iScan System User Guide FOR RESEARCH USE ONLY ILLUMINA PROPRIETARY Part # 11313539 Rev.
This document and its contents are proprietary to Illumina, Inc. and its affiliates (ʺIlluminaʺ), and are intended solely for the contractual use of its customer in connection with the use of the product(s) described herein and for no other purpose. This document and its contents shall not be used or distributed for any other purpose and/or otherwise communicated, disclosed, or reproduced in any way whatsoever without the prior written consent of Illumina.
Revision History iScan System User Guide Part # Revision Date 11313539 B February 2011 11313539 A May 2008 11308663 A April 2008 Description of Change Update to reflect iScan Control Software (ICS) version 3.2, including automated genotype calling functionality and other features. Initial release.
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Table of Contents Revision History . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . iii Table of Contents . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . v List of Tables . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . ix Chapter 1 iScan System Overview . . . . . . . . . . . . . . . . . . . . . . .1 Introduction . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Table of Contents Chapter 4 Configuring iScan Control Software. . . . . . . . . . . . . 31 Introduction . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .32 Omitting BeadChips from a Scan . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .33 Preventing Sections of a BeadChip from being Scanned . . . . . . . . . . . . . .34 Changing Scan Settings . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Chapter 9 71 73 75 77 Maintenance and Service . . . . . . . . . . . . . . . . . . . . .79 Introduction . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 80 Maintenance . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 81 Service . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 82 Index . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
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List of Tables Table 1 Table 2 Table 3 Table 4 Table 5 Table 6 Table 7 iScan System User Guide Status Lights. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5 Hard Drive Configuration of the iScan System. . . . . . . . . . . . . . . . . . . . . . . 6 User-Supplied Consumables . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 9 Image Toolbar Icons. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
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Chapter 1 iScan System Overview Introduction . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2 Audience and Purpose. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3 iScan System Components . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 4 Consumables Required . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
iScan System Overview Introduction The iScan System is an easy‐to‐use, laser‐based, high‐resolution benchtop optical imaging system that can rapidly scan and collect large volumes of data from Illumina DNA analysis and RNA analysis high‐density BeadChips. With powerful scanning tools for gene expression and genotyping applications, the iScan System supports the rapid, sensitive, and accurate imaging of all of Illumina’s BeadChip‐ based genetic analysis products.
This guide describes the instrument components, software interface, consumables, and operational procedures for scanning Illumina BeadChips on the iScan System. This guide is for laboratory personnel and other individuals responsible for: ` Operating the iScan System ` Performing instrument and component maintenance ` Training personnel WARNING Using controls, making adjustments, or performing procedures other than those specified herein may result in hazardous laser light or radiation exposure.
iScan System Overview iScan System Components The iScan System consists of the following components: ` iScan Reader ` Dedicated computer workstation ` BeadChip carrier(s) ` Power cords and other accessories In addition to these components, BeadChips developed for your application are required. NOTE You can also purchase and use the AutoLoader System (AutoLoader2 or AutoLoader 2.x model) to automate BeadChip loading. iScan Reader The iScan Reader is a laser‐based, high‐resolution optical imaging system.
The barcode scanner is internal to the iScan Reader, and allows you to accurately identify each BeadChip. Status Lights The iScan Reader status indicator lights and scan bar on the front panel show the current status of the Reader. Figure 2 Status Lights and Scan Bar Table 1 Status Lights Status Light Description Power (blue) Steady blue indicates that the instrument is on. Ready (green check) Steady green indicates that the instrument has been initialized and is ready to scan.
iScan System Overview Hard Drive Configuration The iScan System contains two permanent drives (C: and D:) on the computer and one removable drive (H:) within the iScan Reader. Drives C: and D: are physically separate drives; they are not part of one large drive partitioned into two. Table 2 Hard Drive Configuration of the iScan System Drive C: Drive C: is about 75 GB in size and is installed with all of the generic scanner software needed to run the iScan System.
iScan System Components Figure 3 iScan Control Software, Setup Screen BeadChip Carriers The iScan System comes with one BeadChip carrier. The carrier holds up to four BeadChips for scanning at one time.
iScan System Overview NOTE Some BeadChip carriers have barcodes affixed to each slot. These slot barcodes enable the iScan Reader to tell if a slot contains a BeadChip. For more information, see Carrier and BeadChip Barcodes on page 8. Carrier and BeadChip Barcodes BeadChip carrier barcodes are used to identify the individual BeadChip carriers and determine if a BeadChip position is occupied or empty.
This section lists the Illumina‐supplied kits and user‐supplied consumables required to scan arrays using the iScan System. Illumina-Supplied Consumables Before you begin scanning, complete the appropriate assay for your BeadChip and application.
iScan System Overview iScan System Requirements Lab Equipment Requirements If you are a current Illumina customer and already have the correct hardware package for the assay you plan to run, you do not need to purchase any additional lab equipment besides the iScan System itself. For example, if you already have the Infinium upgrade package for a BeadArray™ Reader, you do not need to purchase any additional equipment to scan Infinium BeadChips on a new iScan Reader.
This section provides an overview of the steps involved in scanning BeadChips with the iScan System. See the referenced sections for detailed instructions. NOTE This process does not describe how to use the AutoLoader with the iScan System to automate BeadChip loading. For information on the AutoLoader, see the AutoLoader2 User Guide or the AutoLoader 2.x User Guide, depending on your AutoLoader system. 1 Start the iScan System. (See Chapter 2, Starting the iScan System.
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Chapter 2 Starting the iScan System Procedure Summary . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 14 Powering Up the iScan Reader . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 15 Powering Up the iScan System Computer . . . . . . . . . . . . . . . . . . . . . . . . . . . . 16 Starting the iScan Control Software . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 17 Using LIMS with the iScan System . . . . . . . . . . .
Starting the iScan System Procedure Summary There are three steps to starting the iScan System, and they must be performed in the following order: 1 Power up the iScan Reader. 2 Power up the iScan System computer. 3 Start the iScan Control Software. These steps are described in the following sections, along with information on using LIMS with the iScan System. 14 Part # 11313539 Rev.
Powering Up the iScan Reader Powering Up the iScan Reader To power up the iScan Reader: 1 Ensure that the iScan Reader has been off for at least 2 minutes. 2 Press the Power switch on the back panel. Figure 8 iScan Reader Power Switch The iScan Reader status indicator lights on the front panel show the current status as the Reader powers up. For more information on the status lights, see Status Lights on page 5.
Starting the iScan System Powering Up the iScan System Computer To power up the iScan System computer: 16 1 Press the Power button on the iScan System computer. 2 Log on to Windows. The login procedure is the same as that required to log on to other computers connected to the network. Part # 11313539 Rev.
NOTE To ensure adequate disk space, before starting the software, archive the data on the computer from all previous runs to a network location. To start the iScan Control Software: 1 Do one of the following: • Double‐click the iScan Control Software (ICS) icon on the computer desktop. • From the Windows Start menu, select iScan Control Software. The iScan Control Software automatically connects to and initializes the iScan Reader. The software takes a few minutes to initialize.
Starting the iScan System NOTE The colored strip at the top of each ICS screen provides “breadcrumbs” to help you identify where you are in the scan process: • Dark orange with small text—Indicates step has been completed. • Dark orange with large text—Indicates step is in progress. • Light orange—Indicates step has not been completed.
The iScan Control Software is compatible with the following laboratory information management software (LIMS) programs: ` Infinium LIMS ` llumina LIMS Enabling and Disabling LIMS If you use a LIMS, be sure to enable it for use with the iScan System before beginning a scan. 1 Click the Menu button Tools | Options. in the upper left corner of the ICS screen and select 2 In the Options dialog box, click the LIMS tab. 3 On the LIMS tab, select the Enable LIMS check box and click OK.
Starting the iScan System Removing a LIMS Server 20 1 Click the Menu button Tools | Options. in the upper left corner of the ICS screen and select 2 In the Options dialog box, click the LIMS tab. 3 On the LIMS tab, highlight the name of the LIMS server you want to remove, click Delete, and then click OK. Part # 11313539 Rev.
Chapter 3 Loading BeadChips Procedure Summary . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 22 Cleaning a BeadChip . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 23 Loading BeadChips onto a Carrier . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 24 Loading a Carrier into the iScan Reader . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 26 Rescanning Barcodes . . . . . . . . . . . . . . . .
Loading BeadChips Procedure Summary There are three steps to loading BeadChips: NOTE Always wear gloves when handling BeadChips. 1 Clean the BeadChips. 2 Load the BeadChips onto a BeadChip carrier. 3 Load the carrier into the iScan Reader. These steps are described in the following sections, along with instructions on how to rescan barcodes. 22 Part # 11313539 Rev.
To prevent damage to BeadChips or the iScan Reader, the BeadChips must lie completely flat in the BeadChip carrier. To ensure this, always wipe off all protective coating and residue from the back side of the BeadChip before placing it on the carrier. ` Using an alcohol wipe or a lint‐free tissue moistened with ethanol or isopropanol, carefully wipe the back side of the BeadChip to remove the XC4 protective coating or other residue. NOTE Let the surface air dry before loading the BeadChip onto a carrier.
Loading BeadChips Loading BeadChips onto a Carrier BeadChip carriers hold the BeadChips in place during the scan process. 1 Hold the BeadChip by the barcode end. 2 Place it in a slot so that the non‐barcode end presses up against the raised stop. Figure 13 Placing BeadChips 3 Place up to four BeadChips onto the carrier in this way, each in its own slot. The BeadChips might not lie perfectly flat in their individual slots, but each BeadChip should fit between the sides of the slot.
Gently press either of the two Lift buttons to open the latches and raise the pins beneath the BeadChips, then release the button. Figure 15 Correcting BeadChip Flatness in Carrier The BeadChips should settle down firmly into the slots. If any remain uneven, press and release the Lift button again.
Loading BeadChips Loading a Carrier into the iScan Reader You can access the iScan Reader tray using either the iScan Control Software or the Open/ Close Tray button on the front of the iScan Reader. When loading a BeadChip carrier, be sure to orient it properly in the iScan Reader tray. NOTE You can use the AutoLoader to automate the process of loading BeadChip carriers into the iScan Reader. For more information, see the AutoLoader2 User Guide or the AutoLoader 2.
A B Adapter Plate iScan Reader Tray NOTE The adapter plate is specific to each individual iScan Reader. Do not switch adapter plates between iScan Readers. 2 Line up the notches on the carrier with the silver beads on the adapter plate in the iScan Reader tray. Figure 19 Loading BeadChips .
Loading BeadChips 3 Lower the carrier gently onto the tray (BeadChip barcode ends near front of tray) and lightly jiggle it from side to side to ensure that it fits securely. Do not press down on the iScan Reader tray. Figure 20 Placing the BeadChips You may notice some back‐and‐forth play in the carrier after placing it into the iScan Reader tray; this is acceptable. The iScan Reader will automatically center and position the BeadChips for proper scanning.
Loading a Carrier into the iScan Reader Figure 21 BeadChip Barcodes Displayed on the ICS Setup Screen NOTE If the barcode scanner finds neither an empty slot barcode nor a BeadChip barcode on the first scan attempt, the iScan Control Software automatically attempts to rescan the barcode once. If the scanner does not successfully find the barcode after a second scan, nothing will appear in the Barcode box for the missed BeadChip position.
Loading BeadChips Rescanning Barcodes To rescan barcodes in the Setup screen, click the Menu button of the ICS screen and select Scanner | Scan Barcodes. in the upper left corner Figure 22 Rescanning Barcodes NOTE You can manually enter the barcodes into the position that corresponds to the BeadChip’s location in the carrier. You can also manually delete barcodes to remove BeadChips from a scan. 30 Part # 11313539 Rev.
Chapter 4 Configuring iScan Control Software Introduction . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 32 Omitting BeadChips from a Scan . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 33 Preventing Sections of a BeadChip from being Scanned . . . . . . . . . . . . . . . . . 34 Changing Scan Settings . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Configuring iScan Control Software Introduction This chapter explains how to configure the iScan Control Software to perform a scan. If the default configuration values are already correct, you do not need to change them. You can simply click Scan to continue. 32 Part # 11313539 Rev.
Omitting BeadChips from a Scan Omitting BeadChips from a Scan To remove a BeadChip from a scan: ` Delete the BeadChip’s barcode number from the ICS Setup screen.
Configuring iScan Control Software Preventing Sections of a BeadChip from being Scanned If you want, you can deselect individual strips within a BeadChip, preventing them from being scanned. NOTE All sections of a BeadChip must be scanned when using LIMS. You cannot remove sections from the scan. 1 On the ICS Setup screen, at the top of the BeadChip Preview area, select the BeadChip whose scan settings you want to change.
If you want to use scan settings other than the default settings automatically selected based on the BeadChip type, first create a custom scan settings file, then associate it with the BeadChip on the ICS Setup screen. These processes are described in the following sections. Creating a Custom Scan Settings File 1 Click the Menu button Tools | Options. in the upper left corner of any ICS screen and select Figure 24 ICS Tools Menu 2 In the Options dialog box, click the Scan Settings tab.
Configuring iScan Control Software — Export Bead Type Data – Set to True or False. — Image Format – Select Jpg, Png, or Tiff. JPG and PNG files are compressed image files. They are useful for reviewing the array surface for defects that might have affected data quality. Intensity data cannot be extracted from JPG or PNG files. TIFF files are uncompressed image files. They consume more hard drive space than JPGs or PNGs, but their benefit is that intensity data can be extracted from them.
A BeadChip scan generates intensity data (*.idat) files. These files contain raw intensity data values for every bead on the scanned image. (See Generated Files on page 57.) You can configure ICS to normalize the data in these files. Normalization is a process by which the range of intensity values for a BeadChip stripe is transformed to match a target range. This results in faster downstream processing times and optimized workflow.
Configuring iScan Control Software Figure 28 ICS AutoConvert Mapping Dialog Box b c d e f 6 38 Highlight the mapping you want to edit or click New to create a new mapping. For a new mapping, the row is populated with default entries. Click the PartNumber field in the right pane and enter or edit the product part number of the BeadChip. The product part number can be found on the BeadChip packaging.
The iScan System obtains processing file information from the input path. The output path is the location where all files will be saved upon scan completion. NOTE When the iScan System is running under LIMS, you cannot change the input or output paths. These paths are designated by the LIMS project management software. Refer to the LIMS Project Manager Guide for instructions on how to change input and output path locations. 1 On the ICS Setup screen, next to the Input or Output Path, click Browse.
Configuring iScan Control Software Verifying DMAP File Integrity The iScan Reader can be configured to check the integrity of *.dmap files at the start of each scan. (File integrity may become compromised if the files transfer incorrectly to the network during downloading.) NOTE Enabling this feature increases the amount of time before the iScan Reader begins performing the scan. 1 Click the Menu button Tools | Options.
Chapter 5 Scanning BeadChips Introduction . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 42 Starting a Scan . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 43 Monitoring the Scan Progress . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 44 Pausing, Resuming, and Stopping a Scan . . . . . . . . . . . . . . . . . . . . . . . . . . . . 46 Completing a Scan . . . . . . . . . .
Scanning BeadChips Introduction This section describes how to start, monitor, pause, stop, and complete scanning of BeadChips. NOTE Before starting a scan, the lasers must stabilize. Ensure that the iScan Reader has been on for at least 30 minutes before beginning a scan. 42 Part # 11313539 Rev.
After selecting the BeadChips to scan and confirming their settings, click Scan on the ICS Setup screen. Before scanning, the iScan Control Software: ` Checks available disk space The iScan Control Software warns you if there is less than 75 GB of free disk space for the image and intensity files and will not perform the scan if there is less than 12 GB of free disk space on the drive. ` Loads the *.dmap files for each BeadChip in the carrier The iScan Control Software warns you if any *.
Scanning BeadChips Monitoring the Scan Progress You can monitor scan progress by observing the following indicators as the iScan Reader scans: ` Progress Indicator ` Status bar ` Information bar ` Image Preview Progress Indicator The Progress Indicator is located on the left side of the screen. Figure 31 Progress Indicator on the ICS Scan Screen (left) The Progress Indicator shows which strips on the BeadChip have been or are being scanned or registered.
Monitoring the Scan Progress ` Output paths where intensity files and images are being saved Figure 32 Information Bar on the ICS Scan Screen (bottom) The Information Bar also indicates an LED showing the Initialization status: ` Green—The iScan Reader initialized successfully. ` Yellow—The iScan Reader has been conditionally initialized. ` Red—The iScan Reader did not initialize. If the status LED is yellow or red, refer to iScan Reader Issues on page 73.
Scanning BeadChips Pausing, Resuming, and Stopping a Scan While a scan is in progress, you can pause or stop the scan at any time. ` To pause the scan, click Pause. The scan continues to the end of the current array section, and then stops. The scan remains suspended until you click Resume. ` To stop the scan, click Cancel. A confirmation message appears. If you confirm the command, the scan process stops immediately and does not complete the current section. All completed sections are saved to disk.
When all the BeadChips have been scanned, a completion message appears. Click OK to continue to the Review screen. Figure 34 Scan Completed Message When using LIMS, if all sections of a BeadChip were successfully scanned, the BeadChip data are automatically submitted to LIMS. If any section on a BeadChip was not successfully scanned, either these sections can be rescanned, the entire scan can be cancelled, or the scan can be submitted to LIMS.
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Chapter 6 Viewing Scan Results Introduction . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 50 Log Files. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 51 Scan Metrics . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 52 Images . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Viewing Scan Results Introduction This chapter describes how to review the results of your scan using: ` Log Files ` Scan Metrics ` Images ` Generated Files 50 Part # 11313539 Rev.
During each run, the iScan Control Software creates a log file listing each step in the scanning process. These logs are also copied into the data output folder for each BeadChip for troubleshooting purposes. Figure 35 Log File in Data Output Folder To view the current log file: 1 Click the Menu button Tools | Show Log. in the upper left corner of any ICS screen and select 2 Navigate to the folder named Logs in the iScan Control Software application folder to view the archived log files.
Viewing Scan Results Scan Metrics The scan metrics for each BeadChip appear in the Scan Metrics table at the top of the Review screen. This table allows you to review intensity values in both the red and green channels, check the registration and focus metrics for each stripe on the BeadChip, and determine whether intensity data was normalized for each BeadChip section that was scanned. ` The focus metric ranges between 0 and 1.
This section describes how to review images of the scanned BeadChips in the iScan Control Software before closing the software. NOTE Once you click Done on the Review screen, you are returned to the ICS Welcome screen and will no longer be able to view the images in the iScan Control Software. Selecting Images to View 1 Select the BeadChip whose images you want to review, in the BeadChip carrier schematic at the top left side of the screen. 2 Click a scanned stripe in the BeadChip summary.
Viewing Scan Results Using the Toolbar Buttons to Adjust the Image Use the icons on the Image toolbar for the following functions: Table 4 Image Toolbar Icons Icon Description Auto Contrast—Resets the image contrast, brightness, pixels, and color ratio to default settings. Auto Zoom—Adjusts the zoom on the image so that the full swath is visible in the Image window. Zoom In—Zooms in on the image in the Image window, so the image gets larger.
Click in the image, in the area you wish to zoom. 2 Scroll down with the wheel to zoom in on the image, and scroll up with the wheel to zoom out on the image. Using the Control Bars to Adjust the Image The image control icons ( and ) enable you to toggle which control bars are displayed for adjusting the image in the main window. The Color control bar is available in both control bar views.
Viewing Scan Results Adjusting the Brightness 1 Click the image control icon to display the Brightness control bar. 2 Move the Brightness slider up to increase image brightness or down to decrease image brightness. Adjusting the Contrast 1 Click the image control icon to display the Contrast control bar. 2 Move the Contrast slider up to increase the image contrast or down to decrease the contrast. Adjusting the Color ` Move the slider on the Color control bar up to shift the image to be more red.
After images are scanned, they are registered and intensities are extracted for every bead type. If the AutoConvert feature was enabled, ICS normalizes the intensity data and generates genotype calls. ` Registration — Registration identifies beads by correlating their locations on the scanned image with information in the bead map (*.dmap) file. ` Intensity Data — Intensity extraction is the process by which intensity values are determined for every bead on the image.
Viewing Scan Results Image Files Each image file (*.tiff, *.jpeg, or *.png) is also saved on the iScan System computer or network under the Array ID (barcode identifier) folder in the output path folder. Filenames for each individual node are generated based on the position of the section in the BeadChip. The files are named according to the following nomenclature: ID_LABEL_STRIPE_SWATH_CHANNEL.
Chapter 7 Shutting Down the iScan System Procedure Summary . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 60 Ejecting BeadChips . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 61 Closing the iScan Control Software . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 62 Shutting Down the iScan System Computer . . . . . . . . . . . . . . . . . . . . . . . . . . . 63 Shutting Down the iScan Reader. . . . . .
Shutting Down the iScan System Procedure Summary There are four steps to shutting down the iScan System, and they must be performed in the following order: 1 Eject BeadChips. 2 Close the iScan Control Software. 3 Shut down the iScan System computer. 4 Shut down the iScan Reader. These steps are described in the following sections. 60 Part # 11313539 Rev.
` Open the iScan Reader tray and remove the BeadChip carrier by lifting it straight up and out of the tray.
Shutting Down the iScan System Closing the iScan Control Software ` Click the Menu button 62 in the upper left corner of the ICS screen and select Exit. Part # 11313539 Rev.
Shutting Down the iScan System Computer Shutting Down the iScan System Computer ` From the Windows Start menu, select Shut Down.
Shutting Down the iScan System Shutting Down the iScan Reader ` Press the Power switch on the back panel of the iScan Reader. NOTE Leave the power off for at least two minutes before turning on the iScan Reader again. 64 Part # 11313539 Rev.
Chapter 8 Troubleshooting Handling Errors . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 66 Issue Types . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 68 Registration Issues. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 69 Auto-Alignment Issues . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Troubleshooting Handling Errors The iScan Control Software records system errors to a log file as they occur. The log provides a record of system events that you can send to Illumina Technical Support for evaluation. If an error occurs, you can view error details in the error message box as well as in the log file.
Click Properties. Handling Errors b Figure 40 Selecting Properties The location of the event log is displayed in the Start in box of the iScan Control Software Properties dialog box.
Troubleshooting Issue Types Issues that may appear when using the iScan System fall into the following general categories: ` Registration issues ` Auto‐alignment issues ` iScan Reader issues ` Image quality issues ` iScan Control Software display issues The following sections describe these types of issues, with solutions for each. 68 Part # 11313539 Rev.
Cannot find IDAT files / No IDAT files are created / Cannot register images Cause Resolution Network error may have prevented files from being created. Note: Only applies to networked readers. Use Windows Explorer or another application to verify network accessibility. If network errors exist, ask IT for assistance. Sections may be broken or dirty. Eject the BeadChips and visually inspect sections to ensure that none are broken or dirty.
Troubleshooting BeadChips with registration errors are put onto the AutoLoader output stack instead of the error stack 70 Cause Resolution Carriers can contain a percentage of red stripes less than or equal to the error threshold percentage specified in the AutoLoader Options screen. Adjust (decrease) the error threshold percentage in the AutoLoader Options screen. See the AutoLoader2 User Guide or the AutoLoader 2.x User Guide, depending on your AutoLoader system. Carrier barcode cannot be read.
Auto-Alignment Issues Auto-Alignment Issues Unable to successfully complete auto‐alignment Cause Resolution BeadChips not properly seated in iScan Reader tray. Eject the tray and remove the BeadChips. Reload the BeadChips and ensure proper seating flat on the carrier tray. Ensure that the BeadChip is securely and properly snapped onto the tray. Its notches should match the posts built into the carrier tray, and the long edge of the carrier closest to the iScan Reader should push down the sensor button.
Troubleshooting Cause Resolution Sections may be broken or dirty. Eject the BeadChips and visually inspect sections to ensure that none are broken or dirty. Follow lab protocols for cleaning sections, and report broken sections to the responsible scientist. Try scanning the BeadChip again. Low intensity or poor‐ performing samples. Review scan metrics to uncover potential issues. Stripe turns red instead of green. One of the four swaths within the stripe is not being imaged correctly.
iScan Reader Issues iScan Reader Issues Cannot connect to iScan Reader Cause Resolution Cable between iScan Reader and PC might be unplugged. Inspect the cable between the iScan Reader and the dedicated workstation to confirm that the cable is securely connected at both ends. Initialization failure error while starting the iScan Control Software. Remove any external hard drive or other USB device before turning on the iScan Reader and its computer. This allows the override.
Troubleshooting iScan Control Software displays FPGA timeout errors Cause Resolution Problems with emission filter slide, excitation filter wheel, tilt motor, tray switch, and/or laser safety switch. Take a screen capture of the error and save it. Close the iScan Control Software and power cycle the scanner to clear the FPGA. Restart the iScan Control Software to see if the error repeats. If the error occurs again, contact Illumina Technical Support and schedule a field service call.
Image Quality Issues Image Quality Issues The iScan Reader is producing low intensity images Cause Resolution Low assay signal. Review the history of assay preparation with the responsible scientist. Evaluate the length of time since preparation, concentration of signal source due to evaporation, and adverse environmental conditions including humidity, temperature, and amount of direct sunlight. Bad focus.
Troubleshooting System displays “Cannot initialize camera frame grabber” error Cause Resolution Camera cable on back of scanner is loose. Tighten connection, then start the scanner and restart the iScan Control Software. You may need to power cycle the scanner and/or PC several times before the frame grabber is able to initialize successfully. Bead images are blurred Cause Resolution Auto‐tilt values are out of range, slide is not seated properly, or a problem exists with the z‐control board.
Buttons covered by text boxes or inaccessible / Text or icons distorted or truncated Cause Resolution Monitor resolution too low. Set monitor resolution to a minimum of 1280 x 1024, and 16‐bit color. Computer displays blue screen Cause Resolution Loose cable connection Check to see if the camera link cable leading to the between camera and frame frame grabber card has become loose. If the cable seems grabber card. tight, the frame grabber card may need to be reseated.
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Chapter 9 Maintenance and Service Introduction . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 80 Maintenance . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 81 Service . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Maintenance and Service Introduction This chapter describes maintenance and service recommendations for the iScan System. 80 Part # 11313539 Rev.
To clean the equipment, dampen a cloth with water and a mild detergent and wipe down all external surfaces. There are no internal surfaces that require cleaning.
Maintenance and Service Service CAUTION There are no user‐serviceable items inside the equipment. Please refer any service requests to qualified Illumina service personnel. 82 Part # 11313539 Rev.
Index Index A E auto contrast 54 auto zoom 54 auto‐alignment issues 71 AutoConvert 37 effective.
Index iScan Control Software 6 auto contrast 54 auto zoom 54 breadcrumbs 18 configuring 31 copy to clipboard 54 custom scan settings file 35 display issues 77 icon on desktop 17 image control icons 55 image toolbar 54 information bar 44 Menu button 10 overlay cores 54 progress indicator 44 show green and red channels 54 starting 17 status bar 44 zoom in 54 zoom out 54 zooming in/out 54 iScan Reader 4 issues 73 loading a carrier into 26 powering up 15 reinitializing 18 iScan Reader tray 5 iScan System air t
Technical Assistance Technical Assistance For technical assistance, contact Illumina Customer Support. Table 6 Illumina General Contact Information Illumina Website http://www.illumina.com Email techsupport@illumina.com Table 7 Illumina Customer Support Telephone Numbers Region Contact Number North America toll‐free 1.800.809.ILMN (1.800.809.4566) United Kingdom toll‐free 0800.917.0041 Germany toll‐free 0800.180.8994 Netherlands toll‐free 0800.0223859 France toll‐free 0800.
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Illumina, Inc. 9885 Towne Centre Drive San Diego, CA 92121-1975 +1.800.809.ILMN (4566) +1.858.202.4566 (outside North America) techsupport@illumina.com www.illumina.