Agilent's performance-leading microarray scanner just got better
Agilent has been in the microarray scanning business for over a decade. In 1997, Agilent unleashed the power of Affymetrix technology with the Agilent, then HP, GeneArray scanner. In 2001, Agilent launched it's next generation scanner that provided enhanced sensitivity for Agilent's microarray platform, and followed this release with improved performance for non-Agilent slides in 2002. Now as Agilent prepares for its next wave of high-density microarrays, the microarray scanner has evolved to meet the challenge with the introduction of high-resolution scanning capability.
Key Technologies
High-Resolution scanning
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The image on the left shows a region of a 30 micron feature array scanned at 5 micron resolution. The image on the right shows the same region of the array scanned at 2 micron resolution on the new high-resolution Agilent scanner. Note the improvement in the image quality.
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As illustrated by the diagram above, the number of pixels useable for image analysis decreases dramatically as the feature size decreases. Increasing the scan resolution regains the number of pixels available for analysis.
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Industry-first Dynamic Autofocus
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Even the most revered glass manufacturer can't manufacture a glass slide without some warpage, curvature or changes in glass thickness. All of these glass variations can cause problems with microarray scanner laser focus calibration. Many manufacturers have incorporated a single focus laser calibration, but this only occurs on one part of a glass slide and doesn't compensate for potential variability across the slide.
Agilent has engineered a better approach to remove this variable in microarray analysis. Agilent's Dynamic Autofocus feature delivers increased sensitivity by continuously adjusting the focal plane, correcting for common
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glass surface abnormalities and gradients as well as any potential slide movement within the scanner.
Incredibly, this Dynamic Autofocus feature is able to adjust over 1 million times during the course of a microarray scan and helps keep every feature/spot in focus.
Extended Dynamic Range (XDR) and 20 bit scanning
Extended Dynamic Range (XDR)
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For many applications, including gene expression and miRNA, the sample's dynamic range exceeds the 16-bit range that traditional scanners have offered. This forces users to make decision between a high-sensitivity setting in which many features on the array will saturate, and a low-sensitivity setting in which few or no features saturate but the ability to detect weak probes is limited. In 2006, Agilent solved this dilemma with the introduction of extended dynamic range (XDR). In XDR mode, the scanner performs a dual scan, the first at the most sensitive PMT setting, and the second at a lower PMT setting. Agilent's Feature Extraction software then combines the data in a robust manner by checking the data in the overlap region for consistency and reporting any discrepancy that may occur. As a result, users can realize a 10-20 fold increase in dynamic range which more closely matches the dynamic range of the microarray and the biological sample.
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20 bit scanning
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With the introduction of the high-resolution scanner, Agilent is has improved upon XDR scanning by increasing the dynamic range of a single scan from 16-bit to 20-bit thereby realizing the same dynamic range as with XDR scanning but with a single scan. Now instead of saturating at 65,535 counts as with a 16-bit scan, the new saturation value is 12 times larger at over 780,000.
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