Image Quality Issues

Cause

Resolution

Low assay signal.

Review the history of assay preparation with the responsible scientist. Evaluate the length of time after preparation, concentration of signal source due to evaporation, and adverse environmental conditions including humidity, temperature, and amount of direct sunlight.

Bad focus.

Stop the scan and eject the BeadChips. Check the sections for foreign matter that can affect focus. Make sure that the BeadChips are flat in the carrier and that their back sides are clean.

Broken section.

If a section is broken, it cannot produce high-quality data. However, the rest of the BeadChip is not affected.

Contrast bars are not set for optimal viewing of images.

Select the Auto Contrast checkbox. If images are still not optimal, adjust the contrast sliders. For more information on viewing images, refer to View Scan Results.

Images are present but intensity data are low, even though registration is successful.

Data are acceptable and uncompromised.

Cause

Resolution

Contrast is not set for optimal viewing of images.

Select the Auto Contrast checkbox. If images are still not optimal, adjust the contrast sliders. For more information on viewing images, refer to View Scan Results.

Cause

Resolution

Monitor is not adjusted for displayed resolution.

The appearance of the section has no effect on your data. Use the horizontal and vertical size controls of your monitor to manipulate the appearance of a section so it appears regular (all sides are the same length).

Make sure that your video driver resolution is set to 1280 x 1024.

Cause

Resolution

Camera cable on back of scanner is loose.

Tighten connection, then restart the scanner and restart the iCS. Power cycle the scanner and/or PC as many times as necessary until the frame grabber is able to initialize successfully.

Cause

Resolution

Autotilt values are out of range, slide is not seated properly, or a problem exists with the z-control board.

Remove the BeadChip carrier from the iScan Reader tray. Reseat the BeadChips. Make sure that the BeadChips lie flat within the slots on the carrier. Power cycle the scanner and restart the iCS. Reload the carrier and attempt to scan again. If the error still occurs, schedule a field service call to examine the scanner hardware.

Cause

Resolution

Red or green laser is near its end of life.

Contact Illumina Technical Support and schedule a field service call.