SureScan System User Guide
78
Locked
When a protocol is locked, it cannot be changed.
Scan Settings
Dye channel
Determines whether only red (for example, Cy-5 dye), only green (for example, Cy-3 dye), or both
dye channel information is gathered. The selection has no effect on the scan time, but selecting
only one dye channel does reduce file size up to a factor of 2.
Scan region
The
scan region
determines the area of the slide that is scanned. It must be large enough to
capture the entire print region of the microarray. It must be small enough to avoid scanning too
close to the barcode or other nontransparent border areas of the slide and affecting the ability of
the scanner to auto focus properly. Minimizing the scan region also reduces scan time and save
storage space.
Agilent provides a scan region suitable for all Agilent High Density and G3 slides, and another
suitable for scanning full 1 x 3 slides without barcode labels.
For non-Agilent slides, you may need to use a custom scan region that better matches the printed
region. See
“Creating and Changing Scan Regions”
Resolution
Sets the scan resolution (pixel size) to 2, 3, 5 or 10 microns.
For 10-micron scans, each row of pixels in the TIFF image represents the average of two scan
lines, one acquired in each direction. For 5-, 3- and 2-micron scans, you can select double-pass
scanning to perform this averaging, or acquire only a single scan line for each image row.
A high-sensitivity scan mode is also available at all scan resolutions. The high-sensitivity mode
provides sensitivity comparable to the double-pass mode but with scan times reduced by 25%.
The high-sensitivity mode can be selected in the Resolution pull-down menu of the Scan Protocol
Editor.
TIFF Dynamic
Range
Sets the dynamic range to 16-bit or 20-bit. The G4900DA scanner has extended the dynamic
range of the PMT and signal processing electronics. When you select the 20-bit TIFF file option,
you can access this extended range, enabling quantitation of high and low signal features in a
single scan.
The Scan Control software still enables conventional XDR 16-bit scanning, as described below.
shows the storage space and scan time for single and double pass scans for each
resolution selected, for either a 16-bit TIFF dynamic range or a 20-bit range. The Scan Region is 61
X 21.6 mm.
The status bar at the bottom of the Scan Control main window shows an estimate of the storage
space and run time required for the current queue of slides.
NOTE
If 20-bit option is selected, no XDR option is allowed; if an XDR option is
selected already, it is reset automatically.
Table 11
Storage space and scan time
Resolution
Storage Space,
Mb, 16-bit
Storage Space,
Mb, 20-bit
Scan Time,
min.
2-micron single pass
1300
1600
24
3-micron single pass
620
760
16
