( (return path) beams (Figure 2). As a r...)The Affymetrix GeneChip Scanner 3000,,, New Advances in Scanner Design for Superior Performance, Reliability, and Dynamic Range

(return path) beams (Figure 2). As a result of this geometry, optical path length and alignment are independent of scan-arm rotation. Thus, optical performance (i.e., excitation spot size and emission focus) is quite uniform across the width of the scan field. These relationships hold throughout the slow, Y-axis translation that completes the array-scan operation. The beneficial result is that excitation/emission path lengths and optical alignments are always optimal over the entire two-dimensional field of view.

FOL technology addresses limitations observed in prior scanners in several ways:

High-accuracy position detectors, used in the X and Y axes, accurately locate each fluorescent pixel. Optic aberrations and galvanometer imperfections no longer dominate scan linearity; thus, consistently accurate scan linearity and excellent gridding performance are ensured.
The scan arm is physically small, enabling the objective, a low-mass, high-Numerical Aperture (NA) lens, to be located within a millimeter of the probe array. The large NA (0.62) objective provides a four-fold improvement in collection efficiency, which eliminates the need for multiple pass scans; only a single pass is required to deliver consistently high performance. Since line-scan speeds greater than fifty lines per second are easily achieved, Affymetrix largest format chips scan in just about half the time of that of the previous scanner.
The confocal optics structure results in an emission beam (a point instead of a line) detection path. This configuration allows emission detection to be implemented with a fixed-collection lens and pinhole that greatly facilitate simple and robust optical alignment. Taken as a whole, FOL technology consistently delivers outstandingly crisp, uniform, and geometrically accurate images.

A SOLID STATE GREEN LASER

Regardless of scanning technology, the laser is one of the most critical compone
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