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The Affymetrix GeneChip Scanner 3000,,, New Advances in Scanner Design for Superior Performance, Reliability, and Dynamic Range

The Affymetrix GeneChip Scanner 3000
New Advances in Scanner Design for Superior Performance, Reliability, and Dynamic Range

The Affymetrix GeneChip Scanner 3000 design lays the foundation for continued evolution of the GeneChip platform as an integrated genetic analysis system, supporting continued feature size reduction for higher resolution and greater information content of microarray-based products. The Affymetrix GeneChip Scanner 3000 will seamlessly incorporate future developments as GeneChip technology continues to evolve. In order to address the requirements of new and emerging applications, advancements within the Affymetrix GeneChip system will build upon the GeneChip Scanner 3000. This document will describe the technical aspects of the GeneChip Scanner 3000 and provide details on the innovative technologies used to incorporate advanced design improvements. These advances have resulted in dramatic space savings, increased scan speeds, increased signal resolution, reduced noise, wider dynamic range, and real-time laser monitoring and adjustment.

Previous Scanner System

PRE-OBJECTIVE LINE SCANNING SYSTEM

This technology employs a mirror mounted on the end of a galvanometera limited rotation, oscillating motor. The term pre-objective scanning is derived from the fact that the scanning is accomplished by moving (scanning) the laser beam before a fixed objective lens. The galvanometer enables a laser beam to scan back and forth along a straight-line path, referred to as the excitation line-scan. The excitation linescan, in turn, is directed to, and focused on, the array through a multi-element objective lens located several inches away from the array. Emission is collected by another lens/filter/lens system positioned at an angle to the excitation beam. This
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