capture, a 5.6 mm × 3.7 mm field is imaged on a 22.3 mm × 14.9 mm (18 megapixels) CMOS sensor. Therefore, the microarray can be scanned with ~ 1μm
²
spatial resolution which is high enough to distinguish borders of spots with less than 50μm diameter. To characterize the scanner performance, we have used molecules labeled with fluorescent cyanine dyes, including Cy3 and Cy5; however, the proposed scanner can be modified to detect any other fluorescent dye with emission spectra within 400-800 nm. We believe it is the most cost-efficient microarray scanner ever achieved.