Scan BeadChips

Before starting a scan, the lasers must stabilize. Make sure that the iScan Reader has been on for at least 5 minutes before beginning a scan.

After selecting the BeadChips to scan and confirming the settings, start the scan. For instructions on omitting one or more BeadChips from a scan, refer to Omit BeadChips and Stripes from a Scan.

To start a scan:

1. On the iScan Control Software Setup screen, select Scan.

The iCS performs the prescan steps described in the Prescan Steps table below. The scan process begins automatically after these steps are complete.

As each section is scanned, image and intensity data are saved on the instrument control computer or in a network location in the output path specified on the iCS Setup screen. Unless a serious error halts the scan process, the scanning process continues until all sections are scanned or until you pause or stop the scan.

Steps

Description

Checks available disk space

If there is less than 75 GB of free disk space for the image and intensity files, the iCS displays a warning. If there is less than 12 GB of free disk space on the drive, the scan is not performed.

Loads the DMAP files from the user-defined input folder for each BeadChip in the carrier

If any DMAP files are missing, the iCS displays a warning.

Calibrates the iScan Reader

Calibration includes the following processes:

• An autofocus process at three corners of the BeadChip to make sure that the images are clear.
• An autocenter process to make sure that the BeadChip is properly positioned relative to the optics.

Calibration can take several minutes to complete.

If there are defective or dirty sections at any of the three alignment corners, the software attempts to use alternate sections until satisfactory calibration is achieved. If no alternate sections are available, calibration fails and an error message is displayed. For troubleshooting information, refer to iScan Reader Issues.

Tilts and aligns the BeadChips in the carrier

The iScan Reader Autofocus feature records the Z-position (height) of three corners of the BeadChip to determine its current tilt, and adjusts the BeadChip until it is flat.

The iScan Reader then identifies the X-Y position (lateral location) of the fiducials (focus points) on the BeadChip edges, and adjusts the stage to align the BeadChips under the optics.