HELIOS: High-speed sequence alignment in optics
Fig 6
Schematic illustration of the HELIOS optical architecture.
(A) The optical beam provision unit provides a collimated beam to feed the whole system. In this manner, the wideband laser beam, produced by a laser source, passes through the laser line bandpass filter and the pinhole to be cleaned. Afterward, the clean beam is diverged and collimated with passing through the objective and imaging lenses, respectively. Finally, the collimated beam is directed to the optical modulation and mechanism unit. (B) In the optical modulation and mechanism unit, passing collimated beam through WSF #1 modulates the wavelength of the optical beam based on the self-label coding of S2 and S1 on the first and second rows of a 2 × N pixels image, respectively; while PSF #1 performs their polarization selection based on their nearby-label coding scheme. Afterward, the objective and imaging lens arrays diverge and recollimate the optical beam through a horizontal direction to perform the shifting process of the alignment procedure. Moreover, WSF #2 and PSF #2 code S1 and S2 on the first and second rows of a 2 × N pixels image, respectively. By passing the expanded beams through WSF #2 and PSF #2, the proposed architecture compares the shifted coded S2 with S1 at the first row, implementing the S1-align operation, and compares the shifted coded S1 with S2 at the second row, implementing the S2 -align operation. Finally, each pixel is directed to two distinct pixels via a chiral medium to compensate for false mismatches. (C) Finally, in the output capturing unit, optical thresholdder eliminates wavelength cross-talks and speckle noises of the output before capturing. Afterward, the output is captured by a bi-convex lens and a charged-coupled device (CCD) camera.