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Agilent G2565AA and Agilent G2565BA Microarray Scanner System

1. 12 Check that you have the following required items prior to installing and using Agilent Scan Control software v 7 0 Software e Windows XP Professional or Windows 2000 with SP2 or SP3 e Internet Explorer 5 5 or later Hardware e Pentium IV 2 4 GHz or higher Pentium IV 3 2GHz or higher recommended e 1 GB RAM required 2 GB RAM recommended e 50 GB available disk space for programs and data generation Agilent G2565AA G2565BA Microarray Scanner System User Manual v 7 0 Introduction 1 Scanner front view Air filter vent Access lid and access door Status indicator lights Power switch Figure 2 Microarray Scanner Front View Scanner top view Slide holder Access lid autoloader arm Information label Carousel support base Figure 3 Microarray Scanner Top View Agilent G2565AA G2565BA Microarray Scanner System User Manual v 7 0 13 1 Introduction Scanner rear view Air vent Power fuses holder Line voltage indicator window Line voltage setting Diagnostic port Ethernet port for Agilent use only Laser fuse holder Figure 4 Microarray Scanner Rear View Site preparation Make sure the environment meets the Microarray Scanner specifications on page 120 of Chapter 6 If you have any questions contact your local Agilent sales and support center or www agilent com chem dnasupport Make sure the access lid has sufficient clearance Place on stur
2. Read Barcode from Carousel qj J xj This operation will be completd in 4 minutes Do you want to continue D 4 Click Yes The main window now looks like this 56 Agilent G2565AA G2565BA Microarray Scanner System User Manual v 7 0 How Do l 3 Pq Agilent Scan Control File Settings Help Current carousel settings Operator dt T eXtended Dynamic Range Scan Mode DR Red PMT 2 DR Green PMT 2 Hi fioo Lo i0 Hi fioo Lo 10 Start slot fi End slot fis Check Carousel Slot Slide ID Barcode Scan Regionimm Red PMT Green PMT Scan Resolution um Dye Channel 201209735301 Scan region option Use selected scan region for the slides in the carousel Aum scanning mode Single Pass Reset Selection Hide Editing lt lt Edit slot values Red Green Scan Slot Slide D Barcode Scan region mm PRT 22 PMT 9 resolution um Dye channel Mo 257209735301 Scan Area 61 x 21 6mm jho ziho zho ffRectGreen Read Barcode from Carousel Description Output path fes Browse l Scanner status are ready Scan Slot 1 15 Abort Figure 31 Main window after bar code reading If you reset a selection to a default setting the bar code will disappear Agilent G2565AA G2565BA Microarray Scanner System User Manual v 7 0 57 3 How Do l Enter bar code slide identifier information manually You can also enter Agilent supported bar codes or
3. Agilent recommends that the Microarray Scanner be placed ona sturdy lab bench or table The Microarray Scanner is a potential source of vibration The Microarray Scanner is potentially sensitive to external vibration The Microarray Scanner is potentially sensitive to condensing humidity conditions Follow precautions stated in product documentation See Tips to prevent problems on page 116 of Chapter 5 Agilent G2565AA G2565BA Microarray Scanner System User Manual v 7 0 Introduction 1 Principles of operation This section describes the operating features of the Microarray Scanner Slide positioning The Microarray Scanner uses a circular carousel that holds up to 48 slides 1 in x 3 in The carousel can be removed to load or remove slide holders or store for later use When a scan run is initiated the scanner rotates the carousel to the first scheduled slot number that contains a slide After the carousel reaches the loading position the Microarray Scanner transports the first slide and holder into the scanning position scans the slide and then returns the slide and holder to the carousel Laser excitation The Microarray Scanner uses two lasers a SHG YAG laser 532 nm and a helium neon laser 633 nm The lasers excite Cyanine 3 Cy 3 and Cyanine 5 Cy 5 labeled RNA or DNA to measure fluorescence after biological and chemical processes have bound the target sample to specific locations on a glass substrate Other
4. Height 97 cm 88 in with lid closed 55 cm 21 5 in Width 91 cm 86 in Depth 71 cm 28 in These dimensions account for maximum height and width when access doors are open and for an 80 mm 3 in clearance in depth to provide adequate venting 99 Kg 218 lbs 100 120 220 or 240 VAC at4 A 50 60 Hz Two power supply fuses T4A 250 VAC One laser fuse T500mA 250 VAC Operating 15 to 30 C Storage 20 to 50 C Operating 15 to 95 RH at 30 C Potentially sensitive to condensing humidity conditions Follow precautions stated in Chapter 5 Operating maximum 2 300 m 7 500 ft Storage maximum 4 600 m 15 000 ft Indoor use Excitation wavelengths e SHG YAG laser 532 nm e Helium Neon HeNe laser 633 nm Power 23 20 mW at laser orifices nominal 20 mW at 532 nm and 23 mW at 633 nm 120 Agilent G2565AA G2565BA Microarray Scanner System User Manual v 7 0 Maximum scan region Suggested microarray print region Dyes supported Resolution pixel size Pixel placement error Uniformity Scan time Dynamic range Data transfer rate Reference 6 Agilent G2565AA 67 2 mm x 21 6 mm Agilent G2565BA 71 mm x 21 6 mm 1 mm smaller than scan region on the right 2 mm on the left and 0 6 mm on the top and bottom For non Agilent slides the print region is smaller than this by an amount equal to the array printing tolerance Cyanine 3 Cy 3 and cyanine 5 Cy 5 and dyes similar to Cy
5. Output path The Browse button allows you to select a directory to store the data from each scan The directory can be on the local hard disk or a storage area over the network although Agilent recommends that the data be acquired to a local directory on the secondary hard drive i e Drive D You cannot type a directory name into the Output Path text box You must browse to an existing directory Automatic file For standard scans the Scan Control program uses three naming text boxes to determine the file name generated while scanning and merges them to form the file name Prefix1_Prefix2_scannumber tif The default prefixes are the instrument serial number and the bar code You can change Prefix 1 to a custom name and you can change Prefix 2 to either the slot number or a custom name The Scan Control program automatically assigns the scan number Other file names in the selected data directory with the same Instrument and Bar code IDs are detected and compared If no match is found the scan number is set to S01 If a match is found the scan number is incremented by one until the file name is unique This feature avoids duplicate file name conflicts For XDR scans an additional suffix either _H or _L is added to the filename to distinguish the XDR Hi image from the XDR Lo image Prefix1_Prefix2_scannumber_H tif Prefix1_Prefix2_scannumber_L tif Agilent G2565AA G2565BA Microarray Scanner System User Manual v 7 0 63 3
6. instead It will also evaluate several result parameters to decide if a warning should be issued For example an abnormally high Autofocus Hold value will yield one of two warning messages depending upon its magnitude Agilent G2565AA G2565BA Microarray Scanner System User Manual v 7 0 21 1 Introduction More robust scanning algorithms If a slide fails to load Scan Control Version 7 0 will attempt to eject the slide and skip to the next scheduled slot in the scan run Previous versions would simply stop the scan run If desired the Laser Saver feature will now turn off the lasers at the end of a scan run and turn them back on at a scheduled time on another day Hardware enhancements G2565BA This edition of the user guide identifies 2 major improvements to the G2565BA hardware since its introduction Carousel Indexing System The Carousel Indexing System which is a major part of the Autoloader has been redesigned to reduce the frequency of load and eject failures Many tolerances have been tightened and some components completely redesigned to eliminate failure modes that have been reported Autoloader Arm and Motor Assembly The Autoloader Arm and Motor Assembly has been completely redesigned as well One assembly is now compatible with both G2565AA and G2565BA scanners Some components have been redesigned and are now manufactured out of metal instead of plastic And most significantly the most common source of fa
7. 25 4 0 7 25 4 0 7 58 0 Print region for Agilent G2565BA Figure 55 Agilent G2565AA G2565BA Microarray Scanner System User Manual v 7 0 1 0 j 60 122 Reference 6 Slide specifications Slide specifications include glass thickness and bar code information Glass specifications The Microarray Scanner uses slide holders to move the microarrays in and out of the carousel These slide holders are designed to accept a 1 in x 3 in nominal piece of glass The detailed specifications of the glass are as follows e 1 inch wide 25 4 mm 0 45 mm or 0 7 mm e 3 inches long 76 2 mm 0 25 mm or 1 4 mm e Version A slide holder 1 mm thick 1 mm 0 025 mm Version B slide holder 1 mm thick 0 2 mm or 0 1 mm e No mirrored slides e Glass should be of high quality with low intrinsic fluorescence e Index of refraction from 1 510 to 1 515 Bar code specifications The bar code specifications vary for Agilent or non Agilent slides Agilent slide specifications Agilent slides have had the bar code on the side opposite the microarray From mid 2002 Agilent slides contain two bar codes one on each side of the slide Agilent G2565AA G2565BA Microarray Scanner System User Manual v 7 0 123 6 Reference If you are using non Agilent slides for your microarrays the bar code is not read by the G2565AA Microarray Scanner unless you place a bar code on the side opposite the microarray surfa
8. 3 Pull out the fuse holder and check the fuse integrity 4 If a fuse is blown replace the fuse with a T500mA 250 VAC rated fuse 5 Push the fuse holder back into place and screw on the cap Agilent G2565AA G2565BA Microarray Scanner System User Manual v 7 0 Troubleshooting Using HyperTerminal to Capture Diagnostic Data The Agilent Scanner comes with a diagnostic cable that allows Agilent service personnel to do troubleshooting To capture information that comes through the cable you will need to set up a HyperTerminal session These instructions apply to Windows 2000 systems To set up HyperTerminal 1 Click Start gt Programs gt Accessories gt Communications gt HyperTerminal 2 Inthe Connection Description dialog box a Type Scanner in the Name text box b Click OK Connection Description 2 x Ball a New Connection Enter a name and choose an icon for the connection Name Scanned Icon 3 Inthe Connect To dialog box a From the Connect using drop down list select COM1 b Click OK Agilent G2565AA G2565BA Microarray Scanner System User Manual v 7 0 99 4 4 Troubleshooting Connect To 4 From the COM1 Properties dialog box a Select 19200 as Bits per second b Select None as Flow Control c Click OK 7COM1 Properties i Te a a et hirege D r DRS per ong j me B k Ce Ce CL ERAY COMETI The Scanner HyperTerminal window appea
9. 44 Agilent G2565AA G2565BA Microarray Scanner System User Manual v 7 0 The scan time is defined as the time it takes the scanner to load scan and replace the slide Details of the Feature Extraction software can be found in the Feature Extraction Software User Guide which ts included with your scanner materials CAUTION Getting Started 2 Scan Progress M Current scan information e SLPJAN14B4 SLOTO1_S32 tif File name Barcode Slot number 1 Status Scanning m Progress Slide progress 16 Carousel progress 0 0 of 1 slides completed Tum laser power off after the current carousel run completed View Report Abort Close Figure 24 Scan Progress dialog box Note the messages in the Status window of the Scan Progress dialog box that keep you informed of the progress of each scan and of the carousel run The scan time for a 61 mm x 21 6 mm scan region at the 10 micron resolution setting or the single pass 5 micron resolution setting is approximately 8 minutes It s 15 minutes for the double pass 5 micron resolution setting After each scan is complete the data automatically transfers to the directory specified as your output directory See Change the storage directory and check drive capacity on page 76 of Chapter 3 2 Optional When the data for one scan is fully transferred display the file in the Agilent Feature Extraction software or another pr
10. 64 How Do l Split and rotate TIFF image Compress TIFF image Some analysis programs use data from only one color dye and images rotated 90 degrees If you mark this check box the color file is split into two color files and the images are rotated 90 degrees and flipped An example of the image is shown below mo gt g w The split files now have the names of itleName_green and FileName_red where FileName is the name that was automatically given to the file before it was split If you only select one dye channel for your output file you must still mark this check box to rotate the image even if you do not need to split the file This option is not available for XDR scan mode You can reduce the final amount of storage space occupied by scan images if this check box is marked for a carousel run First a temporary uncompressed file is created then after the scan is finished the file is compressed and named according to the default file naming settings If for any reason the software fails to complete the compression step the original uncompressed data file will be renamed according to the default file naming settings The compression algorithm used LZW reduces the storage space on the order of 20 to 70 percent The data in compressed image files can be displayed and extracted only with Feature Extraction 9 1 Click OK 4 Change the scan table settings to the new default settings See Chang
11. This feature allows you to have the laser warmed up and ready for scanning at a specified time or turned off automatically under specified conditions Regardless of how the various automatic ON OFF settings are set the software always allows the following You can turn the scanner on or off manually anytime If you open the Scan Control program the lasers will turn on If the scanner is scanning at the specified turn off time the scanner will finish the carousel run before turning off 1 Select Settings gt Laser Power Saver from the menu bar Li x Laer Poe Sav um Lamers UN Mow Turn Lassers UEF How FY Enable late power automalically ON OFF tacks Laner powe automatically OM AOFF taks Tum ONAOFF dai OM at 1230F OFF al F Tum OFF on weekends l Tum OFF alte a carousel mn completed Tum OFF alter a period of non use Penod fi x hourls and f gt minutels Tum OFF alter exiting the application Fiestas Manulactune Settings Figure 29 Laser Power Saver dialog box 2 Mark the Enable laser power automatically ON OFF tasks check box Agilent G2565AA G2565BA Microarray Scanner System User Manual v 7 0 53 3 How Do l 3 Change the settings using the choices below Turn ON OFF Allows you to specify daily times for turning the lasers on daily and off Turn OFF on If you have set daily times for turning the lasers on and off weekends this option allows you to specify that those t
12. When corresponding with your local Agilent sales and support center about your Microarray Scanner be sure to include the model number and the full 10 character serial number Please make a note of the serial number of your Agilent Microarray Scanner and the installation date in the spaces below if you print this page or on a sheet of paper that you keep close to your scanner 90 Agilent G2565AA G2565BA Microarray Scanner System User Manual v 7 0 Troubleshooting 4 Scanner information Model Serial Installation Date Software Version Software Update Version Date Software Update Version Date Agilent G2565AA G2565BA Microarray Scanner System User Manual v 7 0 91 4 Troubleshooting Frequently Asked Questions FAQs Table 2 FAQs The following are frequently asked questions FAQs and the corresponding answers that can help you operate and maintain the Microarray Scanner System and troubleshoot issues that occur FAQ want to move the Microarray Scanner to another area Can save files over the network while scanning How do obtain the Scan Control program revision information Where do find support information such as drivers guides and troubleshooting solutions for my PC workstation cannot open the top lid to access the carousel Answer If you need to move the scanner there is a chance that its performance could be adversely affected Call your local Agilent sales and
13. information contained herein Should Agilent and the user have a separate written agreement with warranty terms covering the material in this document that conflict with these terms the warranty terms in the sep arate agreement shall control Technology Licenses The hardware and or software described in this document are furnished under a license and may be used or copied only in accor dance with the terms of such license Restricted Rights Legend U S Government Restricted Rights Soft ware and technical data rights granted to the federal government include only those rights customarily provided to end user cus tomers Agilent provides this customary commercial license in Software and techni cal data pursuant to FAR 12 211 Technical Data and 12 212 Computer Software and for the Department of Defense DFARS 252 227 7015 Technical Data Commercial Items and DFARS 227 7202 3 Rights in Commercial Computer Software or Com puter Software Documentation Safety Notices CAUTION A CAUTION notice denotes a haz ard It calls attention to an operat ing procedure practice or the like that if not correctly performed or adhered to could result in damage to the product or loss of important data Do not proceed beyond a CAUTION notice until the indicated conditions are fully understood and met A WARNING notice denotes a hazard It calls attention to an operating procedure practice or the like that if not
14. 3 and Cy 5 and Alexa 647 555 and 660 dyes 5 or 10 microns lt 1 pixel at 10 micron resolution 5 CV global non uniformity average local non uniformity is typically 1 based upon 100um features For two colors simultaneous data acquisition about 8 minutes per scan at 10 micron resolution scan region of 61 mm x 21 6 mm and 5 micron resolution single pass mode and about 15 minutes for 5 micron resolution double pass mode per scan Includes slide loading and ejection Single scan dynamic range gt 104 16 bit data format Dual scan extended dynamic range XDR gt 10 The data transfer rate between the scanner and the PC is 10 MB sec Agilent G2565AA G2565BA Microarray Scanner System User Manual v 7 0 121 76 2 0 25 1 4 dimensions are in millimeters and the reference point is the The scan and print regions for the Agilent G2565BA are lower right side of the glass described in Figure 54 and Figure 55 In the figures all IMmensions Reference Scan and print d 1 K r 20 4 N 2 5 WR ww AA al lt o LO co LO N i SM QQ IARI QQQQQQA MM QQ QAI QQQQQQYA 2 SR QE QQ ab D ARRALI SS RNR RRN N oO D Y xX gt lt r or as co Lo SI QQ AWW QQQQQ QDR pE LQ QQ LQ QQ N QQ QQAN oO N ARRALI QQ QQ QA lt i O N q LO O kez Laden WAAR y O y j qe spooeg l qe1 povieg v or 0 45 pe or 0 45 ES
15. Agilent supported bar codes 56 Enter bar code slide identifier information manually 58 Change scan settings 59 Agilent G2565AA G2565BA Microarray Scanner System User Manual v 7 0 Change the default scan settings 60 Change scan table settings 65 Select a scan region for Agilent slides 67 Select a scan region for non Agilent slides 69 Create a new scan region for non Agilent slides 71 Change the sensitivity resolution or dye channel settings 75 Change the storage directory and check drive capacity 76 Change the prefixes for automatic file naming 78 Rotate the scan image and split the color file 79 Compress TIFF image 80 Do other useful tasks 81 Set the URL to reach technical support 81 Automatically display Report Log after carousel run 82 Find the version information for scanner software components 83 Remove a slide from a version B slide holder 84 Mount or remove the carousel 86 4 Troubleshooting Technical Support 90 PC workstation support 90 Microarray Scanner support 90 Scanner information 91 Frequently Asked Questions FAQs 92 Hardware Troubleshooting 94 Troubleshooting with the status indicator lights 94 Checking and replacing scanner fuses 96 Using HyperTerminal to Capture Diagnostic Data 99 To setup HyperTerminal 99 To start a HyperTerminal capture session after initial set up 103 Agilent G2565AA G2565BA Microarray Scanner System User Manual v 7 0 7 Software Troubleshooting 104 Microarra
16. Default Settings dialog box e Non default settings Changes that you have made in the scan table that differ from the default settings Default settings When you first enter the Scan Control main window the scan table shows the shipped default settings You cannot save changed default settings into a file but you can have your own default settings When you start the Scan Control program after changing the default settings you see the default settings that you entered or changed previously If other users start the Scan Control program they see their own changed default settings not yours See Change the default scan settings on page 60 Non default You can change a default setting in the scan table to a settings non default setting with the Edit slot values panel in the main window You can also edit the non default settings in the same panel See Change scan table settings on page 65 You can always change a non default setting back to a default setting See Change scan table settings to default settings on page 66 Agilent G2565AA G2565BA Microarray Scanner System User Manual v 7 0 59 3 How Do l Change the default scan settings Scan region 1 Select Settings gt Modify Default Settings from the menu bar When you first start the Scan Control program the default Scan configuration settings are selected for Agilent slides Default Settings k Scan configuration Scan region Dye channel R
17. Manual v 7 0 81 3 How Do l Automatically display Report Log after carousel run You can set a preference option to automatically display the Carousel Report Log after each carousel run We recommend that you check the log for errors before beginning the next carousel run because the previous log is erased once you start the new carousel run 1 Select Settings gt Preferences from the menu bar Preferences Sti Current technical support hyperlink Use Default Automatically display the report log at the end of carousel run Cancel Figure 44 Preferences dialog box 2 Select the Automatically display the report log at the end of carousel run check box 3 Click OK 82 Agilent G2565AA G2565BA Microarray Scanner System User Manual v 7 0 How Do l 3 Find the version information for scanner software components 1 Select Help gt About from the menu bar to find version information 2 To close the program click OK About Agilent Scan Control E 3 oe ee gilent Technologies Agilent Scan Control Version 4 7 0 1 May 8 2006 11 24 05 Additional Information Scanner Model G 25056 Scanner SM U51470PPB1 BSPScan DLL Version 4 7 0 1 May 8 2006 11 23 13 Runtime Version4 6 1 1 Sep 09 2002 15 50 45 Scan DSF Version 4 6 1 1 Sep 10 2002 YE DSF Version4 6 1 1 Sep 9 2002 AF DSP AFOCUS Version A621 Nov 14 2002 Boot ROM Version A 7 0 2 Dec 20 2005 05 52 24 RAM Size 010000
18. Microarray Scanner e Place the Microarray Scanner on a sturdy lab bench or table e Avoid leaning on the Microarray Scanner e Leave the instrument powered off when not in use for over 4 hours to extend the life of the lasers Use the laser power save feature to automatically power on and off your lasers See Set Laser Power Saver Agilent G2565BA only on page 53 of Chapter 3 Agilent G2565AA G2565BA Microarray Scanner System User Manual v 7 0 117 5 Maintaining Your System e After turn on allow time for laser warm up and stabilization The maximum warm up time is 20 minutes e Keep carousel floor clean using a wipe and no solvent e Do not use acetone or other solvents for cleaning e Do not touch gearing in the carousel area WARNING Do not remove the covers Do not attempt to repair or gain access to internal components You might expose yourself to high voltage and harmful laser radiation Tip to prevent scanner software miscommunication when using the Recovery CD on a PC running Windows 2000 Agilent supplies a recovery CD that lets you reload the hard drive image that Agilent ships with the PC In order to re establish the LAN connection with the scanner after you reload the image you must restart the connection manager program Keep the recovery CD in a safe 1 Select Administrative Tools in the Windows 2000 Control place You may need the CD to Panel re image the hard drive later 2 Select Services gt
19. Modify Default Settings from the menu bar The Default Settings dialog box appears See Figure 35 2 Under Scan Region clear the check box Attempt to retrieve from XML GEML files 3 In the Region mm drop down list box select an Agilent supplied scan region or an existing one that you or someone else created Agilent Supplied Scan Regions Scan Area 71 x 21 6 mm Agilent G2565BA only Scan Area 67 2 x 21 6 mm Scan Area 61 x 21 6 mm Scan Area 55 x 21 6 mm Scan Area 50 x 21 6 mm Scan Area 45 x 21 6 mm Scan Area 40 x 21 6 mm 4 Click OK Change the scan table scan region to the new default settings See Change scan table settings to default settings on page 66 Agilent G2565AA G2565BA Microarray Scanner System User Manual v 7 0 69 3 70 How Do l Select an existing scan region for slides in the scan table 1 Click Edit Slot Values on the Scan Control main window The Edit slot values panel appears below the main window for you to change the scan region for individual slides See Figure 30 2 Select the slide whose region you want to change 3 Select the scan region from the list and click Set Values You can also press Enter to place the new setting in the scan table 4 Repeat steps 2 and 3 for all the slides whose scan region you intend to change 5 Click Hide Editing To change a setting back to its default setting select the slide or slides in the scan table and click
20. Reset Selection You apply the default settings to all slides when you click Slot in the upper left of the scan table and click Reset Selection See Change scan table settings to default settings on page 66 Agilent G2565AA G2565BA Microarray Scanner System User Manual v 7 0 How Do l Create a new scan region for non Agilent slides If you use non Agilent slides you can create your own scan region or change a scan region up to the maximum scan region of 71 mm x 21 6 mm for the Agilent G2565BA and 67 2 mm x 21 6 mm for the Agilent G2565AA Follow the instructions below Start the Scan Region Editor from the Scan Control main window The Scan Region Editor is not available from the Scan Control main window when the scanner is scanning See Start the Scan Region Editor from the Start menu on page 74 e Select Settings gt Customize Scan Region from the menu bar Agilent G2565AA Agilent G2565BA Agilent T echnologers eeu Fegin E gulir Agilent Technologies Scan Region Editor File Help b x Scanner G2505A Scanner G2505B Temte ne mem eee ee WOT assesses E E ty E C a ka i A Scan Region H 6 00 1 3 10 1 90 E bin upper latt camar Min upper left comer G ne H Meo law right comer Max lower right corner 7 R20 23 50 i 74 10 23 50 Y XS Slide Holder X Pos mm Pos mm width mm 45 00 15 00 20 00 6 00 Figure 37 Scan Region Editor Agilent G
21. and data on your hard drive Refer to this topic to learn about important error messages and solutions Agg Agilent Technologies 89 4 Troubleshooting Technical Support Technical support is available for the Agilent Microarray Scanner System Please read the rest of this chapter prior to calling your local Agilent sales and support center PC workstation support If you have a problem with your PC workstation see the documentation that came with the PC If you are still unable to resolve the problem contact your local Agilent sales and support center or see Agilent support at www agilent com chem dnasupport Microarray Scanner support If you have a problem with your Microarray Scanner that requires assistance from your local Agilent sales and support center you may be asked to provide the latest diagnostic log files that the Scan Control program created These files are located in the folder C Program Files Agilent Microarray Logs Additional diagnostic information including results of the Power on Self Test can be captured using the HyperTerminal program See Using HyperTerminal to Capture Diagnostic Data on page 99 for more information on setting up and using this communication protocol Each Agilent Microarray Scanner is identified by a unique 10 character serial number The serial number is located on a label in two places on the Microarray Scanner one in the carousel bay and one behind the filter door
22. dyes similar to Cy 3 and Cy 5 can be used such as Alexa 647 555 and 660 dyes The Microarray Scanner is optimized for high signal to noise performance in the Cy 3 550 610 nm and Cy 5 650 750 nm emission channels with a wide dynamic range up to five orders of magnitude and low spectral cross talk This allows for measurement of a very broad range of gene expression levels and for higher data confidence at lower signal levels Scanning The laser excitation is scanned rapidly back and forth across the microarray Movement of the microarray in the orthogonal coordinate is accomplished by the slow linear stage The dynamic tracking auto focus assembly keeps the slide in focus with the scan lens ensuring that the microarray is always Agilent G2565AA G2565BA Microarray Scanner System User Manual v 7 0 17 1 18 Introduction positioned in the detection plane These features maximize the signal to noise ratio by providing superior linearity uniformity and noise performance while scanning across the microarray surface Fluorescence detection Fluorescent emissions from the labeled samples are detected using a high performance PMT design Very low noise amplifiers and analog to digital converters process the PMT signal witha high signal to noise ratio Signal to noise performance is maintained by integrating multiple analog to digital samples within a single pixel Maximum scan region for non Agilent slides The maximu
23. file into two separate one color files automatically 1 Select Settings gt Modify Default Settings from the menu bar The Default Settings dialog box appears See Figure 35 2 Under scan image file handling mark the check box Split and Rotate TIFF Image 3 Click OK The image will be flipped as below m gt YBCD Figure 42 Result of the flip rotation Agilent G2565AA G2565BA Microarray Scanner System User Manual v 7 0 79 3 How Do l The split files now have the names of FileName_green and FileName_red where FileName is the name that was automatically given to the file before it was split If you only select one dye channel for your output file you must still mark this check box to rotate the image even if you do not need to split the file This option is not available for XDR scan mode Compress TIFF image You can reduce the final amount of storage space occupied by scan images if this check box is marked for a carousel run First a temporary uncompressed file is created then after the scan is finished the file is compressed and named according to the default file naming settings If for any reason the software fails to complete the compression step the original uncompressed data file will be renamed according to the default file naming settings 1 Select Settings gt Modify Default Settings from the menu bar The Default Settings dialog box appears See Figure 35 2 Under scan imag
24. for one or more slides Or you may need to perform a particular operation on the scanner only occasionally All of the tasks in this chapter are optional if you need to scan Agilent slides The tasks may be necessary if you need to scan non Agilent slides If you have any problems see Chapter 4 for troubleshooting information See Chapter 2 Getting Started for The tasks in this chapter assume that you have already started instructions to start the software the Scan Control program Freq Agilent Scan Control File Settings Help Curent carousel settings T eXtended Dynamic Range Scan Mode Operator amp OR Red PMT 2 SOR Green PMT Hi ion Lo 10 Hi fioo Lo 10 Start slot fi End slot as Check Carousel Slot Slide IDB arcade Scan Region rnm Red PMT Green PMT 4 Scan Resolution umn Ove Channel ut oC an Area 6 al D0 4 n an E aa j ma j al al al al al al ali me 1 ly z i Scan region option Use selected scan region for the slides in the carousel Aum scanning mode Single Pass Reset Selection Edit Slot Values gt gt Scanner status o ready Scan Slot 1 48 Abort Figure 28 Scan Control main window and scan table 52 Agilent G2565AA G2565BA Microarray Scanner System User Manual v 7 0 How Do l 3 Set Laser Power Saver Agilent G2565BA only You can activate the laser power saver which extends the life of your lasers
25. input voltage setting on the rear of the instrument is set to the correct value The input voltage setting can be set to one of four values 100 VAC 120 VAC 220 VAC 240 VAC Go to the rear of the Microarray Scanner View the input voltage setting through the small window Input voltage setting view window Figure 5 Input voltage setting view window 3 If the input voltage setting matches the line voltage you can safely turn on the Microarray Scanner If the input voltage setting does not match the line voltage go to step 4 Disconnect the power cord WARNING Always disconnect the power cord before changing the input voltage setting 24 Agilent G2565AA G2565BA Microarray Scanner System User Manual v 7 0 Getting Started 2 5 Use a small flat edge screwdriver to pry up the small plastic tab located on the bottom edge of the fuse holder until it releases Fuse holder Figure 6 Removing the fuse holder for the power supply 6 Pull out the fuse holder Agilent G2565AA G2565BA Microarray Scanner System User Manual v 7 0 25 2 Getting Started 7 Use needle nose pliers to remove the voltage selector Voltage selector Fuse holder Figure 7 Removing the voltage selector from the fuse holder 8 Insert the voltage selector so that the number showing matches the line voltage 9 Push the fuse holder back in until it clicks into place 10 Plug in the power cord Step 1 Turn on the Micro
26. rotate TIFF image Compress TIFF image Figure 41 Scan image file handling section of the Default Settings di alog box 2 Under Prefix1 select from the following choices Instrument Serial Number Customize 3 Enter your own custom prefix in the Customized box if you selected Customize Maximum characters 36 4 Under Prefix2 select from the following choices Bar code Slot Number Customize 5 Enter your own custom prefix in the Customized box if you selected Customized Maximum characters 36 78 Agilent G2565AA G2565BA Microarray Scanner System User Manual v 7 0 How Do l 3 6 Click OK Example 2583_02506190000015_S503 tif e Instrument serial number 2583 e Bar code 02506190000015 e Scan Number S03 This is the third scan file in the directory with the same instrument and bar code The Scan Control program automatically assigns the Scan Number Other file names with the same Instrument and Bar code IDs are detected and compared If no match is found the scan number is set to SO1 If a match is found the scan number is incremented by one until the file name is unique This feature avoids duplicate file name conflicts Rotate the scan image and split the color file Some post scan analysis programs need to have the scan image rotated 90 degrees and can only analyze data of one color So the Agilent Scan Control program lets you tell the system to rotate the image and split the two color composite
27. scanner model and click OK 5 Select scanner RTTE Select a scanner to edit scan regions Change the sensitivity resolution or dye channel settings This section covers how to change the default settings and scan table settings Change the default settings 1 Select Settings gt Modify Default Settings from the menu bar The Default Settings dialog box appears See Figure 35 2 Select the sensitivity scan resolution or dye channel setting that you need Use the definitions in Change the default scan settings on page 60 to help make your selections 3 Click OK 4 Change the scan table settings to the new default settings See Change scan table settings to default settings on page 66 Agilent G2565AA G2565BA Microarray Scanner System User Manual v 7 0 75 3 How Do l Change the scan table settings 1 Click Edit Slots Values on the Scan Control main window The Edit slot values panel appears below the main window See Figure 30 2 Select the slot whose settings you want to change You can select more than one slot at a time by dragging the cursor up and down the table 3 Select the new settings for this slide See the definitions of the settings in the topic Change the default scan settings on page 60 to help you select the ones to change 4 Click Set Values You can also press Enter to place a setting in the scan table 5 Click Hide Editing To change a setting back to its def
28. scans each row of pixels twice when 5 micron resolution is selected As a result typical 5 micron scans required approximately 15 minutes to complete Scan Control Version 7 0 offers a single pass option that reduces scan time by about half Post processing of the data has been implemented with this option to eliminate direction dependent noise DDN The DDN information is stored into the image file and can be viewed with Feature Extraction Version 9 1 software Automatic image file compression option Scan Control Version 7 0 software provides an option in the Default Settings dialog box for you to compress the scan image file at the time the image is generated The compression algorithm used LZW reduces the storage space on the order of 20 to 70 percent This feature is customizable separately for each User of the system The data in compressed image files can be displayed and extracted only with Feature Extraction 9 1 More robust communication algorithms Bootp and Connection Manager Services have been reprogrammed to be more accommodative to various networking environments For example it is no longer necessary to disable the house network adapter if the house connection doesn t exist or the house network is disabled New Carousel Report Log messages Previous versions of Scan Control software report that a scan is successful simply because it scans to completion Scan Control Version 7 0 will report Scan completed
29. settings for Agilent slides that let you scan right away to produce usable results If you do not need to change any of the default settings for any slide and you usually don t for Agilent slides wait until the Scanner status message says Scanner Ready and move on to Step 8 Start the carousel run on page 44 Before you start the carousel run review this checklist of tasks to make sure that you check or change any available scan setting that you need to You can do the tasks in any order You can find instructions for each of the listed tasks in Chapter 3 Table 1 Pre scan checklist S Pre scan task Read bar codes for slides with Agilent supported bar codes or Enter bar code slide identifier information manually Change the default scan settings Change scan table settings Select a scan region for Agilent slides or Select a scan region for non Agilent slides or Create a new scan region for non Agilent slides Change the sensitivity resolution or dye channel settings Task location in Chapter 3 page 56 page 58 page 60 page 65 page 67 page 69 page 71 page 75 Agilent G2565AA G2565BA Microarray Scanner System User Manual v 7 0 Getting Started 2 Table 1 Pre scan checklist continued Pre scan task Task location in Chapter 3 VY Change the storage directory and page 6 check drive capacity VY Change the prefixes for automatic file page 78 naming VY Rotate
30. slides Select an individual slide Drag the cursor down multiple slides to select more than one slide 4 Change the setting Agilent G2565AA G2565BA Microarray Scanner System User Manual v 7 0 65 3 How Do l See Change the default scan settings on page 60 for information on the selections in the Edit slot values panel or see the individual task in this section that relates to the setting that you intend to change Change scan table settings to default settings 1 Select the slot or slots to contain the new default settings Select one slot in the scan table Select more than one contiguous slot by dragging the cursor over the slots Select the Slot header in the upper left hand corner of the table to select all the slots in the scan table 2 Click Reset Selection The Reset Selection message appears Reset Default Settings xi AN You are trying to set selected slot s fitem s to default settings Any customized settings you have made will be lost Continue anyway 3 Click Yes After applying the default settings to one or more slots the remaining non default settings appear in bold Agilent G2565AA G2565BA Microarray Scanner System User Manual v 7 0 How Do l 3 Select a scan region for Agilent slides The scan region determines the area of the slide that is scanned The larger the region the longer the scan time Scan regions vary because of factors such as bar code label place
31. support center for assistance in moving the scanner and assuring proper operation afterwards Save your data files directly to the local hard disk Saving to a storage device over the network can cause data loss or other problems if network traffic becomes congested When communicating with Agilent Technical Support you might be asked to obtain the Scan Control program revision information This is done by selecting Help gt About in the main menu If you have a problem with your PC workstation see the documentation that came with the PC If you are still unable to resolve the problem contact your local Agilent sales and support center Do not attempt to force the lid open Forcing the lid could damage the Microarray Scanner 1 Push down on the lid to reduce any existing spring tension and then attempt to open the lid If this fails then go to step 2 2 Close and then restart the Scan Control program Try opening the lid 4 Ifthe lid still does not open close the Scan Control program and turn the Microarray Scanner off then back on 5 Try opening the lid 6 Ifthe lid still does not open contact your local Agilent sales and support center oo 92 Agilent G2565AA G2565BA Microarray Scanner System User Manual v 7 0 Table 2 FAQs continued Troubleshooting 4 FAQ Answer The Scan Control program does not The Scan Control program has stopped responding no changes in the status respond message for more than 15 minu
32. the dark offset without incorrectly skewing the data towards zero A constant level of signal offset is not noise and does not negatively impact the detection of low level signals Agilent G2565AA scanners that shipped with version 5 0 scanner software or earlier An Agilent support engineer must perform an on site calibration to enable this feature on existing scanners prior to version 5 1 with the updated version of the software version 5 1 or later Until this calibration is done the dark offset remains unchanged Agilent G2565AA scanners that shipped with version 5 1 scanner software or later or Agilent G2565BA scanners The dark offset subtraction is enabled and provides scans that appear to have lower background levels than scans performed on earlier scanners that do not have this feature enabled Agilent G2565AA G2565BA Microarray Scanner System User Manual v 7 0 19 1 Introduction Software enhancements Version 7 0 For hardware enhancements to the G2565BA see Hardware enhancements G2565BA on page 22 This edition of the user guide covers changes to the software from version 6 3 to version 7 0 With version 6 1 the hardware changed from Agilent G2565AA to Agilent G2565BA Version 6 1 6 3 and 7 0 software can be used on Agilent G2565AA hardware but some of the features may be different because of differences in hardware The differences are marked in this user guide Agilent Scan Control software vers
33. the lid until you hear the lid unlock Attempting to lift the lid while the Microarray Scanner is unlocking the lid can cause a jam Agilent G2565AA G2565BA Microarray Scanner System User Manual v 7 0 49 2 Getting Started 50 Agilent G2565AA G2565BA Microarray Scanner System User Manual v 7 0 Agilent G2565AA G2565BA Microarray Scanner System User Guide v 7 0 3 How Do l Set Laser Power Saver Agilent G2565BA only 53 Enter bar code or slide identifier information 55 Read bar codes for slides with Agilent supported bar codes 56 Enter bar code slide identifier information manually 58 Change scan settings 59 Change the default scan settings 60 Change scan table settings 65 Select a scan region for Agilent slides 67 Select a scan region for non Agilent slides 69 Create a new scan region for non Agilent slides 71 Change the sensitivity resolution or dye channel settings 75 Change the storage directory and check drive capacity 76 Change the prefixes for automatic file naming 78 Rotate the scan image and split the color file 79 Compress TIFF image 80 Do other useful tasks 81 Set the URL to reach technical support 81 Automatically display Report Log after carousel run 82 Find the version information for scanner software components 83 Remove a slide from a version B slide holder 84 Mount or remove the carousel 86 ee Agilent Technologies 51 3 How Do l Before you scan a set of slides you may want to modify scan settings
34. the number showing in the voltage selector on the back of the scanner matches the input power supplied 2 Ifyou rebooted the PC workstation you may need to turn the Microarray Scanner off and then back on after Windows has restarted 3 Ifthe problem persists contact your local Agilent sales and support center Do the following 1 If you have a backup copy of your customized ChipRegions ini file copy it to C Program Files Agilent Microarray Having a backup copy of ChipRegions ini will avoid loss and re creation of custom scan regions 2 Ifyou don t have a backup copy search the folder for ChipRegions bak and rename it to ChipRegions ini 3 If neither file exists re install the Scan Control program 4 Contact your local Agilent sales and support center The hard drive does not have enough disk space to create a file to store scan data You can do one of the following e Go to the Scan Control main menu and set the output directory to another directory on another hard drive e Delete or transfer files from the current hard drive See Step 9 Transfer files and archive data on page 48 Contact your local Agilent sales and support center Agilent G2565AA G2565BA Microarray Scanner System User Manual v 7 0 109 4 Troubleshooting Table 4 Error Messages continued Error Message PMT calibration lost Using factory default settings The autoloader loading arm is in an unknown location It is unclear i
35. the scan image and split the page 9 color file VY Compress TIFF image page 80 Agilent G2565AA G2565BA Microarray Scanner System User Manual v 7 0 43 2 Getting Started Step 8 Start the carousel run A carousel run scans all the specified slides in the carousel Before you start Make sure that the Microarray Scanner has finished warming up maximum 20 minutes Verify that the Scanner status message in the main window says Scanner Ready Once the carousel run is started the Carousel Report Log from the previous carousel run is erased and a new report log is started If you haven t reviewed the report log from the previous carousel run we recommended that you review the report log before you begin the new carousel run You can set a preferences option to automatically display the report log at the end of a carousel run See Automatically display Report Log after carousel run on page 82 of Chapter 3 Start the carousel run 1 Click Sean Slot m n on the Scan Control main window The letter m represents the Start slot where your first slide is located and the letter n represents the End slot where your last slide is located Two actions take place when you start the scan The scanner lid locks The Scan Progress dialog box opens showing you the status of the scan Agilent G2565BA only From the Scan Progress dialog box you can also set the software to automatically turn off the lasers after the carousel run
36. you must synchronize scan regions From doesn t show up as one of the choices the main Scan Control menu select Settings gt Refresh Scan Region from the for the scan regions top menu Agilent G2565AA G2565BA Microarray Scanner System User Manual v 7 0 93 4 Troubleshooting Hardware Troubleshooting 94 The Microarray Scanner has very few parts that you can service yourself You can take actions based on the errors shown by the status indicator lights on the front You can also replace the fuses that protect the system Any other problems including jams should be handled by contacting your local Agilent sales and support center If you are having a problem with your PC workstation see PC workstation support on page 90 for support information Troubleshooting with the status indicator lights The front panel holds three status indicator lights indicating the current status of the Microarray Scanner Status indicator lights Figure 48 Location of the status indicator lights Table 3 describes the actions that you take given the status of the indicator lights Agilent G2565AA G2565BA Microarray Scanner System User Manual v 7 0 Troubleshooting 4 Table 3 Indicator Light Status LED Status Possible Suggested Causes Action Green Yellow Red Off Off Off No power to the scanner Check the following e power switch is on e power cord is plugged in and there is power at the source e power fuses are
37. you want to change You can select more than one slide at a time Just drag the cursor up and down the list of slides You cannot select non contiguous slides 3 Change the path and enter a description for the slides that you want to change See the topic Change the default scan settings on page 60 for more information 4 Click Hide Editing To change a setting back to its default setting select the slide or slides in the scan table and click Reset Selection You apply the default settings to all slides when you click the Slot header in the upper left of the scan table and click Reset Selection See Change scan table settings to default settings on page 66 Agilent G2565AA G2565BA Microarray Scanner System User Manual v 7 0 77 3 How Do l Change the prefixes for automatic file naming The Scan Control program uses three text boxes to determine the file name generated while scanning and merges them to form the file name Prefixl_Prefix2_scannumber tif The default prefixes are the instrument serial number and the bar code If you want to change these prefixes do the following 1 Select Settings gt Modify Default Settings The Default Settings dialog box appears Scan image file handling Output path E temp Browse Automatic file naming the format is Prefix Prefit_scannumber TIF Prete Instrument Serial Mum Customized Frefisz Barcode k Customized T Split and
38. 000 Copyright 1999 2006 Agilent Technologies Figure 45 Example of version information for software components Agilent G2565AA G2565BA Microarray Scanner System User Manual v 7 0 83 3 How Do l Remove a slide from a version B slide holder Fingerprints cause errors in the fluorescence detection For accurate readings touch only the The version B slide holder can be used only in the Agilent G2565BA For instructions on inserting the slide see Inserting a slide into a version B slide holder on page 29 of Chapter 2 1 Hold the slide holder on the sides with the Agilent logo facing up 2 Place one thumb on the center of the slide holder cover edges of the slide and always use gloves when handling slides 84 3 Gently press down on the cover and push toward the top of the slide holder until the cover releases ANN Released slide holder cover 4 Release the cover Agilent G2565AA G2565BA Microarray Scanner System User Manual v 7 0 How Do l 3 5 Push up on the bar code end of the slide from underneath the slide holder to avoid fingerprints on the sample area 6 Grasp the slide from the sides and remove from slide holder Push up from underneath Figure 46 Proper removal of slide Agilent G2565AA G2565BA Microarray Scanner System User Manual v 7 0 85 3 How Do l Mount or remove the carousel If you have placed the slide holders into a carousel that was rem
39. 23 split and rotate tiff image 64 starting carousel run 44 software 38 status indicator lights 13 27 94 95 status in Scan Progress dialog box 44 stopping during ascan 46 stopping the scan 46 storage directory setting 6 support technical 90 system features 10 12 T technical support 90 changing URL to reach 81 82 technical support calling 90 temperature considerations 117 tiff image split and rotate 64 top view of scanner 13 transferring files 48 116 troubleshooting error messages 105 to 112 hardware 94 to 98 replacing fuses 96 to 98 technical support 90 V Version 7 0 enhancements 20 version A slide holder description 28 inserting slide 33 Agilent G2565AA G2565BA Microarray Scanner System User Manual v 7 0 version B slide holder description 28 inserting 29 removing slide 84 version information finding 83 view report 46 voltage setting input 24 W warm up time 27 X XDR 20 62 65 XML GEML path set 67 XML database 67 Agilent G2565AA G2565BA Microarray Scanner System User Manual v 7 0 Index 131 www agilent com Information descriptions and specifications are subject to change without notice Please register online with Agilent to receive new product updates at www agilent com chem dnasupport Agilent Technologies Inc 2003 2006 Printed in USA Sixth Edition May 2006 Part Number G2566 90017 fhe Agilent Technologies
40. 2565AA G2565BA Microarray Scanner System User Manual v 7 0 71 3 3 How Do l Create a new scan region with the Scan Region Editor When creating a new scan region or using existing scan regions make sure the scan region is at least 4 mm away from the bar code label and does not overlap any other opaque or translucent areas of the slide 1 Select File gt New Region from the menu bar Agilent G2565AA Agilent G2565BA w Add New Region Bil x w Add New Region olx Name oo Name PO Ranges mm Ranges mm x mm 6 00 68 20 x mm 310 6910 Y mm 190 23 40 Y ooo mm 1 90 23 40 Width mm 5 00 67 20 Width mm 5 00 71 00 Height mm 0 10 21 60 Height mm 0 10 21 60 ca sa Figure 38 Add New Region dialog box 2 Enter the name or size of the region 3 Enter the measurements in mm for the region using the criteria listed below Invalid ranges are marked in red X X axis measurement for the upper left hand corner You enter this measurement and that of the Y axis in mm to position the region on the slide Y Y axis measurement for the upper left hand corner Width Width of the scan region measured from the end of the X axis measurement in the upper left hand corner Height Height of the scan region measured from the end of the Y axis measurement in the upper left hand corner Ranges Range of values that you can enter for each measurement 72 Agilent G2565AA G2565BA Microarray Scanner Sys
41. 5BA Microarray Scanner System User Manual v 7 0 Maintaining Your System 5 Tips to avoid environmental damage to the scanner e Keep liquids and vapors away from the Microarray Scanner e Minimize and control temperature fluctuations Do not place the Microarray Scanner in direct sunlight Do not locate the Microarray Scanner near windows even if they have blinds or window coverings The hot sun can heat up the Microarray Scanner s housing in a non uniform fashion which may cause problems with the alignment of the optics Scan only when the laboratory temperature is consistent with the operating temperature specifications for the Microarray Scanner To assure optimal Microarray Scanner performance operate the scanner only in the specified temperature ranges see Microarray Scanner specifications on page 120 e Control the humidity The Microarray Scanner is potentially sensitive to condensing humidity conditions To ensure optimal performance operate the Microarray Scanner only in the specified humidity ranges see Microarray Scanner specifications on page 120 Always allow 10 hours thermal equilibration time on site before opening the shipping box Tips to maintain hardware performance e Avoid moving the Microarray Scanner If you need to move the Microarray Scanner there is a chance that its performance could be adversely affected Call your local Agilent sales and support center for assistance in moving the
42. Agilent G2565AA G2565BA Microarray Scanner System User Manual v 7 0 Getting Started 2 Step 3 Insert slide holders into the carousel When the slides are properly inserted in the slide holders you can insert the slide holders into the carousel The carousel is designed so that you can easily insert a slide holder correctly This step assumes that the carousel has not been removed from the Microarray Scanner To mount or remove the carousel see Mount or remove the carousel on page 86 of Chapter 3 CAUTION The Agilent G2565AA uses only the version A slide holder Using the wrong slide holder may damage the Microarray Scanner The Agilent G2565BA uses only the version B slide holder Using the wrong slide holder will alter scan region alignment The Microarray Scanner scans 1 Insert a slide holder into carousel slot 1 the first slot located slides in the order that they are clockwise from the home position detected as it rotates the carousel from lower numbered slots to higher numbered slots The carousel run skips over any empty slots Do not place a slide in the carousel home slot The home slot is wider than the other slots and labeled Home 2 Make sure that the tapered end of the slide holder points toward the center of the carousel Agilent G2565AA G2565BA Microarray Scanner System User Manual v 7 0 35 2 Getting Started 3 Make sure that the slide holder is seated in the bottom of the carousel slot Ta
43. Agilent G2565AA and Agilent G2565BA Microarray Scanner System with SureScan Technology User Guide v 7 0 Sixth Edition May 2006 Research Use Only fhe Agilent Technologies Notices Agilent Technologies Inc 2003 2006 No part of this manual may be reproduced in any form or by any means including elec tronic storage and retrieval or translation into a foreign language without prior agree ment and written consent from Agilent Technologies Inc as governed by United States and international copyright laws Manual Part Number G2566 90017 Edition Sixth Edition May 2006 Printed in USA Agilent Technologies Inc 5301 Stevens Creek Blvd Santa Clara CA 95051 USA Windows is a U S registered trademark of Microsoft Corporation Pentium is a U S registered trademark of Intel Corporation Warranty The material contained in this docu ment is provided as is and is sub ject to being changed without notice in future editions Further to the max imum extent permitted by applicable law Agilent disclaims all warranties either express or implied with regard to this manual and any information contained herein including but not limited to the implied warranties of merchantability and fitness for a par ticular purpose Agilent shall not be liable for errors or for incidental or consequential damages in connec tion with the furnishing use or per formance of this document or of any
44. Connection Manager Click on the Start button The connection between the scanner and the PC restarts 118 Agilent G2565AA G2565BA Microarray Scanner System User Manual v 7 0 Microarray scanner specifications Slide specifications Regulatory information Agilent G2565AA G2565BA Microarray Scanner System User Guide v 7 0 6 Reference Microarray Scanner specifications 120 Slide specifications 123 Regulatory information 127 The Microarray Scanner System includes the following e Microarray Scanner e 48 position carousel e 50 slide holders e Crossover LAN cable e Scan Control software e Feature Extraction software e PC workstation with recovery software on CD e Declaration of Conformity This section describes the specifications for the Microarray Scanner instrument For specifications for the PC workstation see the user guide that came with the PC This section presents the glass and bar code specifications that the scanner is designed to accept This section lets you know which regulations for acoustic noise recycling and disposal electromagnetic interference and safety that the Microarray Scanner complies with fhe Agilent Technologies 119 6 Reference Microarray Scanner specifications Approximate dimensions Weight Power input Fuses Temperature range Humidity Altitude Usage Laser information The Microarray Scanner operates within the following specifications
45. Laser Product e UL CSA Approved Product 128 Agilent G2565AA G2565BA Microarray Scanner System User Manual v 7 0 Index A aborting during a scan 46 Agilent slides entering bar codes manually 58 entering barcodes 55 reading bar codes before or during carousel run 56 selecting scan region 67 air filter cleaning 115 inspecting 114 archiving data 48 76 114 automatic file naming 63 78 bar codes entering manually 58 read before carousel run 56 reading Agilent supported bar codes before or during carousel run 56 specifications 123 barcode reader formats 127 C carousel checking slots 41 covering 36 inserting slides into 28 35 mounting 86 removing 86 Report Log 46 carousel run 40 checklist pre scan 42 cleaning air filter 115 computer hardware system requirements 12 computer system requirements 12 create scan region non Agilent slides 71 D dark offset subtraction calibration required 19 description 19 data archiving 48 76 114 saving 48 76 default scan settings 53 60 design files finding 67 drive capacity checking 76 dye channel setting 61 75 E enhancements Version 7 0 software 20 error messages 105 Extended Dynamic Range 20 F FAQs frequently asked questions 92 features of system 10 12 file naming automatic 63 78 file size 18 files finding design 67 files finding XML GEML 67 files saving 48 116 fluorescence detection 18 frequentl
46. array Scanner 26 1 Turn on the PC but do not start the Scan Control program The Microsoft Windows logon prompt appears 2 Enter your account user name and password at the Windows logon prompt The default logon information is the following User Account User Generic password none Privilege User The logon information can be changed if you have Windows administrator privileges Agilent G2565AA G2565BA Microarray Scanner System User Manual v 7 0 Getting Started 2 3 Turn on the Microarray Scanner using the power switch located on the front of the instrument You will notice the following a A fan turns on and the lid locks b The Microarray Scanner begins an initialization routine that takes about four minutes During the initialization a self test is run during which the lights flash on and off as different functional checks are made c The yellow and green status indicator lights remain lit for about 20 minutes until the lasers are fully warmed up and ready to scan d When the Microarray Scanner is ready to scan the yellow status indicator light turns off and the green status indicator light remains on Status indicator lights Power switch Figure 8 Location of power switch and status indicator lights Agilent G2565AA G2565BA Microarray Scanner System User Manual v 7 0 27 2 Getting Started Step 2 Insert slides into slide holders A slide must be mounted in a slide holder before insertin
47. ault setting see Change scan table settings to default settings on page 66 Change the storage directory and check drive capacity This section covers how to change settings in the storage directory and how to check the drive capacity Check the drive capacity e Determine the free space on the hard disk a In Windows Explorer right click on the data drive and select Properties from the shortcut menu b Click the General tab The total drive capacity as well as remaining free space are displayed on the General tab A 10 micron scan is 50 MB and a 5 micron scan is 200 MB Agilent recommends that you do not use the system partition usually drive C to store data and that you scan to the local hard drive first and then move or archive the scan files to a network or CD drive later 76 Agilent G2565AA G2565BA Microarray Scanner System User Manual v 7 0 How Do l 3 Change the default settings for the storage directory 1 Select Settings gt Modify Default Settings from the menu bar The Default Settings dialog box appears See Figure 35 2 Change the path and enter a description for the slides that you want to change You can use the cut and paste functions for the description 3 Click OK Change the scan table settings for the storage directory 1 Click Edit Slot Values The Edit slot values panel appears under the Scan Control main window See Figure 30 2 Select the slide or slides whose output path
48. ce 124 The microarrays are printed on the active side of the slide containing the bar code labelled Agilent The numeric bar code alone is on the inactive side of the slide Double barcoded slide example Inactive Glass Surface SIDE 1 vc0007vr00091 Active Active Microarray Microarray Surface Surface SIDE 2 uaj y Figure 56 Agilent slide bar code orientation vs microarray surface Non Agilent slide specifications Non Agilent slides may have the microarray deposited on the same side as the bar code To place a bar code on the side opposite the microarray surface for a non Agilent slide you must consider the following requirements e Bar code placement tolerance is 1 0 mm e The bar code label maximum thickness is 0 2 mm Make sure there are no bubbles in the label Do not add labels on top of old labels or replace labels that are beginning to peel off e Do not place bar codes on slides whose scan region exceeds 61 mm You must enter the slide identifier or bar code manually for slides whose scan regions exceed 61 mm Agilent G2565AA G2565BA Microarray Scanner System User Manual v 7 0 Reference 6 e For a bar coded slide the distance between the edge of the microarray scan region and the edge of the bar code can be no less than 4 mm Nominal scan region ho 2 amp 5 ho fee gt 4 mm Figure 57 Bar code location on non Agilen
49. cks and the lasers continue warming up The lasers are still warming up If you have to wait for the lasers to warm up move on to Step 5 Enter your name and the location of your slides on page 40 You need to select Settings gt Laser Power Saver and click the Turn Lasers ON Now button You can begin your scan 38 Agilent G2565AA G2565BA Microarray Scanner System User Manual v 7 0 Getting Started 2 You cannot start a carousel run until both lasers are warmed up E Agilent Scan Control File Settings Help Curent carousel settings Operator T eXtended Dynamic Range Scan Mode DR Red PMT 2 SDR Green PMT fico Lo fia Start slot E End slat as Check Carousel Slot Slide IDB arcade Scan Region rnm Red PMT Green PM T Scan Resolution um Ove Channel 0 4 an E a rag EEE DEE EEEE Scan region option Use selected scan region for the slides in the carousel Aum scanning mode Single Pass Reset Selection Edit Slot Values gt gt Scanner status o ready Scan Slot 1 48 Abort Figure 22 Scan Control main window when lasers are ready Agilent G2565AA G2565BA Microarray Scanner System User Manual v 7 0 39 2 Getting Started Step 5 Enter your name and the location of your slides A scan refers to the laser traversal ofa If you have not filled the carousel with slides in all 48 slots you single slide A carousel r
50. correctly per formed or adhered to could result in personal injury or death Do not proceed beyond a WARNING notice until the indicated condi tions are fully understood and met 2 Agilent G2565AA G2565BA Microarray Scanner System User Manual v 7 0 In This Guide This user guide contains instructions to get started with use troubleshoot and maintain your Agilent Microarray Scanner System 1 Introduction This chapter describes the Microarray Scanner preparation for its operation and enhancements to the software 2 Getting Started In this chapter learn how to safely operate the Microarray Scanner and use the Scan Control program 3 HowDol Learn how to enter bar codes change scan settings and perform other useful tasks 4 Troubleshooting Learn how to troubleshoot problem situations 5 Maintaining Your System This chapter describes maintenance procedures and tips 6 Reference This chapter presents glass and slide specifications as well as regulatory compliance information Agilent G2565AA G2565BA Microarray Scanner System User Manual v 7 0 3 Agilent G2565AA G2565BA Microarray Scanner System User Manual v 7 0 Contents 1 introduction A powerful tool for gene expression analysis 10 System description 12 Parts list 12 Computer system requirements 12 Scanner front view 13 Scanner top view 13 Scanner rear view 14 Site preparation 14 Safety symbols on scanner 15 Safety guideli
51. ct a scan region for non Agilent slides on page 69 4 Select Set Values 5 Start the scan or carousel run To enter a default scan region into the scan table 1 Select the slot or slots whose region you intend to enter 2 Click Reset Selection Enter the scan region set in the Default Settings dialog box 1 Select the slot or slots whose dye channel you intend to change 2 Click Edit Slot Values in the Scan Control main window 3 Select a dye channel setting from the list See Change the sensitivity resolution or dye channel settings on page 75 4 Select Set Values Microarray Scanner initialization and scan operations cannot be performed with the Microarray Scanner lid open Close the lid Wait the required warm up time about 20 minutes when the yellow indicator light turns off If this message still appears contact your local Agilent sales and support center In most cases this error indicates that the maximum laser power achieved is below a threshold value required to maintain an internal set point In these cases treat the error as an early warning message The PMT voltage will be elevated precisely to compensate for lower laser power levels that are as much as 20 below the set point Agilent G2565AA G2565BA Microarray Scanner System User Manual v 7 0 111 4 Troubleshooting If an error message does not appear in the table This table does not list all the possible error messages If you have an error
52. ctive Glass Surface SIDE 1 oD ao oO P P N N gt eo Active Active Microarray Microarray Surface Surface SIDE 2 Figure 12 Slide orientation 6 Let go of other end of slide and allow it to drop into the slide holder It is OK if the slide is slightly tilted against the tabs on the side of the slide holder Tab Figure 13 Slide dropping into slide holder 7 Place one thumb on the cover to gently press down on the slide holder cover and pull the cover back until it locks Agilent G2565AA G2565BA Microarray Scanner System User Manual v 7 0 31 2 Getting Started Figure 14 Lock in the cover 8 Verify that the slide holder lid is fully locked into place Cover locked underneath the side tabs Figure 15 Properly locked cover 32 Agilent G2565AA G2565BA Microarray Scanner System User Manual v 7 0 Getting Started 2 Inserting a slide into a version A slide holder Fingerprints cause errors in the fluorescence detection For accurate readings touch only the edges of the slide and always use gloves when handling slides Also do not write on the slides with markers or place any labels on the slide other than an appropriate bar code See Bar code specifications on page 123 to apply a second readable bar code CAUTION The version A slide holder can be used only in the Agilent G2565AA 1 Place the slide holder on a flat surface with the inset buttons facin
53. does reduce file size up to a factor of 2 Scan resolution Sets the scan resolution pixel size to 5 or 10 microns pm Ten micron scans and 5 micron single pass scans require about the same amount of time to complete but a 10 micron scan consumes only one fourth as much storage space Agilent G2565AA G2565BA Microarray Scanner System User Manual v 7 0 61 3 62 How Do l 5 pm scanning mode PMT sensitivity level Five micron double pass scans do not require more storage space than 5 micron single pass scans but they take twice as long to complete Agilent recommends a 10 micron scan for features 70 microns or greater Choose between Single Pass and Double Pass scanning when 5 micron resolution is selected The two modes differ with respect to how direction dependent noise DDN is eliminated and as a consequence the time required to complete a scan Double pass mode averages signal intensities from two distinct oppositely directed scans of the same line Single pass mode scans each line only once determines the average DDN magnitude for the entire scan and post processes the data to compensate for it Consequently single pass scans take about half as long to complete Sets the sensitivity level of the photo multiplier tube PMT The PMT detects fluorescence emitted by the microarray Different PMT settings are available depending on whether eXtended Dynamic Range scan mode XDR is marked With the check bo
54. dy lab bench or table 14 Agilent G2565AA G2565BA Microarray Scanner System User Manual v 7 0 Introduction 1 Safety symbols on scanner A AN CAUTION symbol This CAUTION symbol is placed on the product where it is necessary for you to refer to the product guide in order to understand a potential hazard It calls attention to an operating procedure practice or the like that if not correctly performed or adhered to could result in damage to the product or loss of important data WARNING symbol This WARNING symbol is placed on the product within the area where hazardous voltage is present or electrical shock can occur Only trained service persons should perform work in this area Agilent G2565AA G2565BA Microarray Scanner System User Manual v 7 0 15 1 16 Introduction Safety guidelines CAUTION CAUTION CAUTION The Microarray Scanner has been designed for safety and ease of use Be sure you understand and observe all the warnings and cautions before operating the Microarray Scanner Do not attempt to repair or gain access to Microarray Scanner internal components You might expose yourself to high voltage and harmful laser radiation Removing the covers voids the warranty If you are turning on the Microarray Scanner for the first time or have moved it to a new site verify that the voltage setting is correct and the voltage is grounded See Before you start on page 24 of Chapter 2
55. e fuses Checking and replacing the power supply fuses If the Microarray Scanner cannot be powered on even though the power outlet is active when tested you should check and replace the fuses if needed You do this from the rear of the unit 1 Disconnect the power cord 2 Useasmall flat edge screwdriver to pry up the small plastic tab located on the bottom edge of the fuse holder until it releases 96 Agilent G2565AA G2565BA Microarray Scanner System User Manual v 7 0 Troubleshooting 4 Fuse holder Figure 49 Removing the fuse holder for the power supply 3 Pull out the fuse holder and check the fuse integrity 4 Ifa fuse is blown replace the fuse with a T4A 250 VAC rated fuse 5 Push the fuse holder back in until it clicks into place 6 Plug in the power cord CAUTION Replace the fuses with only the same or equivalent rated fuses If you are unsure about the fuses contact your local Agilent sales and Support center before installing Agilent G2565AA G2565BA Microarray Scanner System User Manual v 7 0 97 4 Troubleshooting Checking and replacing the red laser fuse If the Microarray Scanner can be powered on but the red laser is not on you can easily check and replace the laser fuse from the rear of the unit 1 Disconnect the power cord 2 Useasmall flat edge screwdriver to unscrew the small plastic circular cap until it releases Laser fuse holder Figure 50 Laser fuse holder location
56. e air filter If excessive dirt has built up or six months have passed since the air filter was cleaned clean the air filter 1 Wash the air filter in warm water 2 Squeeze the air filter to wring out the water All excess water should be wrung out of the air filter Agilent G2565AA G2565BA Microarray Scanner System User Manual v 7 0 115 5 Maintaining Your System 3 Allow the air filter to dry completely before installing You can use paper towels to blot the filter dry 4 Re install the air filter in the air filter access door housing and close the door Verify that the air filter was replaced after drying Failure to replace the air filter can cause dust buildup inside the instrument that could adversely affect performance Air filters p n 3150 0956 can be ordered directly from your local Agilent sales and support center Tips to prevent problems Perform the scheduled maintenance tasks described on the previous pages and follow these tips to help you maintain the Microarray Scanner and its performance Tips to avoid data loss e Avoid loading software programs that cause high CPU workload as this might affect the acquisition of data during scanning e During scanning save your data files directly to the local hard disk Saving to a storage device over the network can cause data loss or other problems if network traffic becomes congested Transfer the files when the scanning is complete 116 Agilent G2565AA G256
57. e file handling mark the check box Compress TIFF Image 3 Click OK The compression algorithm used LZW reduces the storage space on the order of 20 to 70 percent The data in compressed image files can be displayed and extracted only with Feature Extraction 9 1 Agilent G2565AA G2565BA Microarray Scanner System User Manual v 7 0 How Do l 3 Do other useful tasks This section covers the following useful tasks you will need to know e Setting the technical support URL e Automatically displaying the Carousel Report Log e Finding version information e Removing a slide from a version B slide holder e Mounting or removing the carousel Set the URL to reach technical support The software arrives with a default URL that lets you access Agilent technical support for the Microarray Scanner You can change this support URL if you want to have users go through your own support or another support organization first 1 Select Settings gt Preferences from the menu bar LT x Curent technical support hyperlink Use Default T Automatically display the report log at the end of carousel run Cancel Figure 43 Preferences dialog box 2 Enter the URL of your choice and click OK When you select Help gt Technical Support from the menu bar you access the Web site with the URL you entered To return to the original Agilent URL click Use Default Agilent G2565AA G2565BA Microarray Scanner System User
58. e scan table settings to default settings on page 66 Agilent G2565AA G2565BA Microarray Scanner System User Manual v 7 0 How Do l 3 Change scan table settings 1 Check that the eXtended Dynamic Range Scan mode check box is marked or cleared appropriately to enable the scan mode you want to use With XDR enabled the PMT sensitivity settings are determined by the XDR Red PMT and XDR Green PMT values located above the scan table The same sensitivity settings are applied to all slides in the carousel run You can set all the other scan table parameters individually For the standard scan mode i e when the eXtended Dynamic Range Scan mode check box is clear you can change any of the scan settings for individual slides in the scan table To return an individual setting to the setting that was entered in the Default Settings dialog box highlight the setting and click the Reset Selection button 2 Click Edit Slot Values to change individual scan table settings The window expands to show the Edit slot values panel Edit slot values Red Green Scan Slot Slide D Barcode Scan region mm PMT PMT resolution iim Dye channel Description Output path Browse Ie Scanner status Scanner ready Scan Slot 1 1 id Figure 34 Edit slot values panel 3 Select the slide or slides whose setting you intend to change Click the Slot header in the upper left corner of the table to select all the
59. ed amp Green Region mm SEA Scan resolution pm fio Options PMT sensitivity level Attempt to retrieve from ML GEML files eXtended Dynamic Range scan mode SEAME GEME File Path Red Green Standard fio fio OR Hi fioo fioo Bum scanning mode Single Pass ADR Lo fio x fio x Description Scan image file handling Output path fes Browse Automatic file naming the format ix Frefist_FPrefis2_scannumber TIF Prefix Instrument Seral Num Customized Frefis2 Slot Number ki Customized T Split and rotate TIFF image Compress TIFF image Heb coca Figure 33 Default Settings dialog box 2 Change the settings using the choices below and on the next pages The scan region determines the area of the slide that is scanned It should be large enough to capture the entire print region of the microarray It should be small enough to avoid scanning too close to the bar code or other non transparent 60 Agilent G2565AA G2565BA Microarray Scanner System User Manual v 7 0 How Do l 3 border areas of the slide which would affect the scanner s ability to autofocus properly Minimizing the scan region will reduce scan time and save storage space For Agilent slides the default scan region is 61 x 21 6mm You can also select from the regions that you or others created with the Scan Region Editor You can select from the other Agilent provided scan reg
60. ed for empty slots before scanning the first slide It only attempts to scan slots that have slides in them 1 Enter the slots that you want to check See steps 3 and 4 on the previous page 2 Click Check Carousel Pq Agilent Scan Control File Settings Help Current carousel settings Operator dt eXtended Dynamic Range Scan Mode DR Red PMT 2 DRA Green PMT 2 Hi fioo Lo 110 Hi fioo Lo 10 Start slot fi End slot as Check Carousel Slot Slide ID Barcode Scan Aegion rmm Red PMT Green PMT Scan Resolution um Ove Channel J F H Scan region option Use selected scan region for the slides in the carousel Aum scanning mode Single Pass Reset Selection Edit Slot Values gt gt Figure 23 Example of scan table after the carousel check See Chapter 3 for more details on If you later place a slide into an empty slot select the row in the changing scan table settings scan table and then click Reset Selection to enter the default settings for the slide You can then change its settings if you want Agilent G2565AA G2565BA Microarray Scanner System User Manual v 7 0 41 2 Getting Started Step 7 Check or change the scan settings in the scan table Easy scan option for Agilent slides Pre scan checklist Agilent and non Agilent slides 42 When you first start the software the Scan Control scan table in the main window contains the original default
61. error messages you may encounter Sources of error messages The computer monitor shows error messages for the Microarray Scanner hardware the scanning and feature extraction software Microsoft Windows and the PC workstation Check the title bar of the error message to determine the source of the error message The title bar of the error message indicates that this message is related to the carousel hardware Browsing carousel x Description The chip carousel is not present Please place the carousel in the scanner and try again Figure 51 Title bar of a Scan Control error message This topic presents the error messages for the Microarray Scanner hardware and the Scan Control program If the title bar indicates that you are having a problem with your PC workstation or Windows see PC workstation support on page 90 for support information Where scanner error messages can appear Error messages can appear in the following places e Errors during the Microarray Scanner initialization appear in the Scanner status message in the Scan Control window See Step 4 Start the Scan Control program on page 38 of Chapter 2 e Errors before the scan starts are shown in message boxes Agilent G2565AA G2565BA Microarray Scanner System User Manual v 7 0 105 4 Troubleshooting e Some errors during the scan are shown in the Status message in the Scan Progress dialog box Error messages are logged in the Carou
62. f the slide holder until the cover releases an L Released slide holder cover Figure 10 Release the cover 4 Place the slide into the slide holder with the end of the slide supported fully on the rear ledge The active microarray surface must be facing up toward the cover Agilent G2565AA G2565BA Microarray Scanner System User Manual v 7 0 29 2 Getting Started Active microarray surface Ledge of slide holder Figure 11 Proper placement of slide on ledge 5 Align the slide with the slide holder following these two rules The end without the bar code label is placed on the rear ledge The slide surface on which the microarray is deposited is facing the cover The microarray is scanned through the glass Make sure these rules are always followed when you align a slide Agilent slides have two bar codes one on each side of the glass See Figure 12 Typically non Agilent slides have only one bar code Place the active microarray side of the slide facing toward the slide holder cover See Bar code specifications on If you have a slide whose spotted array is on the opposite page 123 to apply a second side of the slide as the bar code the scanner cannot read the readable bar code bar code CAUTION An improperly inserted slide can damage the Microarray Scanner 30 Agilent G2565AA G2565BA Microarray Scanner System User Manual v 7 0 Getting Started 2 Double barcoded slide example Ina
63. f it is safe to move the carousel The chip carousel is not present Please place the carousel in the scanner and try again The carousel may be misaligned Please remove the carousel make sure that its opening is aligned with home position and reinsert the carousel Slide skipped because it is outside the allowable thickness range or the selected scan region contains an obstruction to the initial focus positions The slide failed to eject Pressing OK will re initialize the instrument The software has detected a serious sensor error that may have existed prior to the installation of this version of software 110 Description or Solution Contact your local Agilent sales and support center Do the following 1 2 3 4 Open the scanner lid lf the Autoloader Arm is partially extended into the carousel compartment gently push it back into the scanner until it comes to a stop Close and restart the Scan Control program If the problem persists contact your local Agilent sales and support center Put the carousel in the Microarray Scanner and reinitiate the carousel run See Mount or remove the carousel on page 86 Do the following 1 Check the skipped slide for a bar code hybridization residue or other non transparent obstruction that has interfered with the initial focus position The primary initial focus position is located 1 to 2 mm to the left of the scan region on the top row of the scan re
64. g it into the carousel The slide holder protects the slide during scanning Two types of slide holders are available e Version A p n G2505 60500 for the Agilent G2565AA e Version B p n G2505 60525 for the Agilent G2565BA CAUTION The Agilent G2565AA uses only the version A slide holder The Agilent G2565BA uses only the version B slide holder Using the wrong slide holder will alter scan region alignment and may cause loading failures that may damage the Microarray Scanner Version A slide holder use only in Agilent G2565AA Version B slide holder use only in Agilent G2565BA Figure 9 Loading slides into the two types of slide holders 28 Agilent G2565AA G2565BA Microarray Scanner System User Manual v 7 0 Getting Started 2 Inserting a slide into a version B slide holder Fingerprints cause errors in the fluorescence detection For accurate readings touch only the edges of the slide and always use gloves when handling slides Also do not write on the slides with markers or place any labels on the slide other than an appropriate bar code The version B slide holder can be used only in the Agilent G2565BA For instructions on removing the slide see Remove a slide from a version B slide holder on page 84 1 Hold the slide holder on the sides with the Agilent logo facing up 2 Place one thumb on the center of the slide holder cover 3 Gently press down on the cover and push toward the top o
65. g up Buttons Dual bar code labels For Agilent slides bar code labeled Agilent facing down Figure 16 Slide alignment with slide holder 2 Align the slide with the slide holder following these two rules The end without the bar code label is inserted into the slide holder first The slide surface on which the microarray is deposited is face down in the slide holder The microarray is scanned through the glass Agilent slides have two bar codes one on each side of the glass Non Agilent slides have only one bar code Place the active microarray side of the slide upside down in the holder If you have a slide whose spotted array is on the same side of the slide as the bar code the scanner will not be able to read the bar code An improperly inserted slide can damage the Microarray Scanner Agilent G2565AA G2565BA Microarray Scanner System User Manual v 7 0 33 2 Getting Started Double barcoded slide example Inactive Glass Surface SIDE 1 oD ao oO P P N N gt eo Active Active Microarray Microarray Surface Surface SIDE 2 quajiiy Figure 17 Slide orientation 3 While pressing the two inset buttons on the slide holder with one hand gently push the slide into the holder with the other hand Figure 18 Slide fully inserted into slide holder 4 Verify that the slide is pushed all the way into the slide holder and the slide is underneath the four tabs 34
66. gion Measure the glass thickness and verify that it meets with the specifications in Slide specifications on page 123 When you press OK the Microarray Scanner re initializes If this fails do the following 1 2 3 4 Open the scanner lid lf the Autoloader Arm is partially extended into the carousel compartment gently push it back into the scanner until it comes to a stop Do not force it if it does not move easily Close and restart the Scan Control program lf the problem persists contact your local Agilent sales and support center Contact your local Agilent sales and support center Agilent G2565AA G2565BA Microarray Scanner System User Manual v 7 0 Troubleshooting 4 Table 4 Error Messages continued Error Message Description or Solution Unable to lock instrument specified by connection manager You must select a region to scan first You must select at least one dye channel You must close the door first Warning The laser power does not fall within expected thresholds Please contact an Agilent representative Do the following 5 Reboot the PC workstation 6 Turn the Microarray Scanner off and then back on 7 Start the Scan Control program To enter a non default scan region into the scan table 1 Select the slot or slots whose region you intend to enter 2 Click Edit Slot Values in the Scan Control main window 3 Select a scan region from the Scan region list See Sele
67. iate scan region For some non Agilent slides with translucent or opaque borders the scan region selected may be located too near to the non transparent areas of the glass See Select a scan region for non Agilent slides on page 69 Contact your local Agilent sales and support center 106 Agilent G2565AA G2565BA Microarray Scanner System User Manual v 7 0 Table 4 Error Messages continued Troubleshooting 4 Error Message Autofocus error No PSD signal is detected Make sure there is a slide in the chip holder Autofocus was unable to retain focus as it travelled to the scan start position Cannot eject chip There is already a chip in the slot Cannot load chip moving the arm may be unsafe Command timed out Description or Solution Do the following 1 Verify that the slide is inserted properly in the slide holder See Step 2 Insert slides into slide holders on page 28 2 Verify that the slide meets the Agilent specifications See Slide specifications on page 123 3 Ifthe problem persists with one slide then there might be something wrong with that slide 4 Forsome non Agilent slides with translucent or opaque borders the scan region selected may be located too near to the non transparent areas of the glass See Select a scan region for non Agilent slides on page 69 5 Contact your local Agilent sales and support center Do the following 1 Verify that a bar code has not obstruc
68. ic levels Agilent G2565AA G2565BA Microarray Scanner System User Manual v 7 0 127 6 Reference Canada This ISM Industrial Scientific Medical device complies with Canadian ICES 001 Cet appareil ISM est conforme a la norme NMB 001 du Canada Safety information This scanner complies with the following safety standards CAN CSA No 22 2 No 1010 1 92 CAN CSA C22 2 No 1010 1B 97 UL Std No 3101 1 UL Std No 3111 1 ISA 82 01 1994 IEC 61010 1 IEC 825 1 EN60825 1 Safety Requirements for Electrical Equipment for Measurement Control and Laboratory Use Part 1 General Requirements Includes Amendment 1 Amendment 2 to CAN CSA C 22 2 No 1010 1 92 Safety Requirements for Electrical Equipment for Measurement Control and Laboratory Use Part 1 General Requirements Electrical Equipment for Laboratory Use Part 1 General Requirements Equipment for Measurement Use Part General Requirements Safety Standards for Electrical and Electronic Test Measuring Controlling and Related Equipment General Requirements Safety Requirements for Electrical Equipment for Measurement Control and Laboratory Use Part 1 General Requirements Safety of laser products Part 1 Equipment classification requirements and user s guide Including Amendment 1 1992 and Amendment 2 1995 e Pollution Degree 2 e Installation Category II e Class 1 Equipment requires a grounding system e Class 1
69. ilure in the past has been corrected by using a direct drive motor and a more robust external drive gear 22 Agilent G2565AA G2565BA Microarray Scanner System User Manual v 7 0 Agilent slides Non Agilent slides Agilent G2565AA G2565BA Microarray Scanner System User Guide v 7 0 2 Getting Started Before you start 24 Step 1 Turn on the Microarray Scanner 26 Step 2 Insert slides into slide holders 28 Step 3 Insert slide holders into the carousel 35 Step 4 Start the Scan Control program 38 Step 5 Enter your name and the location of your slides 40 Step 6 Check the carousel for empty slots 41 Step 7 Check or change the scan settings inthe scan table 42 Step 8 Start the carousel run 44 Step 9 Transfer files and archive data 48 Step 10 Shut down the system 49 This chapter gives you instructions to set up and scan your slides quickly and easily If you have Agilent slides just follow the steps in this chapter and use the shipped default settings You can change scan settings if you want If you have non Agilent slides you may have to change the shipped default settings See Step 7 Check or change the scan settings in the scan table on page 42 If you have any problems see Chapter 4 for troubleshooting information ee Agilent Technologies 23 2 Getting Started Before you start Before turning on the Microarray Scanner for the first time or after it has been moved to another site verify that the
70. imes are active only on weekdays Turn OFF after a Turns off the lasers after every carousel run carousel run completed Turn OFF after period of Allows you to specify a specific time span of scanner non use inactivity to turn off the lasers Turn OFF after Turns off the lasers when you close the Scan Control exiting the program application 4 Click OK 54 Agilent G2565AA G2565BA Microarray Scanner System User Manual v 7 0 How Do l 3 Enter bar code or slide identifier information This section covers how to read in Agilent supported bar codes and how to enter bar codes manually Agilent slides If you have Agilent slides you do not have to enter bar codes into the scan table before the carousel run The scanner automatically reads Agilent bar codes into the scan table as it scans each slide You also do not have to change any settings on the scanner after it is shipped from the factory Just follow the instructions in Chapter 2 You have the choice however of reading bar codes into the scan table before you start scanning This section gives you instructions on how to read bar codes into the scan table either automatically or manually before you scan Non Agilent Ifyou have non Agilent slides with Agilent supported bar codes slides you can either have the scanner read the bar codes during or before the carousel run or you can enter them manually If you have non Agilent slides with unsupported bar codes you must enter
71. ion 7 0 is designed for use with Agilent Feature Extraction software version 9 1 but is backwards compatible to version 6 1 Although these earlier versions of Feature Extraction can display and extract uncompressed single scan TIF images generated by Scan Control 7 0 only versions 9 1 and later will be able to process compressed images and extract XDR data You can use Feature Extraction software version 9 1 with any version of Scan Control software Extended Dynamic Range scanning Scan Control software 7 0 provides the ability to load a slide once and automatically scan it twice at two different user selected sensitivity settings By using this new feature you can generate an eXtended Dynamic Range XDR scan of up to 5 orders of magnitude Each XDR scan file is named according to the standard Scan Control protocol but in addition a distinguishing suffix is appended The software also creates a unique ID for each pair of XDR scans and saves it to both scan image files Feature Extraction 9 1 uses this XDR ID to link the pair of SCR scans together automatically when extracting data The allowable range of PMT levels for an XDR Hi scan is 100 to 10 and for an XDR Lo scan 50 to 1 The ratio of XDR Hi to XDR Lo is further constrained to be 2 and lt 20 20 Agilent G2565AA G2565BA Microarray Scanner System User Manual v 7 0 Introduction 1 Reduced scanning time for 5 micron scans Scan Control software Version 6 3 always
72. ions as well but in most cases they will not be appropriate For non Agilent slides you can retain the Agilent default setting or select one that better matches the expected print region from the other Agilent provided scan regions or from regions that you or others created with the Scan Region Editor See Select a scan region for non Agilent slides on page 69 or see the Help for the Scan Region Editor Scan region For Agilent slides you can also select Attempt to retrieve options from XML GEML files The system attempts to read the bar code and search for the scan region information in the selected XML database If the scan region is not found the system uses the scan region set in the scan table for each slide You can change the XML GEML path Click Set XML GEML File Path to set or change the path to the location where the XML GEML files are to be found For non Agilent slides this option does not apply Clear the check box and select from the Agilent provided scan regions or from regions that you or others created with the Scan Region Editor For a combination of Agilent slides and non Agilent slides mark this check box if the default scan region is appropriate for the non Agilent slides Dye channel Determines whether only red for example Cy 5 dye only green for example Cy 3 dye or both dye channel information is gathered The selection has no effect on the scan time but selecting only one dye channel
73. it a few minutes and try again e The Microarray Scanner might not be connected to the PC workstation Verify the Ethernet connector is connected to both the Microarray Scanner and PC workstation If the Ethernet connector is disconnected reconnect the cable reboot the PC computer and if needed turn the Microarray Scanner off then on e The Ethernet cable connected to the scanner may be a regular LAN cable and not a crossover cable If the PC Ethernet cables have been disconnected recently the House and Scanner cables may have been switched They are not interchangeable the scanner must be connected to the PC with a crossover cable e The PC network adapter that is connected to the scanner may have failed Verify that the LEDs on the PC adapter are lit or flashing e The Internet Protocol TCP IP networking properties for the scanner may have been altered Verify that the IP address for the scanner s Local Area Connection is 10 0 0 1 and its subnet mask is 255 255 255 0 e Windows XP firewall may be preventing communication Disable the firewall e Ifyou rebooted the PC workstation you may need to turn the Microarray Scanner off and then back on after Windows has restarted e Ifyou are using a version of Scan Control software prior to 7 0 The scanner PC is not connected to the House network but the House network adapter card is enabled Disable the House network adapter card with the Windows operating system The scanner PC is con
74. m scan area for the 1 in x 3 in microscope slide depends on the Microarray Scanner version e G2565AA 67 2 x 21 6 mm e G2565BA 71 x 21 6 mm The file sizes in megabytes for the following uncompressed resolutions are Resolution 67 2 mm x 21 6 mm 71 mm x 21 6 mm 5 microns 232 2 MB 245 4 MB 10 microns 56 7 MB 59 9 MB Sizes of compressed files are variable Agilent G2565AA G2565BA Microarray Scanner System User Manual v 7 0 Introduction 1 Dark offset subtraction The Agilent scanner was designed to offset all signal intensity levels by a few hundred counts This dark offset was introduced to ensure that no detected signal levels would ever fall below zero Without this precaution the signal level could fall below zero either due to electronic noise or even slight fluctuations in the average level of the background Not letting signals fall below zero ensures that an unbiased pixel distribution is reported within the data set thus improving the accuracy of the generated data set Yet the dark offset has created some confusion when users are interpreting the background level from the scanner generated TIFF image files An earlier software release provided a method that improves usability but does not reduce accuracy of the data set The scanner dynamically measures the average electronic offset prior to each scan and calculates a value that can be safely subtracted from each pixel value This calculation is designed to lower
75. ment and size and areas with frosted glass The XML database contains the microarray layout files that have critical information about the microarray The information can include scan region feature extraction settings location of each microarray feature and name and sequence of each microarray probe When you first start the Scan Control program the default settings are selected for Agilent slides The scan region is 61 mm x 21 6 mm and the Attempt to retrieve from XML GEML files check box is not marked You can select a different scan region for one or more slides if you want but normally you do not have to See Change scan table settings on page 65 Set the XML GEML path If the Attempt to retrieve from XML GEML files check box is marked the system attempts to read the bar code and search for the scan region information in the selected XML database If the scan region is not found the system uses the scan region set in the scan table You can modify the XML GEML path 1 Select Settings gt Modify Default Settings on the menu bar The Default Settings dialog box appears Default Settings j m Scan configuration Sean region Dye channel RediGreen gt Region mm ScanArea 61 21 6mm 7 Scan resolution pm ho x Options PMT sensitivity level M Attempt to retrieve from XML GEML files eXtended Dynamic Range scan mode SetXML GEML Fie Path Pedi Si ID Braas S
76. message that is not listed and you are unable to resolve the problem do the following 1 Write down the error message 2 Restart the Scan Control program 3 If step 2 does not solve the problem do the following a Reboot the PC workstation b Turn the Microarray Scanner off then back on c Restart the Scan Control program 4 If step 3 does not solve the problem contact your local Agilent sales and support center 112 Agilent G2565AA G2565BA Microarray Scanner System User Manual v 7 0 Scheduled maintenance tasks Tips to prevent problems Agilent G2565AA G2565BA Microarray Scanner System User Guide v 7 0 5 Maintaining Your System Scheduled maintenance tasks 114 Tips to prevent problems 116 This chapter provides maintenance information for the Agilent G2565AA and Agilent G2565BA Microarray Scanner System This section describes the software and hardware maintenance tasks that you need to perform on a regular basis to keep the Microarray Scanner operating efficiently This section presents hints on the operation and care of the Microarray Scanner to help you avoid problems ee Agilent Technologies 113 5 Maintaining Your System Scheduled maintenance tasks With proper care and maintenance the Microarray Scanner will provide you with trouble free use When in doubt about the use or care of the Microarray Scanner contact your local Agilent sales and support center to answer your questions Scheduled softwa
77. nected to the House network and the network goes down or becomes inaccessible As a temporary fix disconnect the House LAN cable and disable the House network adapter using the Windows operating system The Connection Manager service is stopped To correct this situation set the Connection Manager service recovery options for the First Failure Second Failure and Subsequent Failures to Restart the Service 108 Agilent G2565AA G2565BA Microarray Scanner System User Manual v 7 0 Troubleshooting 4 Table 4 Error Messages continued Error Message Description or Solution Error ejecting chip The chip was ejected into the home slot Failed to communicate with connection manager Lasers never became ready Missing or corrupt ChipRegions ini file Not enough disk space to create file PMT calibration may be unstable Using last known PMT setting Do the following 1 Turn off power to the scanner 2 Open the scanner lid 3 Rotate the carousel by hand until access to the home slot is not blocked by the Autoloader Arm 4 Remove slide from home slot 5 Gently push the Autoloader Arm back into the scanner until it comes to a stop 6 Ifthe problem persists contact your local Agilent sales and support center Do the following 1 Reboot the PC workstation 2 Turn the Microarray Scanner off and then back on 3 After several minutes start the Scan Control program Do the following 1 Verify that
78. nes 16 Principles of operation 17 Slide positioning 17 Laser excitation 17 Scanning 17 Fluorescence detection 18 Maximum scan region for non Agilent slides 18 Dark offset subtraction 19 Software enhancements Version 7 0 20 Extended Dynamic Range scanning 20 Reduced scanning time for 5 micron scans 21 Automatic image file compression option 21 More robust communication algorithms 21 New Carousel Report Log messages 21 More robust scanning algorithms 22 Agilent G2565AA G2565BA Microarray Scanner System User Manual v 7 0 2 3 Hardware enhancements G2565BA 22 Carousel Indexing System 22 Autoloader Arm and Motor Assembly 22 Getting Started How Dol Before you start 24 Step 1 Turn on the Microarray Scanner 26 Step 2 Insert slides into slide holders 28 Inserting a slide into a version B slide holder 29 Inserting a slide into aversion A slide holder 33 Step 3 Insert slide holders into the carousel 35 Step 4 Start the Scan Control program 38 Step 5 Enter your name and the location of your slides 40 Step 6 Check the carousel for empty slots 41 Step 7 Check or change the scan settings inthe scan table 42 Step 8 Start the carousel run 44 Before you start 44 Start the carousel run 44 Abortascan 46 Step 9 Transfer files and archive data 48 Step 10 Shut down the system 49 Set Laser Power Saver Agilent G2565BA only 53 Enter bar code or slide identifier information 55 Read bar codes for slides with
79. ng existing scan regions make sure the scan region is at least 4 mm away from the bar code label 1 Inthe Scan Region Editor select the region to change 2 Select File gt Open Region from the menu bar The Modify Region dialog box appears Agilent G2565AA Agilent G2565BA ms Modify Region Miel x is Modify Region Jof x Name Name Ranges mm Ranges mm x 4 00 mm 6 00 68 20 x 4 00 mm 3 10 690 Y 200 mm 1 90 23 40 Ve 2 00 mm 1 90 23 40 Width 16 00 mm 5 00 67 20 Width 16 00 mm 500 70 10 Height 1 00 mm 0 10 21 50 Height 1 00 mm 0 10 21 50 sa sa Figure 40 Modify Region dialog box Change the name or size of the region 4 Change the measurements for the region using the criteria listed in Create a new scan region with the Scan Region Editor on page 72 5 Click Save Start the Scan Region Editor from the Start menu You cannot access the Customize Scan Region menu item in the main window when the scanner is in operation You can only create and change new scan regions through the Start menu Agilent G2565AA G2565BA Microarray Scanner System User Manual v 7 0 How Do l 3 If you attempt to start the Scan Region Editor when a second one is already running a message appears that says that another Scan Region Editor is running and you cannot open another one 1 Select Start gt Programs gt Agilent Life Sciences gt Scan Region Editor on the taskbar 2 Select your microarray
80. not blown Flash once Flash once Flash once LED test at power on No action required duration lt 1 sec Flashing Flashing Off Power on Self Test in No action required User operation HyperTerminal to capture diagnostic information See Using HyperTerminal to Capture Diagnostic Data on page 99 Off Flashing Off Attempting to connect to PC Install Scan Control software 20 sec off version 7 0 if not already installed 20 sec on Off or On Flashing Off Firmware downloading and No action required period 1 3 DSP initializing or 1 0 sec On On Off Lasers are warming upand Wait Maximum warm up time is 20 are not ready to scan minutes On Off Off Instrument is ready to scan No action required Flashing Off Off Instrument scanning No action required Any condition Any condition On Error detected Contract your local Agilent sales Agilent G2565AA G2565BA Microarray Scanner System User Manual v 7 0 and support center 95 4 Troubleshooting Checking and replacing scanner fuses The Microarray Scanner has three fuses two fuses for the power supply and one fuse for the red laser The fuses can be found on the rear of the Microarray Scanner The power supply fuses are directly above the power cord plug The laser fuse is located ina circular fuse holder to the left of the power cord plug The fuses can be ordered directly from Agilent Technologies WARNING Always disconnect the power cord before checking or replacing th
81. ogram Do NOT attempt to copy or move the file containing the scan data for the current scan while the scanner is still scanning Data will be lost if you do this Agilent G2565AA G2565BA Microarray Scanner System User Manual v 7 0 45 2 Getting Started The Carousel Report Log presents scan information and error messages that occur during the carousel run Abort a scan 3 Optional At any time during the carousel run or after the run is complete select View Report to view the Carousel Report Log File Edit view Favorites Tools Help ay TEDE x E A _ gt Search S 2 Favorites E bs x eS w we rel gt Links Address A C Program Files Agilent MicroArray CarouselRunLog htm Go Eee Agilent Technologies AGILENT SCANNER CAROUSEL REPORT LOG Fri May 05 20 06 23 2006 Carousel run requested from Slot 1 to Slot 3 Carousel Scan Mode Standard 5 Micron Scanning Mode Single Pass Total number of slide s detected 3 Scanning user defined region for Barcode 251209735301 Scanned image c US1470PPB1 SLOTO1 02 tf Scan completed Scanning user defined region for Barcode 16010549047351 Scanned image c US1470PPB1 SLOTO2 S01 tf Scan completed Figure 25 Carousel Report Log Note when the carousel run is complete The Status box reads Carousel run completed You can now remove the slide holders or the carousel After the carousel run you can find the Carousel Report Log in the f
82. ollowing directory C Program Files Agilent Microarray CarouselRunLog htm This file is overwritten each time a new carousel run is started At any time you can stop the scan or carousel run e Click the Abort button on the Scan Progress dialog box The following message appears 46 Agilent G2565AA G2565BA Microarray Scanner System User Manual v 7 0 Getting Started Carousel Run Abort Figure 26 Carousel Run Abort message The Microarray Scanner can take a minute or two to finish aborting the scan even if Yes is selected depending upon the stage at which the command is issued Any collected data is saved for later analysis Scan Progress E Turr laser power off after the current carousel lun completed Figure 27 Scan Progress dialog box after Abort is complete Agilent G2565AA G2565BA Microarray Scanner System User Manual v 7 0 2 47 2 Getting Started Step 9 Transfer files and archive data CAUTION 48 e At the end of the run transfer the files to another directory if needed You can save the file or files in one of four places Original directory on the local drive that you set up for the output path Another directory on the local drive Directory on the network CD or DVD Agilent recommends that scanned data first be saved to the local drive so that network problems do not cause the loss of data A DVD Writer is included with every PC workstation Do NOT attempt to copy or m
83. ove the file containing the scan data for the current scan while the scanner is still scanning Data will be lost if you do this Failure to archive data regularly can result in a completely filled hard disk When the disk is full the Microarray Scanner stops scanning and a caution Is displayed Use only the compression software provided in the Scan Control program to compress the image files Other compression algorithms might cause a loss of data Agilent G2565AA G2565BA Microarray Scanner System User Manual v 7 0 Getting Started 2 Step 10 Shut down the system To extend laser lifetime the Microarray Scanner should be powered off if it is not going to be used for more than four hours Agilent G2565BA only You also have the option to automatically turn off the lasers after a carousel run from the Scan Progress dialog box You can also specify laser on and off conditions from the Laser Power Saver dialog box See Set Laser Power Saver Agilent G2565BA only on page 53 of Chapter 3 for more information 1 Click Exit on the Scan Control main window To avoid intermittent communication lock ups close the Scan Control program before you turn off the Microarray Scanner 2 Wait afew seconds and verify that the Microarray Scanner lid is unlocked 3 Lift the lid 4 Optional Remove the slide holders or the carousel Turn off the power switch on the front of the Microarray Scanner CAUTION Do not attempt to lift
84. oved from the Microarray Scanner follow these steps to remount the carousel CAUTION When mounting the carousel be careful not to knock the carousel against the autoloader arm Knocking the autoloader arm can cause misalignment CAUTION If you need to rotate the carousel manually do so only when the instrument is turned off or you may damage the instrument 1 Mount the carousel so that the carousel alignment pin holes fit in with the alignment pins on the Microarray Scanner carousel mounting area Align the D shaped hole in the bottom of the carousel with the D shaped center post of the scanner tabletop where the carousel fits and gently place the carousel into the scanner straight down 2 Make sure that the carousel is firmly seated 3 Close the Microarray Scanner access lid 86 Agilent G2565AA G2565BA Microarray Scanner System User Manual v 7 0 How Do l 3 Stationary alignment pins Stationary alignment pin slots Movable alignment pin Movable alignment pin slot Figure 47 Alignment pins and slots on scanner and carousel If an error message appears in the Carousel Log Report that says there is a motor time out this time out may be due to an improperly mounted carousel Check the carousel alignment and remount if necessary AGILENT SCANNER CAROUSEL REPORT LOG Fri May 10 15 44 53 2002 Carousel run requested from Slot 1 to Slot 48 Checking carousel failed Description Motor timed out CAUTION Rem
85. oving the carousel when the slide holder autoloader arm Is extended into the carousel will cause serious damage to the Microarray Scanner Call your local Agilent sales and support center for instructions if the autoloader arm is extended Agilent G2565AA G2565BA Microarray Scanner System User Manual v 7 0 87 3 How Do l 88 Agilent G2565AA G2565BA Microarray Scanner System User Manual v 7 0 Technical support Frequently asked questions Hardware troubleshooting Software troubleshooting Scanner error messages Agilent G2565AA G2565BA Microarray Scanner System User Guide v 7 0 4 Troubleshooting Technical Support 90 Frequently Asked Questions FAQs 92 Hardware Troubleshooting 94 Using HyperTerminal to Capture Diagnostic Data 99 Software Troubleshooting 104 Microarray Scanner Error Messages 105 The Agilent Microarray Scanner was designed for low maintenance requirements and high user friendliness If you cannot resolve the problem you are experiencing with the system please read over this chapter before calling your local Agilent sales and support center This topic gives important information about technical support Refer to this section to learn about solutions to frequently asked questions related to support and maintenance This topic describes the indicator lights and how to replace the fuses This topic covers the precautions you must take when you use the Recovery CD to recover the software
86. pered end faces toward center ZS 53 i T NN ne ANNY ie A Slot 1 Figure 19 Carousel CAUTION Improper placement of the slide holder in the carousel can result in severe damage to the Microarray Scanner 4 Optional Place the carousel cover onto the carousel until the two side tabs snap into place Home slot Figure 20 Carousel cover 36 Agilent G2565AA G2565BA Microarray Scanner System User Manual v 7 0 Getting Started 2 5 Close the lid You cannot do any of the following tasks until you close the lid Initialize the scanner Check the carousel for empty slots Read bar codes before the carousel run Start a carousel run Agilent G2565AA G2565BA Microarray Scanner System User Manual v 7 0 37 2 Getting Started Step 4 Start the Scan Control program Initializing Scanner Lasers are warming Lasers are powered off Scanner ready The Scan Control program on the PC workstation controls the Microarray Scanner You can set options and start and abort a scan from the user interface You can also view a scan status messages and display a carousel run report 1 Double click the Agilent Scan Control icon to open the Scan Control program ape Agilent Scan Control Figure 21 Agilent Scan Control icon 2 Check the Scanner status message at the bottom of the main window The scanner is initializing When the initialization is complete the scanner lid unlo
87. pture Files Capture 0601A TXT Browse You can also click Browse to open the Select Capture File dialog box From the Select Capture File dialog box you can create new folders or go to a different folder and create a new file Make sure you choose a new folder or a new file name or else your original capture session file will be overwritten When you are done click Save to continue 5 Turn on the scanner if it s not already on 6 When the scanner is warmed up about 5 minutes after you turn it on start the Scan Control software Agilent G2565AA G2565BA Microarray Scanner System User Manual v 7 0 103 4 Troubleshooting Software Troubleshooting In case your computer crashes or you want to reload the hard drive image that Agilent ships with the PC Agilent supplies a recovery CD that lets you re image the hard drive In order to use this CD successfully you must disconnect the two LAN cables that attach to the LAN cards in the back of the PC before you use the CD One cable is from the scanner and the other is to the company corporate network if the company has one CAUTION If you do not disconnect these cables the Agilent default LAN settings for these cards may be changed and the software will not recognize the scanner when you restart the software 104 Agilent G2565AA G2565BA Microarray Scanner System User Manual v 7 0 Troubleshooting 4 Microarray Scanner Error Messages This section explains how to use
88. r System User Manual v 7 0 Reference 6 Regulatory information This section lists regulatory information for the Micorarray Scanner For research use only The Agilent Microarray Scanner is intended for RESEARCH USE ONLY Acoustic noise information Manufacturer s Declaration English This statement is provided to comply with the requirements of the German Sound Emission Directive from 18 January 1991 Sound Pressure Lp lt 70 dB A at operator s position normal operation according to EN 27779 Type Test Deutsch Die folgende Information wird in Ubereinstimmung mit den Anforderungen der Maschinenlarminformationsverordnung vom 18 Januar 1991 erteilt Schalldruckpegel am Arbeisplatz bei normalem Betrieb Lp lt 70 dB A nach EN 27779 Typprufung Recycling and disposal Contact Agilent Technologies for This device is designed to accommodate recycling at the end of more information on recycling and its useful life Please dispose of this device in accordance with disposal local regulations Electromagnetic interference The scanner is intended for use with shielded cables only Emissions Complies with the emissions levels for Class A equipment as required in LEC 61326 1 This equipment is not intended for use in residential areas Immunity This device complies with the immunity levels required in IEC 61326 1 for a non controlled non industrial environment See accompanying Declaration of Conformity for specif
89. ray Scanner System User Manual v 7 0 101 4 Troubleshooting Select Capture File Save int 6 HyperTerminal Capture Files Of eg My Recent Documents Desktop D My Documents er TE HA y E Bi mputei A0000313 E wo Tne File name Capture 060105 1 Save Flaces Save as type Text file TAT _ Cancel J os h Click Save i Click Start in the Capture Text dialog box Capt ure Text Folder CA Documents and Settings david_baker My File inal Capture Files Capture 0601051 TXT Browse HyperTerminal data will continue to append to this file until HyperTerminal is closed or the Capture Text session is stopped from the Transfer drop down menu HyperTerminal will close when you log off 102 Agilent G2565AA G2565BA Microarray Scanner System User Manual v 7 0 Troubleshooting 4 To start a HyperTerminal capture session after initial set up 1 Log onto the Scanner PC If the shortcut to Scanner ht is in the All Users Startup folder HyperTerminal will start automatically 2 If HyperTerminal does not start double click on the Desktop Scanner ht icon 3 From the HyperTerminal Transfer drop down menu click Capture Text 4 In the Capture Text dialog a Change the file name in the File text box to reflect today s date and capture session b Click Start Capture Text 2x Folder C Documents and Settings david_baker My File inal Ca
90. ray Scanner System and Agilent G2565BA Microarray Scanner System This section describes the features that make the Microarray Scanner a powerful tool in Agilent s gene expression analysis solution In this section learn about the external components of the Microarray Scanner the site preparation information and the safety guidelines This section explains how the Microarray Scanner works This section explains the differences between Version 6 3 Version 7 0 of the Scan Control software This section describes major improvements to the G2565BA hardware ee Agilent Technologies 1 Introduction A powerful tool for gene expression analysis The Microarray Scanner System is part of the Agilent Technologies gene expression analysis solution The Microarray Scanner is a sophisticated laser induced fluorescence scanner designed to read microarrays deposited on standard 1 in x 3 in slides The Microarray Scanner measures the fluorescence intensity of labeled sample nucleic acid DNA and RNA bound to probe arrays The Microarray Scanner s ability to measure fluorescence from two dyes simultaneously facilitates differential gene expression studies This technology provides for rapid high quality automated hands off scanning of microarrays Figure 1 Microarray Scanner 10 Agilent G2565AA G2565BA Microarray Scanner System User Manual v 7 0 Introduction 1 Each slide is scanned in minutes and the files are prepa
91. re maintenance Perform these tasks to help maintain the performance of your PC workstation and MS Windows operating system e At least once a week check disk space and archive data as needed e Once a week delete any temporary files mp tmp files from the c Temp folder e If sluggish performance is observed defragment the hard disk using defragmentation software Scheduled hardware maintenance Perform these tasks to help maintain the performance of your Microarray Scanner Inspecting the vents and air filter Good air flow through the Microarray Scanner is essential to proper operation Blocked vents and dirty air filters can adversely affect performance Vents Check all vents weekly to ensure that they are not blocked by dust debris furniture or other instrumentation Air filter The air filter in the Microarray Scanner should be checked once a month for excessive dirt using the following procedure 1 Turn the Microarray Scanner off 114 Agilent G2565AA G2565BA Microarray Scanner System User Manual v 7 0 Maintaining Your System 5 2 Open and remove the air filter access door which is located on the right side of the Microarray Scanner Removable air _ __ filter access door Figure 52 Opening and removing the air filter access door 3 Remove the air filter from the door housing and inspect the air filter visually Air filter access door Figure 53 Removing the air filter Cleaning th
92. red for feature extraction analysis The Microarray Scanner provides the following features e Internal bar code reading and lets you enter external bar codes e Dynamic auto focus e Automatic PMT gain calibration prior to each scan e Continuous laser power stabilization e Pixel placement error of lt 1 pixel e 5 or 10 micron pixel size e Single scan dynamic range gt 104 maximum non saturating signal detection limit e Dual scan extended dynamic range XDR gt 10 e TIFF image file compression e Uniformity specification of less than 5 CV global uniformity The Scan Control software lets you set scan parameters manage your files and scan your microarrays The Microarray Scanner reads each bar code incorporating ID information from the Agilent pattern file or you can use an external reader for non Agilent slides Agilent G2565AA G2565BA Microarray Scanner System User Manual v 7 0 11 1 Introduction System description Parts list The Microarray Scanner is designed for ease of use and easy access to features The illustrations in this section show all the customer accessible features of the Microarray Scanner The Microarray Scanner System consists of the following components e Microarray Scanner e Carousel and 50 slide holders e Crossover LAN cable e PC workstation e Power cables e Software e Diagnostic serial cable e Norton Ghost backup amp recovery software Computer system requirements
93. rs 5 Click File gt Save to save the file to Scanner ht 100 Agilent G2565AA G2565BA Microarray Scanner System User Manual v 7 0 Troubleshooting 4 6 Create a Scanner ht shortcut icon on the Desktop a Click Start gt Programs gt Accessories gt Communications b From the HyperTerminal submenu right click Scanner ht Note that the HyperTerminal submenu has been added to the bottom of the Communications menu Do not right click the HyperTerminal program icon towards the top of the menu c From the shortcut menu click Create Shortcut d Click and drag Shortcut to Scanner ht to the Desktop 7 Place a Scanner ht shortcut icon in All Users Startup folder a Right click Shortcut to Scanner ht on the Desktop b Select Copy c In Windows Explorer paste the shortcut to C Documents and Settings All Users Start Menu Programs Startup 8 Start a HyperTerminal text capture session a Double click the Scanner ht icon on the Desktop Click Transfer gt Capture Text Click Browse In the Select Capture File dialog box find the Archive E drive Create a new folder named Support a Oo oa f Inthe Support folder create a new folder and call it HyperTerminal Capture Files g In the HyperTerminal Capture Files folder type the file name Capture yymmdd in the File name text box where yymmdd represents today s date and represents the number of the capture session for that day Agilent G2565AA G2565BA Microar
94. sel Report Log as the carousel run progresses See Step 8 Start the carousel run on page 44 of Chapter 2 We recommend that you check the Report Log at least after the first scan and when the carousel run is completed You can set an option in the Preferences menu to automatically show the report log after a run is completed See Automatically display Report Log after carousel run on page 82 of Chapter 3 Troubleshooting with error messages The Microarray Scanner System creates error messages to help you solve issues that may arise Many of the error messages include a solution within the text box follow those instructions The following table contains some of the error messages that appear without instructions These descriptions contain information that can help you resolve your problem Table4 Error Messages Error Message Description or Solution Application Is Already Running You cannot run two copies of the Scan Control program at the same time Autofocus error Did not detect two Do the following reflective surfaces during home 1 Verify that the slide is inserted properly in the slide holder See Step 2 Insert slides into slide holders on page 28 or try another slide holder Verify that the slide meets the Agilent specifications See Slide specifications on page 123 If the problem persists with one slide then there might be something wrong with that slide If needed select or create an appropr
95. t slide e The bar code width should be about 6 mm the recommended bar code width is for use with the 61 mm scan region Larger or longer bar codes can be used by decreasing the scan region proportionally e 21 6 mm scan region will be centered for a 25 4 mm glass width 1 9 mm from the top and bottom or above center by 0 2 mm for a 25 0 mm glass width e Bar codes should be narrow enough so as not to interfere with the slide holder tabs e Maximum allowable tilt in the placement of the bar code label on the slide is 3 The bar code must meet the following requirements e The minimum quiet zone the region between the edge of the label and the start or end of the bar code is 10 times the X dimension on each side of the bar code e Bar code lines must be parallel to the long edge of the slide within tilt tolerance of 3 Agilent G2565AA G2565BA Microarray Scanner System User Manual v 7 0 125 6 Reference e Agilent supports the following bar code formats Code 128 Non Agilent bar codes with 12 digits must not start with 2 CODABAR Maximum of 8 digits minimum line thickness 6 mils Code 39 Maximum of 8 digits minimum line thickness 6 mils Code 93 Maximum of 8 digits minimum line thickness 6 mils e Minimum height of bar code must be Code 128 15 of bar code length for Code 128 Code 39 Code 93 CODABAR 5 mm or 15 of bar code length whichever is greater 126 Agilent G2565AA G2565BA Microarray Scanne
96. t slides 74 creating for non Agilent slides 71 selecting for Agilent slides 67 selecting for non Agilent slides 69 Scan Region Editor 71 scan report 46 130 scan settings automatic file naming 63 change 59 change default 60 default 59 dye channels 61 non default 59 output path 63 scan region 60 sensitivity level PMT 62 split and rotate image 64 scan table settings changing individual slides 76 changing to default 66 scan time 45 121 scanner initializing 27 maintenance tasks 114 to 116 moving 117 ready 44 specifications 120 stopping during scan 46 turning on 26 scanner lid opening 92 sensitivity level PMT setting 62 75 serial number scanner 90 91 shutting down the system 49 signal to noise performance 17 site preparation 14 slide holder differences 28 inserting into version A 33 inserting into version B 29 removing slide from version B 84 version 28 version B 28 slides entering bar codes 55 entering identifier automatically 56 entering identifier manually 58 inserting into carousel 28 inserting into slide holders 28 jammed 93 location 40 specifications 123 slots number containing slides 40 slots selecting 41 software enhancements for Version 7 0 20 icon 38 main window 39 maintenance 114 not responding 93 revision number 92 starting 38 system requirements 12 specifications 15 bar code 123 Microarray Scanner 120 slide glass 1
97. tandard fioo gt fio DR Hi fio 7 fioo z 5pm scanning mode Singe Pass gt xDA Lo fio z U s Description a l m Scan image file handling Output path fes Browse m Automatic file naming the format is Prefix1_Prefix2_scannumber TIF Prefix Instrument Serial Num Customized Prefix2 Slot Number Customized Split and rotate TIFF image I Compress TIFF image Help Cancel Figure 35 Default Settings dialog box Agilent G2565AA G2565BA Microarray Scanner System User Manual v 7 0 67 3 How Do l 2 Make sure that the Attempt to retrieve from XML GEML files check box is marked 3 Click Set XML GEML file path 4 Click Browse to find a directory to add and click OK 5 Click Add and click OK To remove a directory select the directory and click Remove Set ML Path for finding Design Files C Program Files Agilent MicroArray D AcDNA Catalog Design Files Figure 36 Set the XML GEML path 6 Click OK in the Default Settings dialog box 68 Agilent G2565AA G2565BA Microarray Scanner System User Manual v 7 0 How Do l 3 Select a scan region for non Agilent slides If you use non Agilent slides you can select from the already existing scan regions either the Agilent supplied scan regions for non Agilent slides or the scan regions that you or others created Select a default scan region setting 1 Select Settings gt
98. ted the scan start position 2 Choose a smaller scan region 3 Ifthe problem persists with one slide then there might be something wrong with that slide 4 Contact your local Agilent sales and support center Do the following 1 Open the scanner lid 2 Remove the slide holder from the home slot Do the following 1 Open the scanner lid 2 Ifthe AL Arm is partially extended into the carousel compartment gently push it back into the scanner until it comes to a stop 3 Ifthe problem persists contact your local Agilent sales and support center Do the following 1 Verify that the Ethernet cable from the Microarray Scanner to the PC workstation is connected 2 Turn the Microarray Scanner off then on again 3 Verify that the LEDs on the PC network adapter that is connected to the scanner are lit and or flashing 4 Restart the Scan Control program 5 Ifthe problem persists contact your local Agilent sales and support center Agilent G2565AA G2565BA Microarray Scanner System User Manual v 7 0 107 4 Troubleshooting Table 4 Error Messages continued Error Message Description or Solution Connection manager reports that there Possible causes for this error include are no instruments The Microarray Scanner might not be on or you turned on the Microarray Scanner but did not wait long enough for the Microarray Scanner to complete its self test and initialization Select OK to close the Scan Control message wa
99. tem User Manual v 7 0 How Do l 3 4 Click Save If no errors are found the Scan Region Editor appears with the new region listed in the Scan Region Editor Close the Scan Region Editor Select Settings gt Refresh Scan Region from the menu bar The newly created regions now appear in the Scan Region lists Red entries in the table are invalid entries that are not available to the Scan Control program This can occur when you specify that you have a Agilent G2565BA when you really have a Agilent G2565AA Show Custom regions only Pos immi Y Pos frm idth immi Height imm ocan Area 67 2 x 21 6mm 21 60 Scan Area B0 x 21 6mm 12 00 1 90 60 00 21 60 Scan Area 55 x 21 6mm 17 00 1 90 55 00 21 60 Scan Area 50 x 21 6mm 22 00 1 90 50 00 21 60 Scan Area 45 x 21 6mm 27 00 1 90 45 00 21 60 Figure 39 Scan regions list Show Custom When this check box is marked only the created scan regions regions only appear in the list in the Scan Region Editor When the check box is clear you can also see the regions provided by Agilent in the list However you cannot change these regions with the Scan Region Editor Agilent G2565AA G2565BA Microarray Scanner System User Manual v 7 0 73 3 74 How Do l Change an existing scan region for non Agilent slides You can only change the scan regions that you created You cannot change or remove the regions provided by Agilent When creating a new scan region or usi
100. tes and you are unable to close the program Do the following 1 Open the Windows Task Manager Ctrl Alt Del and close the Scan Control What do do if a slide is only halfway 1 inserted in the carousel by the autoloader arm The Microarray Scanner is turned on but 1 the yellow light does not go off after 20 2 minutes program Then restart the Scan Control program If the previous step fails reboot the PC workstation turn the Microarray Scanner off and then back on wait for the yellow status indicator light to go off and then restart the Scan Control program Gently push or pull the autoloader arm whichever resists least to the end of its range Don t force it Close and restart the Scan Control program Call your local Agilent sales and support center if the problem persists Verify that the PC workstation is turned on Verify that the Ethernet cable is connected from the PC workstation to the Microarray Scanner 3 Contact your local Agilent sales and support center Can I use both slide holders version A Agilent G2565AA Use only version A slide holders Version B slide holders may and version B on all Microarray fail to load or eject reliably and could damage the Microarray Scanner Scanners Agilent G2565BA Use only version B slide holders Version A slide holders may fail to load or eject reliably The largest scan region would not be usable created a custom scan region and it After creating a custom scan region
101. the bar codes or slide identifier information manually See Bar code specifications on page 123 in Chapter 6 to learn how to place a bar code onto a non Agilent slide to meet Agilent specifications Agilent G2565AA G2565BA Microarray Scanner System User Manual v 7 0 55 3 How Do l Read bar codes for slides with Agilent supported bar codes Because Agilent supported bar codes are directly attached to the slides the scanner reads the bar codes as it scans If you want the scanner to read the bar code information before the carousel run follow these steps for Agilent supported bar codes attached to the slides 1 Click Edit Slot Values on the Scan Control main window The Edit slot values panel appears below the main window for you to read in the bar codes for each slide Edit slot values Red Green can Slot Slide ID Barcode Scan region mm PMT PMT resolution iim Dye channel SE SSF SS Description Output path E fa Scanner status Scanner ready Scan Slot 1 17 Figure 30 Edit slot values panel below the main window 2 Inthe scan table select the slots or slides whose bar codes you want the scanner to read Drag the cursor to select more than one slide or click the Slide ID Bar code header to select all slides for entry 3 Click Read Bar code from Carousel on the Edit slot values panel of the Scan Control main window The message similar to the one you see below appears
102. un refersto can save time by entering the location of the slots that contain scans of all of the specified slidesin your slides When you start the carousel run the carousel will the carousel then begin scanning the slide in the start slot and stop scanning the slide in the end slot that you enter 1 Inthe Scan Control main window enter your name in the Operator text box optional 2 If you want to scan slides in all 48 slots skip to Step 7 Check or change the scan settings in the scan table on page 42 3 In the Start slot box select the number of the slot where the first slide that you want to scan is located 4 In the End Slot box select the number of the slot where the last slide that you want to scan is located The range of slots that you enter in steps 3 and 4 affects most of the functions in the Scan Control main window e Only the slot range that you enter here appears in the scan table e The Check Carousel function only checks the range of slots that you enter here e The scanner scans only those slides in the slot range that you enter here 40 Agilent G2565AA G2565BA Microarray Scanner System User Manual v 7 0 Getting Started 2 Step 6 Check the carousel for empty slots To update the visual display of the scan table to indicate which slots have slides in them you can run Check Carousel You do not need to do this step because the Scan Control software automatically checks the range of slots select
103. unique IDs through the keyboard or an external bar code reader You must enter bar codes for non Agilent slides with unsupported bar code formats this way 1 Click Edit Slot Values on the Scan Control main window The Edit slot values panel appears below the main window for you to read in the bar codes for each slide before you start the scan Edit slot values Green Red an Slot Slide ID Barcode Scan region mm PMT PMT resolution iim Dye channel Description Output path Scanner status Scanner ready Scan Slot 1 17 zi Figure 32 Edit slot values panel below the main window 2 Select the slots or slides whose bar codes you want to read Move the cursor to select more than one slide or click the Slide ID Bar code header to select all slides for entry 3 Wand in a bar code for the slide with the external reader or enter the bar code through the keyboard Depending on the external reader s settings you may have to press Enter after each wand pass 4 Repeat step 3 until you have entered bar codes for all slides 58 Agilent G2565AA G2565BA Microarray Scanner System User Manual v 7 0 How Do l 3 Change scan settings This section covers several procedures related to changing settings for Agilent and non Agilent slides The scan table in the Scan Control main window can contain two kinds of scan settings e Default settings The scan settings that you set up in the
104. x cleared the Standard sensitivity settings are active The default output level 100 is the recommended setting for Agilent arrays 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 For example an 80 setting reduces the signal intensity of the output TIFF file by 20 above the dark level Alternatively mark the XDR check box to automatically scan the same slide twice at two different sensitivity levels This generates two linked images that Feature Extraction 9 1 can co process to yield a single unified set of extracted intensity data covering up to 5 orders of magnitude There are limitations to the XDR Hi and XDR Lo settings The software automatically resets the selectable levels based on these limitations Agilent G2565AA G2565BA Microarray Scanner System User Manual v 7 0 How Do l 3 Allowable sensitivity ranges XDR Hi 100 to 10 XDR Lo 50 to 1 Ratio range for XDR Hi XDR Lo 2 to 20 Example If XDR Hi 100 the selectable range for XDR Lo is 50 to 5 Microarrays that are too bright may eventually affect the PMT adversely Description Description of each slide being scanned This information becomes part of the file information that can be viewed You can cut and paste within this text box
105. y Scanner Error Messages 105 Sources of error messages 105 Where scanner error messages can appear 105 Troubleshooting with error messages 106 If an error message does not appear in the table 112 5 Maintaining Your System Scheduled maintenance tasks 114 Scheduled software maintenance 114 Scheduled hardware maintenance 114 Tips to prevent problems 116 Tips to avoid data loss 116 Tips to avoid environmental damage to the scanner 117 Tips to maintain hardware performance 117 Tip to prevent scanner software miscommunication when using the Recovery CD ona PC running Windows 2000 118 6 Reference Microarray Scanner specifications 120 Scan and print dimensions 122 Slide specifications 123 Glass specifications 123 Bar code specifications 123 Regulatory information 127 For research use only 127 Acoustic noise information 127 Recycling and disposal 127 Electromagnetic interference 127 Safety information 128 Agilent G2565AA G2565BA Microarray Scanner System User Manual v 7 0 A powertul tool System description Principles of operation Software enhancements Hardware enhancements Agilent G2565AA G2565BA Microarray Scanner System User Guide v 7 0 1 Introduction A powerful tool for gene expression analysis 10 System description 12 Principles of operation 17 Software enhancements Version 7 0 20 Hardware enhancements G2565BA 22 This chapter provides a general introduction to the Agilent G2565AA Microar
106. y asked questions FAQs 92 front view of scanner 13 fuses laser 98 power supply 96 G glass slide specifications 123 H humidity 117 indicator lights 13 27 94 95 initialization process 38 input voltage checking 24 setting 24 inspecting air filter 114 L laser fuse changing 98 laser power saver 53 lasers checking or replacing fuses 98 extending life of 49 types used 1 Log Report 46 M maintenance tasks 114 to 116 moving scanner cautions 117 naming files automatic 63 78 non Agilent slides creating scan region 71 entering bar codes manually 58 entering barcodes 55 reading bar codes before or during carousel run 56 rotating scan image 79 selecting scan region 69 Agilent G2565AA G2565BA Microarray Scanner System User Manual v 7 0 129 Index 0 opening the scanner lid 92 operating scanner 26 output directory selecting 63 output path setting 63 76 P parts list of 12 power supply fuses 96 preparation of site 14 pre scan checklist 42 print dimensions 122 rear view of scanner 14 Report Log 46 revision number of software 92 rotating scan image non Agilent slide 79 S safety guidelines 16 regulations 128 symbols for scanner 15 safety symbols 15 saving files 48 116 scan area See scan region Scan Control software See software scan dimensions 122 Scan Progress dialog box 44 scan region area 60 69 changing for non Agilen

Agilent G2565AA and Agilent G2565BA Microarray Scanner System

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