SureScan System User Guide
79
Double pass scans do not require more storage space than single pass scans, but they take twice
as long to finish.
Red PMT
Sensitivity (%)
and
Green PMT
Sensitivity (%)
Sets the sensitivity level of the red channel and green channel PMTs. The PMT detects
fluorescence emitted by the microarray.
The default output level (100%) sets the gain to the factory-calibrated level; this setting is
recommended for Agilent microarrays. You can reduce each color channel setting independently
to as low as 1%.
If a microarray is so bright that the upper end of the output signal is saturated, the PMT sensitivity
level can be lowered to a sensitivity range that allows all the information to be read.
XDR Ratio
Before 20-bit TIFF file dynamic range was available, the eXtended Dynamic Range function was
used on both the scanner and Feature Extraction program to capture all the data scanned
between very low signal features and very high signal features. Now, instead of using XDR, you
can select the 20-bit TIFF file dynamic range to capture the wide dynamic range of data.
With the XDR function turned on, the scanner automatically scans the same slide twice, at two
different PMT sensitivity levels. It generates two linked images that Feature Extraction
coprocesses to yield a single unified set of extracted intensity data. This data covers up to 6+
orders of magnitude.
The Red or Green PMT Gain sets the high sensitivity level. The XDR function is automatically
turned off at values lower than 10%.
The XDR ratio setting instructs the scanner to perform a second scan at lower PMT settings. For
example, if the Red and Green PMTs are set to 100%, and the XDR ratio is set to 0.1, then the
second scan is performed with the PMTs set to 10%. Available values are: <NoXDR>, 0.5, 0.2, 0.1,
and 0.05.
5-micron single pass
200
300
10
10-micron single pass
52
115
10
2-micron double pass
1300
1600
46
3-micron double pass
620
760
31
5-micron double pass
200
300
19
2-micron high-sensitivity
1300
1600
36
3-micron high-sensitivity
620
760
24
5-micron high-sensitivity
200
300
15
10-micron high-sensitivity
52
115
15
Table 11
Storage space and scan time (continued)
Resolution
Storage Space,
Mb, 16-bit
Storage Space,
Mb, 20-bit
Scan Time,
min.
NOTE
If 20-bit option is selected, no XDR option is allowed.