Roche Nimblegen MS 200, Operator'S Manual

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60 | NimbleGen MS 200 Microarray Scanner Operator’s Manual v1.0
Manually Adjusting the PMT Gain during a Scan
While scanning, Gain 1 and Gain 2 spin boxes appear in the Scan Control to
enable you to adjust the PMT gain for each channel. To increase or decrease
the PMT gain value, click the arrow buttons to incrementally change the
value. In the Image Control, select the respective channel to see the
immediate effects on the acquired signal.
If you adjust the PMT gain value(s) during the scan, Roche
NimbleGen recommends to rescan the slide using the new settings.
For NimbleGen arrays: If using NimbleScan software to extract and
analyze data, ensure the fiducial controls are visible and near or
above the signal intensity of the surrounding experimental features
to help to ensure proper grid alignment. Features with saturated
pixels are drawn in magenta on the image. Saturated fiducial
controls can cause poor alignment quality.
7.3 Aborting a Scan
At any time, you can stop the scan or batch run. Click the Start/Stop Scan
button ( ) in the Scan Control (Figure 19). It can take some time to stop
the scan, depending upon the stage of the scan process. Any collected data
are saved in the default or user-defined file directory for later analysis.
7.4 Saving Log Files
If you encounter errors or exceptions, or if you suspect problems with the
instrument or settings that you are using, save the log files that record
actions of the scanning operation.
Figure 33: QC Tab Showing the Save Logfiles Button
Click the QC tab and click Save Logfiles to save as a .zip file to a user-
defined location.