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Agilent G2565CA Microarray Scanner System (Scan Control Software 8.5) User Guide

1. Agilent G2565CA Microarray Scanner System Scan Control Software 8 5 User Guide Reference 6 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 specific levels 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 C22 2 Safety Requirements for Electrical No 1010 1 92 Equipment for Measurement Control and Laboratory Use Part 1 General Requirements Includes Amendment 1 CAN CSA C22 2 No Amendment 2 to CAN CSA C22 2 No 1010 1 92 1010 1B 97 Safety Requirements for Electrical Equipment for Measurement Control and Laboratory Use Part 1 General Requirements UL Std No 3101 1 Electrical Equipment for Laboratory Use Part 1 General Requirements UL Std No 3111 1 Equipment for Measurement Use Part General Requirements ISA S82 01 1994 Safety Standards for Electrical and Electronic Test Measuring Controlling and Related Equipment General Requirements IEC 61010 1 Safety Requirements for Electrical Equipment for Measurement Control and Laboratory Use Part 1 General Requirements IEC 825 1 Safety of laser products Part 1 Equipment classification requirements and user s guide EN60825 1 Incl
2. Default settings that you see after you install the program Agilent HD 2 color gene expression microarrays Agilent HD 1 color gene expression microarrays Agilent HD CGH CNV ChIP microarrays Agilent HD miRNA microarrays Agilent G3 CGH CNV ChIP microarrays To change all the settings at once you can select one of the Agilent profiles or create your own from any of the existing profiles including the lt Default gt profile To edit an existing profile or create your own profile see Chapter 4 Edit an existing profile on page 55 or Create a new profile on page 56 Agilent G2565CA Microarray Scanner System Scan Control Software 8 5 User Guide 37 2 Getting Started Step 3 Change individual scan settings in the scan table CAUTION If you do not need to change any of the settings in the scan table produced by the selected profile wait until the Scanner status message says Scanner ready and move on to Step 4 Start the carousel run on page 39 1 Click the cell s whose setting s you intend to change Click an individual cell or Click a column header or Drag the cursor down multiple cells in a column to select contiguous cells An arrow appears on the right hand side of the first cell selected Press Ctrl and select non contiguous cells within a column one at a time An arrow appears on the right hand side of the last cell you select 2 Select a new setting from the list The new setting appears in
3. You can reset this warning using the Reset Calibration Warnings tool See Additional Tools on page 65 If this warning persists or reoccurs contact your local Agilent sales and support center Do the following 1 Check the skipped slide for a barcode 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 region 2 Measure the glass thickness and verify that it meets with the specifications in Slide specifications on page 98 Do the following 1 Open the scanner lid 2 Ifthe Autoloader Arm is partially extended into the carousel compartment gently push it back into the scanner until it comes to a stop 3 Close and restart the Scan Control program 4 Ifthe problem persists contact your local Agilent sales and support center Put the carousel in the microarray scanner and reinitiate the carousel run See Step 2 Insert slides into slide holders on page 24 92 Agilent G2565CA Microarray Scanner System Scan Control Software 8 5 User Guide Table 4 Error Messages continued Maintaining and Troubleshooting Your System 5 Error Message Description or Solution The carousel may be misaligned Please remove the carousel make sure that its opening is aligned with home position and reinsert the carousel The slide failed to eject
4. Each slide is scanned in minutes and the files are prepared for feature extraction analysis 10 Agilent G2565CA Microarray Scanner System Scan Control Software 8 5 User Guide Introduction 1 System description In this section you find listings of hardware and software features parts and computer requirements as well as a physical description of the scanner and information on site preparation and safety Hardware and software features The microarray scanner provides the following features e Internal and external barcode reading e Dynamic auto focus e Automatic PMT gain calibration prior to each scan e Continuous laser power stabilization e 2 3 5 or 10 micron pixel size e Dynamic range of gt 104 fora single scan in 16 bit scan mode gt 10 fora single scan in 20 bit scan mode and gt 10 for a dual scan in 16 bit scan mode XDR e TIFF image file compression e Uniformity specification of lt 5 CV Coefficient of Variation The Scan Control software allows you to select the dye fluorescence channels scan regions resolution dynamic range PMT gain and output folders for each of the slides in the carousel run These settings can be automatically loaded from saved application specific profiles or can be individually selected Parts list The Agilent G2565CA Microarray Scanner System consists of the following components e Microarray scanner e Carousel and 50 slide holders e PC workstation with recov
5. Lasers are To turn on the lasers select Tools gt Laser Auto ON OFF powered off Settings and click Turn Lasers ON Now Scanner ready You can begin your scan You cannot start a carousel run until both lasers are warmed up Agilent Scan Control File Tools Help Start slot fi zi End slot fio x Profile ME zl Operator Slot Slide ID Channels Scan Region Resolution TIFF RPMT GPMT XDR Output Path Description lt Auto detect gt Agilent HD 61 x 21 6mm 5 um 20bit 100 100 lt NoXDR gt D ScanData lt Auto detect gt Agilent HD 61 x 21 6mm Sum 20bit 100 100 lt NoXDR gt D ScanData lt Auto detect gt Agilent HD 61 x 21 6mm Sum 20bit 100 100 lt NoXDR gt D ScanData lt Auto detect gt Agilent HD 61 x 21 6mm Sum 20bit 100 100 lt NoXDR gt D ScanData lt Auto detect gt Agilent HD 61 x 21 6mm Sum 20bit 100 100 lt NoXDR gt D ScanData lt Auto detect gt Agilent HD 61 x 21 6mm 5 um 20bit 100 100 lt NoXDR gt D ScanData lt Auto detect gt Agilent HD 61 x 21 6mm 5 um 20bit 100 100 lt NoXDR gt D ScanData lt Auto detect gt Agilent HD 61 x 21 6mm Sum 20bit 100 100 lt NoXDR gt D ScanData lt Auto detect gt Agilent HD 61 x 21 6mm Sum 20bit 100 100 lt NoXDR gt D ScanData lt Auto detect gt Agilent HD 61 x 21 6mm Sum 20bit 100 100 lt NoXDR gt D ScanData Oa Nn om e wne 5 gt Scanner ready Scan Slot 1 10 Compress Off Split Rot
6. Step 3 Change individual scan settings in the scan table on page 38 Step 4 Start the carousel run on page 39 Step 5 Transfer files and archive data on page 42 32 Agilent G2565CA Microarray Scanner System Scan Control Software 8 5 User Guide Getting Started 2 Step 5 Remove the slides After the carousel run is complete you can unload the slide holders from the carousel and then remove the slides from the slide holders 1 Optional Remove the carousel from the scanner If the slide holder autoloader arm is extended into the carousel do not remove the carousel Instead follow the instructions in Troubleshooting an autoloader arm extended into the carousel on page 82 2 Remove the slide holders from the carousel 3 Remove the slides from the slide holders a Hold the slide holder on the sides with the Agilent logo facing up b Place one thumb on the center of the slide holder cover c Gently press down on the cover and push toward the top of the slide holder until the cover releases iV A Released slide holder cover Agilent G2565CA Microarray Scanner System Scan Control Software 8 5 User Guide 33 2 Getting Started d Push up on the barcode end of the slide from underneath the slide holder to avoid fingerprints on the sample area e Grasp the slide from the sides and remove from slide holder Push up from underneath Figure 19 Proper removal of slide 34 Agilent
7. problem is experienced during the scan data will be saved to a temporary local directory and a warning will be included in the carousel run report Slide Description of each slide being scanned This information Description becomes part of the file information that can be viewed in the Feature Extraction software Agilent G2565CA Microarray Scanner System Scan Control Software 8 5 User Guide Agilent G2565CA Microarray Scanner System Scan Control Software 8 5 User Guide 4 Using Tools Creating Editing profiles using the Profile Editor 55 Creating Editing scan regions using the Scan Region Editor 59 Setting up times to turn the lasers on and off 63 Additional Tools 65 If you want to create or modify a profile or a scan region or if you intend to set up times for the lasers to turn on and off automatically you use the tools in the Tools menu This chapter shows you how to use these tools Tools Help Profile Editor Scan Region Editor Laser Auto ON OFF Settings Log File Finder Figure 27 Tools menu at Agilent Technologies 53 4 54 Using Tools Profile Editor lt Default gt AgilentHD GX_ 2Color AgilentHD_GX_1Color AgilentHD_CGH AgilentHD miRNA AgilentG3_CGH Scan Region Editor Lasers Auto On Off Settings With the Profile Editor you can modify the settings for any of the profiles that come with the software The profile whose settings you see loaded upon installati
8. 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 Unable to lock instrument specified by connection manager You must select a region to scan first You must select at least one dye channel See Step 2 Insert slides into slide holders on page 24 When you press OK the microarray scanner re initializes If this fails do the following 1 Open the scanner lid 2 Ifthe 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 3 Close and restart the Scan Control program 4 Ifthe problem persists contact your local Agilent sales and support center 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 Start the Scan Control program To enter a scan region not specified in the selected profile into the scan table 1 Select the slot or slots whose region you intend to enter 2 Click the down arrow next to the selection s 3 Select a scan region from the Scan region list See Change individual scan table settings on page 46 4 Start the scan or carousel run 1 Select the slot or slots whose dye channel you intend to change Click the down arrow next to the selection s
9. Scan Progress x m Current scan information File name e LPJAN14B4_SLOTO1_SO1 tif Barcode 16011535021652 Slot number 1 r Status Scanning a m Progress Scan progress g Carousel progress 0 0 of 1 slides completed Figure 20 Scan Progress dialog box Agilent G2565CA Microarray Scanner System Scan Control Software 8 5 User Guide 39 2 Getting Started The Carousel Report Log presents scan information and error messages that occur during the carousel run 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 When the carousel run is complete the Status box reads Carousel run completed At the end of a carousel run the Carousel Report Log automatically appears AGILENT SCANNER CAROUSEL REPORT LOG Scammer SN US1470PPB1 Carousel run requested from Slot 1 to Slot 29 Total number of slide s detected 29 Slot 1 2 Scanned image D New Folder US1470PPB1_123456789012_S01 tif Scan completed Fri Apr 11 11 01 38 2008 Scanned image D New Folder US1470PPB1_ 251554817094 01 tif Scan completed Scanned image D New Folder US1470PPB1_251554819356_ 01 tif Scan completed Scanned image D New Folder US1470PPB1_ 251554819966 _ 01 tif Scan completed Figure 21 40 Carousel Report Log If you wish to re open the final Carousel Report Log after you have closed t
10. Select a dye channel setting from the list See Dye channel on page 49 w N Agilent G2565CA Microarray Scanner System Scan Control Software 8 5 User Guide 93 5 Maintaining and Troubleshooting Your System Table4 Error Messages continued Error Message Description or Solution You must close the door first Microarray scanner initialization and scan operations cannot be performed with the microarray scanner lid open Close the lid Warning The laser power does not fall Wait the required warm up time about 30 minutes when the status message in within expected thresholds Please the Scan Control program says Status Ready You can reset this warning using contact an Agilent representative the Reset Calibration Warnings tool See Additional Tools on page 65 If this warning persists or reoccurs contact your local Agilent sales and support center The Scan Control program scales the TIFF file to compensate for the lower laser power 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 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 n
11. The Microarray Scanner can take a minute or two to finish aborting the scan even if Yes is selected Any collected data is saved for later analysis Agilent G2565CA Microarray Scanner System Scan Control Software 8 5 User Guide 41 2 42 Getting Started Step 5 Transfer files and archive data e At the end of the run transfer the files to another folder if needed You can transfer the file or files to one of four places New folder under the original folder on the local drive that you set up for the Output Path Another folder on the local drive Folder on the network Eventually you must transfer data to the PC where the Feature Extraction program resides CD or DVD A DVD Writer is included with every PC workstation CAUTION It is important to archive data regularly from the scanner PC to make sure enough disk space is available for future runs When the disk is almost full the microarray scanner stops scanning and a caution is displayed You can improve performance by regularly defragmenting the disk drive Agilent G2565CA Microarray Scanner System Scan Control Software 8 5 User Guide Agilent G2565CA Microarray Scanner System Scan Control Software 8 5 User Guide 3 Changing scan settings Changing Scan Table Settings 44 Change scan table settings through profiles 45 Change individual scan table settings 46 Scan Table Settings 48 Before you scan a set of slides you may want to modify scan or i
12. Use the Web to reach technical support The software arrives with a default URL that lets you access Agilent technical support for the microarray scanner e Click Help gt Technical Support 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 click Help gt Technical Support 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 83 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 When corresponding with your local Agilent sales and support center about your microarray scanner be sure to include the model number and 10 character serial number Agilen
13. definition example of 40 viewing during or after run 41 carousel run 32 cleaning air filter 70 compressing TIFF 57 computer hardware system requirements 12 computer system requirements 12 create scan region non Agilent slides 59 D dark offset subtraction description 18 data archiving 42 68 saving 42 default scan settings 55 63 dye channel setting 49 dynamic range 16 bit or 20 bit 50 TIFF file 50 E empty slots checking for 49 error messages 88 not appearing in table 94 table in alphabetical order 89 where and when they appear 88 F FAQs 76 jammed slides 77 opening the scanner lid 76 program not responding 76 FAQs frequently asked questions 76 features of system 10 file naming automatic 56 fluorescence detection 18 frequently asked questions FAQs 76 front view of scanner 13 fuses laser 81 power supply 80 glass slide specifications 98 high resolution scanning license 20 humidity 71 indicator lights 13 78 79 initialization process 23 input voltage checking 105 setting 105 inspecting air filter 69 L laser excitation 17 laser fuse changing 81 lasers auto On Off settings 54 checking or replacing fuses 81 turning off automatically 35 turning on off automatically 63 turning on off manually 64 types used 17 licensing high resolution scanning 20 non Agilent barcode 21 Log Report 41 M maintenance tasks 68 to 70 moving scan
14. 32 bit or Windows 7 64 bit systems please see the release notes associated with the Scan Control Software Set up HyperTerminal 1 Turn on the scanner to start initialization Start the Scan Control program to turn on the lasers 3 Make sure the scanner is on for at least 30 seconds before starting HyperTerminal step 4 4 Click Start gt Programs gt Accessories gt Communications gt HyperTerminal 5 In the Connection Description dialog box a Type Scanner in the Name text box Connection Description lor New Connection Enter a name and choose an icon for the connection Name Scanner Icon ASs3eur b Click OK Agilent G2565CA Microarray Scanner System Scan Control Software 8 5 User Guide 83 5 Maintaining and Troubleshooting Your System CAUTION When the scanner is turned on and HyperTerminal is running the scanner cannot initialize Wait at least 30 seconds after you turn on the HyperTerminal must be started no earlier than 30 seconds after the scanner has been turned on 6 In the Connect To dialog box a From the Connect using drop down list select the highest COMX number This will usually be COM3 but you can verify this through Windows Device Manager The scanner COM port is listed as USB Serial Port COMX Connect To D Scanner Enter details for the phone number that you want to dial Country region Area code Phone number Corect usino b C
15. Code 128 Code 39 Code 93 CODABAR 5 mm or 15 of barcode length whichever is greater Agilent G2565CA Microarray Scanner System Scan Control Software 8 5 User Guide 101 6 Reference Regulatory information English Deutsch Contact Agilent Technologies for more information on recycling and disposal 102 Emissions This section lists regulatory information for the microarray scanner For research use only The Agilent G2565CA Microarray Scanner is intended for RESEARCH USE ONLY Acoustic noise information Manufacturer s Declaration 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 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 Typpritifung Recycling and disposal This device is designed to accommodate recycling at the end of its useful life Please dispose of this device in accordance with local regulations Electromagnetic interference The scanner is intended for use with shielded cables only Complies with the emissions levels for Class A equipment as required in IEC 61326 1 This equipment is not intended for use in residential areas
16. Export Default configuration settings R G Agilent HD 61 x 21 6mm Sum 16 bit 100 100 lt No XDR gt ree lt Instrument Serial gt lt Slot gt No No Change the scan and image settings using the choices described in Changing Scan Table Settings on page 44 and Profile settings not in the scan table on page 56 Agilent G2565CA Microarray Scanner System Scan Control Software 8 5 User Guide 55 4 56 Using Tools Create a new profile You can create a new profile from any existing profile by saving the existing profile as a new name 1 Select Tools gt Profile Editor Select an existing profile to save as a new one Click Save As to save the existing file to a new name Enter the name then click Save oF WwW N Change the scan and image settings using the choices described in Changing Scan Table Settings on page 44 and Profile settings not in the scan table on page 56 6 Click Save Profile settings not in the scan table Naming prefix 1 and Naming prefix 2 The following settings do not appear in the scan table These parameters apply to all scans in the carousel run For standard scans the Scan Control program uses three name segments to compose the filename Prefix1_Prefix2_ScanNumber tif For XDR scans an additional segment either _H or _L is added to the filename to distinguish the XDR Hi image from the XDR Lo image Prefix1_Prefix2_ScanNumber_H t
17. From the Select Capture File dialog box choose a new folder or a new filename or else your original capture session file will be overwritten When you are done click Save to continue 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 To use this CD successfully you must disconnect the USB cable that attaches to the back of the PC before you use the CD CAUTION If you do not disconnect this cable the Agilent default settings for the USB devices may be changed and the software will not recognize the scanner when you restart the software Agilent G2565CA Microarray Scanner System Scan Control Software 8 5 User Guide 87 5 88 Maintaining and Troubleshooting Your System Microarray Scanner Error Messages This section explains how to use error messages you may encounter Sources of error messages The computer monitor shows error messages for the microarray scanner hardware the Scan Control 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 Q Description The chip carousel is not present Please place the carousel in the scanner and
18. G2565CA Microarray Scanner System Scan Control Software 8 5 User Guide Getting Started 2 Step 6 Set times to automatically turn the lasers off You can extend laser lifetime by having the instrument automatically power off the lasers at specified times See Setting up times to turn the lasers on and off on page 63 of Chapter 4 Using Tools for more information You do not need to turn off the microarray scanner Should you want to turn off the scanner follow these instructions 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 a few seconds and verify that the Microarray Scanner lid is unlocked 3 Lift the lid 4 Turn off the power switch on the front of the Microarray Scanner CAUTION Do not attempt to lift 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 G2565CA Microarray Scanner System Scan Control Software 8 5 User Guide 35 2 Getting Started Scanning Your Slides Step 1 Set slot locations 36 If you want to scan slides in all 48 slots skip to Step 2 Set a profile for changing all settings in the scan table on page 37 1 In the Start slot box select the number of the slot where the first slide that you want to scan is located 2 In the End Slot box select the num
19. Ifthe 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 76 Agilent G2565CA Microarray Scanner System Scan Control Software 8 5 User Guide Table 2 FAQs continued Maintaining and Troubleshooting Your System 5 FAQ Answer What do do if a slide is only halfway inserted in the carousel by the autoloader arm The microarray scanner is turned on but the yellow light does not go off after 20 minutes The microarray scanner is turned on and the Scan Control program is open but the scanner won t scan I m using the Windows 7 64 bit operating system and I m getting a Command timed out message 1 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 If the problem persists call your local Agilent sales and support center w N 1 Verify that the PC workstation is turned on 2 Verify that the USB cable is connected from the PC workstation to the microarray scanner 3 Contact your local Agilent sales and support center 1 Close and then restart the Scan Control program The microarray scanner must be turned on before the Scan Control program is started If you started the Scan Control program first the connection is not made when the scanner is turned on 2 Contact your
20. against the tabs on the side of the slide holder Figure 12 Slide dropping into slide holder 7 To close the slide holder cover gently press down on the cover with your thumb Figure 13 Close the cover 8 To lock the cover in place gently pull the cover back with your thumb until it locks Agilent G2565CA Microarray Scanner System Scan Control Software 8 5 User Guide 27 2 Getting Started Step 1 Turn on the Agilent Microarray Figure 14 Lock in the cover 9 Verify that the slide holder lid is fully locked into place Cover locked underneath the side tabs Figure 15 Properly locked cover 28 Agilent G2565CA Microarray Scanner System Scan Control Software 8 5 User Guide Getting Started 2 Step 3 Load the slide holders into the carousel The Microarray Scanner scans slides in the order that they are detected as it rotates the carousel from lower numbered slots to higher numbered slots The carousel run skips over any empty slots CAUTION When the slides are properly inserted in the slide holders you can load the slide holders into the carousel The carousel is designed so that you can easily load a slide holder correctly You can load the slide holders either with the carousel in the scanner or removed from the scanner 1 Load a slide holder into carousel slot 1 the first slot located clockwise from the home position Do not place a slide in the carousel home slot The home slot is wider t
21. and its subnet mask is 255 255 255 0 Windows XP firewall may be preventing communication Disable the firewall If you rebooted the PC workstation you may need to turn the microarray scanner off and then back on after Windows has restarted Do the following 1 2 3 6 Turn off power to the scanner Open the scanner lid Rotate the carousel by hand until access to the home slot is not blocked by the Autoloader Arm Remove slide from home slot Gently push the Autoloader Arm back into the scanner until it comes to a stop If the problem persists contact your local Agilent sales and support center Do the following 1 2 3 Reboot the PC workstation Turn the microarray scanner off and then back on After several minutes start the Scan Control program Do the following 1 Verify that the number showing in the voltage selector on the back of the scanner matches the input power supplied If you rebooted the PC workstation you may need to turn the microarray scanner off and then back on after Windows has restarted If the problem persists contact your local Agilent sales and support center Agilent G2565CA Microarray Scanner System Scan Control Software 8 5 User Guide 91 5 Maintaining and Troubleshooting Your System Table 4 Error Messages continued Error Message Description or Solution Missing or corrupt ChipRegions ini file Not enough disk space to create file PMT calibrati
22. description 11 Hardware and software features 11 Parts list 11 Computer system requirements 12 Scanner physical description 13 Site preparation 14 Safety symbols onscanner 15 Safety guidelines 16 Principles of operation 17 Slide positioning 17 Laser excitation 17 Scanning 1 7 Fluorescence detection 18 Dark offset subtraction 18 2 Getting Started 19 Licensing 20 Redeeming your high resolution scanning license 20 Installing your high resolution scanning license 20 Non Agilent Barcode Licensing 21 Operating the Scanner 22 Step 1 Turn on the Agilent Microarray Scanner 22 Step 2 Insert slides into slide holders 24 Step 3 Load the slide holders into the carousel 29 Agilent G2565CA Microarray Scanner System Scan Control Software 8 5 User Guide Contents Step 4 Scan your slides 32 Step 5 Remove the slides 33 Step 6 Set times to automatically turn the lasers off 35 Scanning Your Slides 36 Step 1 Set slot locations 36 Step 2 Set a profile for changing all settings in the scan table 37 Step 3 Change individual scan settings inthe scan table 38 Step 4 Start the carousel run 39 Step 5 Transfer files and archive data 42 Changing scan settings 43 Changing Scan Table Settings 44 Change scan table settings through profiles 45 Change individual scan table settings 46 Scan Table Settings 48 Using Tools 53 Creating Editing profiles using the Profile Editor 55 Edit an existing profile 55 Create anew profile 56
23. following 1 Verify that the USB cable from the microarray scanner to the PC workstation is connected 2 Turn the microarray scanner off then on again Restart the Scan Control program 4 Ifthe problem persists contact your local Agilent sales and support center ow 90 Agilent G2565CA Microarray Scanner System Scan Control Software 8 5 User Guide Table 4 Error Messages continued Maintaining and Troubleshooting Your System 5 Error Message Description or Solution Connection manager reports that there are no instruments Error ejecting chip The chip was ejected into the home slot Failed to communicate with connection manager Lasers never became ready Possible causes for this error include 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 wait a few minutes and try again The microarray scanner might not be connected to the PC workstation Verify the USB cable is connected to both the microarray scanner and PC workstation If the USB cable is disconnected reconnect the cable reboot the PC computer and if needed turn the microarray scanner off then on 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
24. in slides in a removable carousel During a carousel run the slides are sequentially transported into scanning position scanned then returned 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 hybridization of the target nucleic acid to the microarray probes Dyes similar to Cy 3 and Cy 5 such as Alexa 647 555 and 660 dyes can also be used 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 bands 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 target concentrations and for higher data confidence at lower signal levels Scanning The laser excitation is scanned rapidly back and forth across the microarray The dynamic tracking auto focus ensures that the microarray is always positioned in the focal plane of the scan lens resulting in scan uniformity Agilent G2565CA Microarray Scanner System Scan Control Software 8 5 User Guide 17 1 18 Introduction Fluorescence detection Fluorescence from the labeled samples is converted to an electrical signal by a high performance PMT Very low noise amplifiers and digital integrators process the PMT signal into a dig
25. operates within the following specifications 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 8 in clearance in depth to provide adequate venting 99 Kg 218 lbs 100 120 220 or 240 VAC at 4 A 50 60 Hz Two power supply fuses T4A 250 VAC Part 2110 1309 One laser fuse T500mA 250 VAC Part 2110 0458 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 20 mW at 532 nm and 23 mW at 633 nm both controlled to 13 mW Maximum scan region Suggested microarray print region Dyes supported Resolution pixel size Pixel placement error Uniformity Scan time Dynamic range Reference 6 Agilent G2565CA 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 3 and Cy 5 and Alexa 647 555 and 660 dyes 2 3 5 or 10 micr
26. slide the distance between the edge of the microarray scan region and the edge of the barcode label can be no less than 4 mm Nominal scan region Barcode label area gt 4mm Figure 42 Barcode location on non Agilent slide e The barcode label width should be about 6 mm the recommended barcode label width is for use with the 61 mm scan region Larger or longer barcode labels can be used by decreasing the scan region proportionally e Barcode labels should be narrow enough so as not to interfere with the slide holder tabs e Maximum allowable tilt in the placement of the barcode label on the slide is 3 The barcode 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 barcode is 10 times the X dimension on each side of the barcode e Barcode lines must be parallel to the long edge of the slide within tilt tolerance of 3 e Agilent supports the following barcode formats Code 128 Non Agilent barcodes with 12 digits must not start with 2 CODABAR Maximum of 8 digits minimum line thickness 6 mils Agilent G2565CA Microarray Scanner System Scan Control Software 8 5 User Guide Reference 6 gt 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 barcode must be gt Code 128 15 of barcode length for
27. sure the scan region is at least 4 mm away from the barcode label and does not overlap any other opaque or translucent areas of the slide 1 Select File gt New Region from the menu bar in the Scan Region Editor is Add New Region Jol x Name Ranges mm X mm 310 6910 Y mm 190 23 40 Width mm 5 00 71 00 Height mm 010 21 60 e Figure 30 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 values will be marked in red Agilent G2565CA Microarray Scanner System Scan Control Software 8 5 User Guide Height Ranges Show Custom regions only Using Tools Change an existing scan region for non Agilent slides 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 axis measurement for the upper left hand corner Width of the scan region measured from the end of the X axis measurement in the upper left hand corner Height of the scan region measured from the end of the Y axis measurement in the upper left hand corner Range of values that you can enter for each measurement Click Save If no errors are found the Scan Region Editor appears with the new region listed in the Scan Region Editor a acca ar A E A Custom Region 1 1 95 70 90 1 50 Figure 31 Scan regions list When this check box is m
28. 3 e ScanNumber S03 This is the third scan file in the directory with the same Instrument Serial and Slide ID Compress TIFF You can reduce the final amount of storage space occupied by scan images by compressing the TIFF files The compression algorithm used LZW reduces the storage space by 20 to 70 percent Agilent G2565CA Microarray Scanner System Scan Control Software 8 5 User Guide 57 4 58 Using Tools Split rotate image Some analysis programs require data from one color images rotated 90 degrees If you set the Split Rotate option to Yes 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 mec gt YBCD 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 select only one dye channel for your output file you must still make this selection to rotate the image even if you do not need to split the file This option is available only for 16 bit TIFF dynamic range scans Agilent G2565CA Microarray Scanner System Scan Control Software 8 5 User Guide UsingTools 4 Creating Editing scan regions using the Scan Region Editor The scan region determines the areaof If you use non Agilent slides you can create your own scan the slide that is scanned The largerthe region or change a scan region up to the maxim
29. Agilent G2565CA Microarray Scanner System Scan Control Software 8 5 with SureScan High Resolution Technology User Guide June 2010 Research Use Only Not for use in Diagnostic Procedures Ee Agilent Technologies Notices Agilent Technologies Inc 2010 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 62505 90021 Edition June 2010 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 o
30. Agilent G2565CA Microarray Scanner System Scan Control Software 8 5 User Guide 4 0 Glass specifications Scan region for Agilent G2565CA Reference Slide specifications 6 25 4 0 7 or 0 45 1 0 Figure 40 98 Reference 6 Barcode and barcode label specifications Barcode specifications for Agilent slides The G2565CA scanner reads barcodes placed on the active side of the slide For backwards compatibility with the G2565AA model scanners Agilent microarrays continue to have barcodes on both sides The label with the text Agilent denotes the active side the label with the numeric value is the inactive side Double barcoded slide example Inactive Glass Surface SIDE 1 a S P p5 N So Ss A ox Active Active Microarray Microarray Surface Surface SIDE 2 quayiby Figure 41 Agilent slide barcode orientation vs microarray surface Barcode specifications for non Agilent slides e The barcode 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 barcode labels on slides whose scan region exceeds 61 mm You must enter the slide identifier or barcode manually for slides whose scan regions exceed 61 mm Agilent G2565CA Microarray Scanner System Scan Control Software 8 5 User Guide 99 6 100 Reference e For a barcoded
31. Guide A powerful tool System description Principles of operation Agilent G2565CA Microarray Scanner System Scan Control Software 8 5 User Guide 1 Introduction A powerful tool for microarray analysis 10 System description 11 Principles of operation 17 This chapter provides a general introduction to the Agilent G2565CA Microarray Scanner System This section describes the features that make the microarray scanner a powerful tool for Agilent s microarray analysis solution In this section learn about the hardware and software features of the microarray scanner the parts and system requirements the site preparation information and the safety guidelines This section explains how the microarray scanner works ee Agilent Technologies 9 1 Introduction A powertul tool for microarray analysis The Agilent G2565CA Microarray Scanner is part of the microarray analysis solution from Agilent Technologies The microarray scanner is a sophisticated laser induced fluorescence scanner designed to read microarrays printed 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 microarrays Its ability to measure fluorescence from two dyes simultaneously facilitates all two color microarray studies This technology provides for rapid high quality automated scanning of microarrays Figure 1 Agilent G2565CA Microarray Scanner
32. Profile settings not inthe scan table 56 Creating Editing scan regions using the Scan Region Editor 59 Start the Scan Region Editor 59 Create a new scan region with the Scan Region Editor 60 Change an existing scan region for non Agilent slides 61 Setting up times to turn the lasers on and off 63 Enable the lasers to turn on or off automatically 63 Turn the lasers on or off manually 64 Additional Tools 65 Unlock Door 65 Agilent G2565CA Microarray Scanner System Scan Control Software 8 5 User Guide Contents Reset Calibration Warnings 65 Extended Laser Calibration 66 5 Maintaining and Troubleshooting Your System 67 Maintaining yoursystem 68 Scheduled software maintenance 68 Scheduled hardware maintenance 69 Tips to prevent problems 71 Troubleshooting your system 73 Technical Support 74 Frequently Asked Questions FAQs 76 Hardware Troubleshooting 78 Using HyperTerminal to Capture Diagnostic Data 83 Software Troubleshooting 87 Microarray Scanner Error Messages 88 6 Reference 95 Microarray scanner specifications 96 Slide specifications 98 Scandimensions 98 Glass specifications 98 Barcode and barcode label specifications 99 Regulatory information 102 Input voltage check 105 Verify input voltage 105 Change the voltage setting 106 Index 109 Agilent G2565CA Microarray Scanner System Scan Control Software 8 5 User Guide 7 Contents 8 Agilent G2565CA Microarray Scanner System Scan Control Software 8 5 User
33. The Agilent G2565CA 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 The microarray scanner must be connected to a grounded power outlet It relies on a protective earth ground for safety CAUTION 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 CAUTION Agilent recommends that the microarray scanner be placed on a sturdy lab bench or table The microarray scanner is a potential source of vibration and is potentially sensitive to external vibration CAUTION The microarray scanner is potentially sensitive to condensing humidity conditions Follow precautions stated in product documentation See Tips to prevent problems on page 71 of Chapter 5 and the relative humidity specifications on page 96 of Chapter 6 Agilent G2565CA Microarray Scanner System Scan Control Software 8 5 User Guide Introduction 1 Principles of operation This section describes the operating features of the Agilent G2565CA Microarray Scanner Slide positioning The microarray scanner holds up to 48 1 in x 3
34. 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 70 Agilent G2565CA Microarray Scanner System Scan Control Software 8 5 User Guide Maintaining and Troubleshooting Your System 5 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 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 temper
35. arked only the custom scan regions 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 Close the Scan Region Editor The newly created regions now appear in the Scan Region lists both in the Profile Editor and the scan table 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 Agilent G2565CA Microarray Scanner System Scan Control Software 8 5 User Guide 61 4 4 62 Using Tools When creating a new scan region or using existing scan regions make sure the scan region is at least 4 mm away from the barcode label 1 In the Scan Region Editor select the region to change 2 Select File gt Open Region from the menu bar The Modify Region dialog box appears a Modify Region el Ea Name Ranges mrm x 4 00 mm 310 6910 ne 2 00 mm 1 90 23 40 Width 16 00 mm 5 00 7010 Height 11 00 mm 010 21 50 co Figure 32 Modify Region dialog box 3 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 60 5 Click Save Agilent G2565CA Microarray Scanner System Scan Control Software 8 5 User Guide UsingTools 4 Sett
36. ate OFF Naming US1470PPB1_ lt Slide ID gt _5 lt Scan gt Total file size 3 0 GB Total run time 1 hr 20 min Figure 7 Scan Control main window when lasers are ready Agilent G2565CA Microarray Scanner System Scan Control Software 8 5 User Guide 23 2 Getting Started Step 2 Insert slides into slide holders A slide must be inserted into a slide holder before loading it into the carousel The slide holder protects the slide during scanning Figure 8 Loading slides into the slide holder Fingerprints cause errors in the 1 Hold the slide holder on the sides with the Agilent logo fluorescence detection For facing up accurate readings touch only the 2 Place one thumb on the center of the slide holder cover edges of the slide and always use gloves when handling slides 3 Gently press down on the cover and push toward the top of the slide holder until the cover releases Also do not write on the slides with markers or place any labels on the slide other than an appropriate For instructions on removing the slides see Step 5 Remove barcode the slides on page 33 24 Agilent G2565CA Microarray Scanner System Scan Control Software 8 5 User Guide Getting Started 2 Released slide holder cover Figure 9 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 Active microarray s
37. ature ranges See Microarray scanner specifications on page 96 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 96 Always allow 10 hours thermal equilibration time on site before opening the shipping box Agilent G2565CA Microarray Scanner System Scan Control Software 8 5 User Guide 71 5 Maintaining and Troubleshooting Your System 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 microarray scanner e Place the microarray scanner on a sturdy lab bench or table e Avoid leaning on the microarray scanner e To extend the life of the lasers set up to automatically power your lasers on and off See Setting up times to turn the lasers on and off on page 63 of Chapter 4 e After turn on allow time for laser warm up and stabilization The maximum warm up time is 30 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 repa
38. ber of the slot where the last slide that you want to scan is located Start slot M End slot 48 x The range of slots that you enter in steps 1 and 2 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 scanner scans only those slides in the slot range that you enter here e The Carousel Check command checks only the range of slots that you enter here for empty slots and for Agilent supported barcodes See Check for Agilent supported barcodes and empty slots on page 49 of Chapter 3 Agilent G2565CA Microarray Scanner System Scan Control Software 8 5 User Guide Getting Started 2 Step 2 Set a profile for changing all settings in the scan table A profile is a collection of scan and image settings that when selected populate the scan table with values you entered in the Profile Editor lt default gt AgilentHD_GX_2Color AgilentHD_GX_1Color AgilentHD_CGH AgilentHD_miRNA AgilentG3_CGH e From the Profile list select one of the existing profiles Profile XSI itn Sm epee a When you open the Scan Control main window you see the columns populated by scan setting values These values are set from the last profile selected for a run before closing the program Agilent supplies six preloaded profiles for your selection and use with Agilent high density microarrays Agilent G3 microarrays and non Agilent microarrays
39. bit one The Scan Region is 61 X 21 6 mm The Status bar at the bottom of the Scan Control main window shows an estimate of the storage space and run time required for the complete carousel of slides Table 1 Storage Space and Scan Time for Single and Double Pass Scans for Agilent HD Scan Region 61 x 21 6 mm Resolution Storage Space Storage Space Scan Time Mb 16 bit Mb 20 bit min 2 micron single pass 1300 1600 20 3 micron single pass 620 760 15 5 micron single pass 200 300 8 10 micron single pass 52 115 8 2 micron double pass 1300 1600 40 3 micron double pass 620 760 30 5 micron double pass 200 300 16 Double pass scans do not require more storage space than single pass scans but they take twice as long to complete Agilent G2565CA Microarray Scanner System Scan Control Software 8 5 User Guide Changing scan settings 3 Red PMT Gain Sets the sensitivity level of the red channel and green and channel PMTs The PMT detects fluorescence emitted by the Green PMT Gain microarray The default output level 100 sets the gain to the factory calibrated level this is the recommended setting for Agilent microarrays 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 XDR Ratio Before the availability of th
40. bold Scan Region F Agilent HD 61 x 21 6mm lt 3 Full Slide 71 x 21 6mm a lent HD 61 x 21 6mm An estimate of the total file size and run time is reported in the status line at the bottom of the Scan Control main window Note that space is required on the C drive for temporary files generated while scanning If the estimated image size plus temporary file size exceed the space available the scanner will not permit the carousel run to begin Agilent recommends that you select an Output Path for storing image files to a local drive If you select a network drive for your output path and the network connection fails then files are stored on the local C drive in the file Program Files Agilent Microarray NetDataBackup 38 Agilent G2565CA Microarray Scanner System Scan Control Software 8 5 User Guide Getting Started 2 Step 4 Start the carousel run A carousel run scans all the selected slides in the carousel 1 Verify that the Scanner status message in the main window says Scanner ready The carousel run cannot be started until the lasers have fully warmed up 2 Click Scan 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
41. can do this for Agilent slides See Slide ID on page 48 To learn about each of the scan settings see Scan Table Settings on page 48 44 Agilent G2565CA Microarray Scanner System Scan Control Software 8 5 User Guide Changing scan settings 3 Change scan table settings through profiles e From the Profile drop down list select the profile whose settings you want to use for the run Profile AEn Sm ep dete a Figure 23 Profile drop down list on Scan Control main window You can change the settings for the selected profile See Edit an existing profile on page 55 or create a new profile from it See Create a new profile on page 56 When you open the Scan Control main window you see the columns populated by scan setting values These values are set from the last profile selected for a run before closing the program Agilent supplies six preloaded profiles for your selection and use with Agilent high density microarrays Agilent G3 microarrays and non Agilent microarrays AgilentHD GX_2Color Agilent HD 2 color gene expression microarrays AgilentHD GX_1Color Agilent HD 1 color gene expression microarrays AgilentHD CGH Agilent HD CGH CNV ChIP microarrays AgilentHD miRNA Agilent HD miRNA microarrays AgilentG3_CGH Agilent G3 CGH CNV ChIP microarrays For Agilent slides you select the profile that applies to your type of Agilent microarray For non Agilent slides you will need to make changes to in
42. cell or cells whose setting s you intend to reset Click an individual cell or Click a column header or Drag the cursor down multiple cells in a column to select contiguous cells or Press Ctrl and select non contiguous cells within a column one at a time or Click the Slot header in the upper left hand corner of the table to select all the cells in the scan table 2 Right click the selected area and select Reset to Profile Value Reset to Profile Value Fit Column s to Window Best Fit Column Sizes Refresh Table Figure 25 Shortcut menu for returning all selected settings to their orig inal values in the current profile The settings in the current profile appear in the selected area Agilent G2565CA Microarray Scanner System Scan Control Software 8 5 User Guide 47 3 Changing scan settings Scan Table Settings This section describes the settings in the scan table that you can change The next section tells you how to change them Agilent Scan Control Eile Tools Figure 26 48 Start slot j1 x Slot Help Slide ID lt Auto detect gt lt Auto detect gt lt Auto detect gt lt Auto detect gt lt Auto detect gt lt Auto detect gt lt Auto detect gt lt Auto detect gt lt Auto detect gt lt Auto detect gt End slot Channels 10 x ile Scan Region Agilent HD 61 x 21 6mm Agilent HD 61 x 21 6mm Agilent HD 61 x 21 6mm Agilent HD 61 x 21 6mm Ag
43. dge screwdriver to pry up the small plastic tab located on the bottom edge of the fuse holder until it releases PZ K Fuse holder Figure 44 Removing the fuse holder for the power supply 3 Pull out the fuse holder 106 Agilent G2565CA Microarray Scanner System Scan Control Software 8 5 User Guide Reference 4 Use needle nose pliers to remove the voltage selector Voltage selector Fuse holder Figure 45 Removing the voltage selector from the fuse holder 5 Insert the voltage selector so that the number showing matches the line voltage 6 Push the fuse holder back in until it clicks into place 7 Plug in the power cord Agilent G2565CA Microarray Scanner System Scan Control Software 8 5 User Guide 107 6 Reference Change the voltage setting 108 Agilent G2565CA Microarray Scanner System Scan Control Software 8 5 User Guide Index A aborting ascan 41 Agilent slides automatic barcode entry 48 manual barcode entry 48 air filter cleaning 70 inspecting 69 archiving data 33 42 68 automatic file naming 56 barcode formats 100 barcodes automatic entry 48 checking for 49 manual entry 48 non Agilent 21 specifications 99 C capturing diagnostic data 83 carousel checking for barcodes and empty slots 49 covering 30 inserting slides into 24 loading slide holders into 29 Report Log 41 starting the run 39 troubleshooting autoloader arm 82 Carousel Report Log
44. dividual scan table settings Or you can create a new profile from an existing one Agilent G2565CA Microarray Scanner System Scan Control Software 8 5 User Guide 45 3 46 Changing scan settings Change individual scan table settings With this scan table you can change entries for individual slides or groups of slides by selecting an item from the drop down menu enabled for each column except the Slide ID and Description columns 1 Click the cell s whose setting s you intend to change Click an individual cell or Click a column header or Drag the cursor down multiple cells in a column to select contiguous cells An arrow appears on the right hand side of the first cell selected Press Ctrl and select non contiguous cells within a column one at a time An arrow appears on the right hand side of the last cell you select 2 Click the arrow to show the drop down list and select the setting Scan Region F Full Slide 71 x 21 6mm a lent HD 61 x 21 6mm Figure 24 Drop down list for scan region settings The changed settings appear in bold letters See descriptions of these column settings in Scan Table Settings on page 48 Agilent G2565CA Microarray Scanner System Scan Control Software 8 5 User Guide Changing scan settings 3 Reset scan table settings to current profile values The profile values that appear when resetting are the original values found in the selected profile 1 Click the
45. e 20 bit TIFF file dynamic range the eXtended Dynamic Range function had to be used on both the scanner and Feature Extraction software to capture all the data scanned between very low signal features and very high signal features Now you can select the 20 bit TIFF file dynamic range to capture the wide dynamic range of data as an alternative to using XDR With the XDR function turned on the scanner automatically scans the same slide twice at two different PMT sensitivity levels This generates two linked images that Feature Extraction can co process to yield a single unified set of extracted intensity data covering up to 6 orders of magnitude The high sensitivity level is set by the Red or Green PMT Gain The XDR function is automatically turned off once on at values lower than 10 Setting the XDR ratio column instructs the scanner to perform a second scan at lower PMT settings For example if the Red and Green PMTs are set to 100 and the XDR ratio is set to 0 1 then the second scan will be performed with the PMTs set to 10 The lowest available PMT setting is 1 Output path The Browse button lets you select a directory to store the data from each scan Agilent recommends that the data be acquired to a local directory on a secondary hard drive You may also select a network directory If a network access Agilent G2565CA Microarray Scanner System Scan Control Software 8 5 User Guide 51 3 52 Changing scan settings
46. e power switch located on the front of the instrument You will notice 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 status indicator lights flash on and off as different functional checks are made c The lasers will not turn on until you start the Scan Control software Status indicator lights Power switch Figure 5 Location of power switch and status indicator lights To learn how to set up to turn the 5 Double click the Agilent Scan Control icon to open the lasers on and off automatically see Scan Control program Setting up times to turn the lasers Or on and off on page 63 in Chapter 4 Select Start gt All Programs gt Agilent gt Scan Control trol Figure 6 Agilent Scan Control icon When the program starts the lasers begin to warm up 22 Agilent G2565CA Microarray Scanner System Scan Control Software 8 5 User Guide Getting Started 2 iray CH 6 Check the Scanner status message at the bottom of the main window Initializing The scanner is initializing When the initialization is Scanner complete the scanner lid unlocks and the lasers continue warming up Lasers are The lasers take about 30 minutes to warm up If you have warming up to wait for the lasers to warm up move on to Step 2 Insert slides into slide holders on page 24
47. ed by the move Call your local Agilent sales and support center for assistance in moving the scanner and assuring proper operation afterwards Agilent recommends that you save your data files directly to the local hard disk Data files may also be saved to a network directory If a network access problem is experienced during the scan data will be saved to a temporary local directory and a warning will be included in the carousel run report 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 If the 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 w The Scan Control program has stopped responding no changes in the status message for more than 15 minutes 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 program Then restart the Scan Control program 2
48. ery software on CD e Power cables and USB cable Agilent G2565CA Microarray Scanner System Scan Control Software 8 5 User Guide 11 1 12 Introduction e Scan Control Software 8 5 e Feature Extraction Software 10 x e Declaration of Conformity Agilent Scan Control Software 8 5 is designed for use with Agilent Feature Extraction Software 9 5 and higher 5 and 10 micron 16 bit scans are backwards compatible with FE 9 5 2 and 3 micron scans and all 20 bit scans require FE 10 x Computer system requirements Check that you have the following required items prior to installing and using Agilent Scan Control software Software e Windows XP Professional with SP2 Windows Vista 32 with SP1 or Windows 7 64 bit e Internet Explorer 5 5 or later Hardware e Pentium IV 3 2GHz or higher e 2 GB RAM required 4 GB RAM required if Feature Extraction software is installed on the same PC e 250 GB available disk space for programs and data generation Agilent G2565CA Microarray Scanner System Scan Control Software 8 5 User Guide Introduction 1 criptio Scanner physical description 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 G2565CA Microarray Scan
49. f this document or of any 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
50. f you have any problems see Chapter 5 for troubleshooting information ot Agilent Technologies 19 2 Getting Started Licensing The Agilent scanner can be ordered in either of two configurations the standard high resolution configuration or with the high resolution capability deleted Without the high resolution license you can select 10 micron 5 micron and 5 micron double pass but the 2 and 3 micron selections are not available If you have purchased the high resolution capability you need the software license to enable this capability In most cases the scanner installation engineer will install the license for you If this is not the case or the capability is purchased later follow the instructions below to redeem the software license Redeeming your high resolution scanning license To redeem your high resolution scanning license 1 Locate the software entitlement certificate SEC that was shipped with the scanner 2 Go to https software business agilent com index stm 3 Select Click here to start software license redemption 4 Follow the instructions to redeem your license Installing your high resolution scanning license When you have received your license via e mail install the license as follows 1 Close the Scan Control software window 2 Locate the license file and place it in the following directory C ProgramFiles Agilent Microarray 3 Restart the Scan Control software The 2 and 3 micr
51. han the other slots and labeled Home 2 Make sure that the tapered end of the slide holder points toward the center of the carousel 3 Make sure that the slide holder is seated in the bottom of the carousel slot Tapered end faces toward center GY f p Figure 16 Carousel Improper placement of the slide holder in the carousel can result in severe damage to the Microarray Scanner 4 If the carousel is already mounted skip to step 5 Otherwise mount the carousel Agilent G2565CA Microarray Scanner System Scan Control Software 8 5 User Guide 29 2 30 Getting Started CAUTION If you have placed the slide holders into a carousel that was removed from the Microarray Scanner follow these steps to remount the carousel a 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 b Make sure that the carousel is firmly seated 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
52. he Scan Progress dialog box it can be found in C Program Files Agilent Microarray Logs CarouselRunLog htm This file is overwritten each time a new carousel run is started Agilent G2565CA Microarray Scanner System Scan Control Software 8 5 User Guide Getting Started 2 After the run is complete you can remove the slides See Step 5 Remove the slides on page 33 View the Carousel Report Log during the run You can also view the Carousel Report Log any time during the carousel run e Click View Report on the Scan Progress dialog box Review the data during or after the run Refer to the Feature Extraction e After the data for one scan is transferred display the file Software Quick Start Guide in the Agilent Feature Extraction software or another included with your scanner program materials If you installed Feature Extraction 10 x on another computer hard drive you must transfer the image files to this drive after the run See Step 5 Transfer files and archive data on page 42 Abort a scan 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 Carousel Run Abort x Q Do you want to abort the carousel run now 3 Click Yes to abort the run now you may lose scan data Click No to abort the run after the current scan is done Click Cancel to cancel your abort command Figure 22 Carousel Run Abort message
53. if Prefix1_Prefix2_ScanNumber_L tif The default Prefix is Instrument Serial but you can select either Slide ID or your own custom prefix The default Prefix2 is Slide ID but you can select Slot Scan Date Time or your own custom prefix Agilent G2565CA Microarray Scanner System Scan Control Software 8 5 User Guide UsingTools 4 E Image File Settings Output path cil Slide description Naming prefix 1 lt Instrument Serial gt Naming prefix 2 lt Customize gt Customized lt Slide ID gt Compress Tiff lt Scan DateTime gt Split rotate image lt Slot gt lt Customize gt Slide ID If selected the entry in the Slide ID cell appears in the filename If lt Auto detect gt is in the Slide ID cell the barcode will appear in the filename Slot The number of the slot in which the scanned slide resides Scan DateTime If you select this option the date and time in format YYYYMMDDHHMM will be used Customize Enter a custom prefix if you select Customize 36 character maximum The Scan Control program automatically assigns the Scan Number The program compares the filename of a new scan with those in the selected data directory If Prefix1_Prefix2 is unique the scan number is set to S01 If a match is found the scan number is increased until the filename is unique Example US4510PP02_251485023883_S03 tif e Instrument Serial US4510PP02 e Slide ID 25148502388
54. ilent HD 61 x 21 6mm Agilent HD 61 x 21 6mm Agilent HD 61 x 21 6mm Agilent HD 61 x 21 6mm Agilent HD 61 x 21 6mm Agilent HD 61 x 21 6mm Slide ID SEE jlentHD_GX_2Color Operator Resolution TIFF RPMT GPMT XDR Output Path Description Sum 20 bit 100 100 lt NoXDR gt D ScanData 5 um 20 bit 100 100 lt NoXDR gt D ScanData Sum 20bit 100 100 lt NoXDR gt D ScanData Sum 20 bit 100 100 lt NoXDR gt D ScanData 5 um 20 bit 100 100 lt NoXDR gt D ScanData Sum 2bt 100 100 lt NoxDR gt D ScanData TT Sum 20 bit 100 100 lt NoXDR gt D ScanData Sum 20 bit 100 100 lt NoXDR gt D ScanData Sum 20 bit 100 100 lt NoXDR gt D ScanData 5 um 20bit 100 100 lt NoXDR gt D ScanData Scan Control main window and scan table with preloaded profile settings An identifier for the slide The Slide ID entries will be used as part of the image file name if specified as part of the file name in the current profile See Naming prefix 1 and Naming prefix 2 on page 56 Automatic entry If your slides have barcodes conforming to the specifications in Barcode and barcode label specifications on page 99 you do not have to enter Slide ID into the scan table before the carousel run The Auto detect function in the Slide ID column means the scanner automatically reads the Agilent supported barcode into the scan table as it scans each slide You also have the choice of e
55. ing up times to turn the lasers on and off To extend the life of the scanner lasers you can enable the Scan Control program to turn the lasers on or off automatically This feature allows you to have the laser warmed up and ready for scanning at a specified time or turned off automatically at a specified time or when idle Regardless of Laser Auto ON OFF settings e You can turn the lasers on or off manually anytime e When you start the Scan Control program the lasers turn on e If the scanner is scanning at the specified turn off time the lasers will remain on Enable the lasers to turn on or off automatically 1 Select Tools gt Laser Auto ON OFF Settings from the menu bar Figure 27 2 Double click No to set Enable laser auto ON OFF to Yes Agilent G2565CA Microarray Scanner System Scan Control Software 8 5 User Guide 63 4 Using Tools Laser Auto ON OFF Settings Enable laser auto ON OFF Yes a Turn ON daily Every day Turn ON at 7 00 AM a E Turn OFF daily Yes Turn OFF at 8 00 PM Turn OFF when idle Yes Idle For hr 1 Turn Lasers on Now Cancel Figure 33 Laser Auto ON OFF Settings properties page If the selection is NO you must turn the lasers on and off manually as described in the next section Turn ON daily Select Weekdays only or Weekends and specify the time for turning the lasers ON on weekdays or weekends Turn OFF daily Select Yes and specify the time for turning the lasers OFF on wee
56. ir or gain access to internal components You might expose yourself to high voltage and harmful laser radiation 72 Agilent G2565CA Microarray Scanner System Scan Control Software 8 5 User Guide Maintaining and Troubleshooting Your System 5 Troubleshooting your system 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 Technical support This topic gives important information about technical support Frequently Refer to this section to learn about solutions to frequently asked questions asked questions related to support and maintenance Hardware This topic describes the indicator lights and how to replace troubleshooting the fuses Software This topic covers the precautions you must take when you troubleshooting use the Recovery CD to recover the software and data on your hard drive Scanner error Refer to this topic to learn about important error messages messages and solutions Agilent G2565CA Microarray Scanner System Scan Control Software 8 5 User Guide 73 5 74 Maintaining and Troubleshooting Your System 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
57. ital measurement that is recorded in the TIFF file Dark offset subtraction At very low signal levels noise can cause negative pixel values Rather than setting these values to zero which results in a biased measurement the Agilent scanner adds a small offset to all pixel values allowing the full pixel distribution to be reported This constant offset is not noise and is removed in a statistically correct manner by Agilent Feature Extraction software Agilent G2565CA Microarray Scanner System Scan Control Software 8 5 User Guide Agilent G2565CA Microarray Scanner System Scan Control Software 8 5 User Guide 2 Getting Started Licensing 20 Redeeming your high resolution scanning license 20 Installing your high resolution scanning license 20 Non Agilent Barcode Licensing 21 Operating the Scanner 22 Step 1 Turn on the Agilent Microarray Scanner 22 Step 2 Insert slides into slide holders 24 Step 3 Load the slide holders into the carousel 29 Step 4 Scan your slides 32 Step 5 Remove the slides 33 Step 6 Set times to automatically turn the lasers off 35 Scanning Your Slides 36 Step 1 Set slot locations 36 Step 2 Set a profile for changing all settings inthe scan table 37 Step 3 Change individual scan settings inthe scantable 38 Step 4 Start the carousel run 39 Step 5 Transfer files and archive data 42 This chapter describes how to operate the scanner including how to set up and scan your slides quickly and easily I
58. kdays and weekends Turn OFF when idle Select Yes and specify a time span of scanner inactivity beyond which the scanner turns off the lasers If No the scanner will not turn off under this condition 3 Click OK Turn the lasers on or off manually 1 Open the Laser Auto ON OFF Settings properties page 2 Click Turn Lasers on Now or Turn Lasers off Now 3 Click OK 64 Agilent G2565CA Microarray Scanner System Scan Control Software 8 5 User Guide UsingTools 4 Additional Tools The following additional tools are available on the Tools menu Unlock Door The unlock door tool Tools gt Unlock Door can be used to attempt to manually unlock the door if the door lock did not operate correctly This can happen for example if the lid is being lifted as the lock operates automatically at the end of a carousel run Reset Calibration Warnings During normal operation the G2505C scanner calibrates the PMTs before every scan and calibrates the lasers during system initialization and after every carousel run If the calibration is unsuccessful or if the calibration changes significantly since the previous time it was performed the scanner software will record that fact and generate warnings in the Carousel Run Log The PMT calibration warning is set when the PMT voltage changes by more than 20 from the previous calibration value The laser calibration warnings are set when the lasers cannot achieve their specified power wi
59. l also reduce scan time and save storage space Agilent provides a scan region suitable for all Agilent High Density and G3 slides and another suitable for scanning full 1 by 3 slides without barcode labels For non Agilent slides you may need to use a custom scan region that better matches the printed region See Create a new scan region with the Scan Region Editor on page 60 Scan resolution Sets the scan resolution pixel size to 2 3 5 or 10 microns m um For 10 micron scans each row of pixels in the TIFF image represents the average of two scan lines one acquired in each direction For 5 3 and 2 micron scans you can select double pass scanning to perform this averaging or acquire only a single scan line for each image row Agilent G2565CA Microarray Scanner System Scan Control Software 8 5 User Guide 49 3 50 Changing scan settings TIFF file Sets the dynamic range to 16 bit or 20 bit The G2565CA dynamic range scanner has extended the dynamic range of the PMT and signal processing electronics By selecting the 20 bit TIFF file option you can access this extended range to enable quantitation of high and low signal features in a single scan The Scan Control software still enables conventional XDR 16 bit scanning as described below Below is a table showing the storage space and scan time for a single and double pass scans for each resolution selected for either a 16 bit TIFF dynamic range or a 20
60. lick OK 7 From the COMX Properties dialog box a Select 19200 as Bits per second b Select None as Flow Control 84 Agilent G2565CA Microarray Scanner System Scan Control Software 8 5 User Guide Maintaining and Troubleshooting Your System 5 COM3 Properties Port Settings Bits per second 19200 Data bits 8 Parity None Stop bits f1 Flow controt D v c Click OK The Scanner HyperTerminal window appears 8 Click File gt Save to save the file to Scanner ht and close the window 9 Click Yes when asked if you want to sever the connection 10 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 Agilent G2565CA Microarray Scanner System Scan Control Software 8 5 User Guide 85 5 86 Maintaining and Troubleshooting Your System 11 Start a HyperTerminal text capture session ao oS 5 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 In the S
61. local Agilent sales and support center Because of the way in which Windows 7 handles connections between the scanner and the PC you need to close the Scan Control software before you turn off the scanner or disconnect the USB cable to the scanner If you don t the Command timed out appears To fix this problem reboot your computer Agilent G2565CA Microarray Scanner System Scan Control Software 8 5 User Guide 77 5 78 Maintaining and Troubleshooting Your System Hardware Troubleshooting 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 74 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 ana ae Status indicator lights Figure 36 Location of the status indicator lights Table 3 describes the actions that you take given the status of the indicator lights Agilent G2565CA Microarray Scanner System Scan Control Software 8 5 User Guide Maintaining and Troubleshoo
62. mage settings This chapter first describes each of the scan table settings then shows you how to change all of them at once or one at a time ot Agilent Technologies 43 3 Changing scan settings Changing Scan Table Settings You can change the scan table settings in two ways A profile is a collection of scanand Change all of the settings at once through profiles image settings that when selected populate the scan table with values you entered in the Profile Editor e Change individual settings through drop down lists in the scan table Although you can change entries in any order you want you may want to change the entries in this order to save some time a If you are scanning non Agilent slides you may want to Create a new scan region with the Scan Region Editor that is more relevant for your slides than the ones offered in the scan table or Profile Editor b Whether you are scanning Agilent or non Agilent slides you may want to Change scan table settings through profiles by selecting a different profile c After selecting a different profile or editing or creating one you can Change individual scan table settings If you select a different profile after changing entries individually the profile entries override the changed individual ones d Be sure to enter Slide IDs either manually or automatically after you have selected a profile You must do this for non barcoded slides You
63. n the 1 Verify that the slide is inserted properly in the slide holder See Step 2 Insert slides into slide holders on page 24 2 Verify that the slide meets the Agilent specifications See Slide specifications on page 98 3 If the problem persists with one slide then something might be wrong with that slide 4 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 Create a new scan region with the Scan Region Editor on page 60 5 Contact your local Agilent sales and support center chip holder Autofocus was unable to retain focus as_ Do the following it travelled to the scan start position 1 Verify that a barcode has not obstructed the scan start position 2 Choose a smaller scan region 3 If the problem persists with one slide then there might be something wrong with that slide 4 Contact your local Agilent sales and support center Cannot eject chip There is already a chip Do the following in the slot 1 Open the scanner lid 2 Remove the slide holder from the home slot Cannot load chip moving the arm may be Do the following unsafe 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 If the problem persists contact your local Agilent sales and support center Command timed out Do the
64. ner cautions 72 naming files automatic 56 Agilent G2565CA Microarray Scanner System Scan Control Software 8 5 User Guide Index naming prefix 1 and 2 56 network drive 38 51 76 non Agilent barcode licensing 21 non Agilent slides creating scan region 59 0 opening the scanner lid 76 operating principles 17 operating scanner 22 output directory selecting 51 output path setting 51 P parts list of 11 power supply fuses 80 preparation of site 14 principles of operation 17 dark offset subtraction 18 fluorescence detection 18 laser excitation 17 scanning 17 slide positioning 17 profile definition 37 44 Profile Editor 54 55 profile settings compressing TIFF 57 naming prefix 1 and 2 56 not in scan table 56 splitting rotating image 58 profiles 54 changing settings 45 creating 56 editing 55 rear view of scanner 14 recovery CD 87 recycling and disposal 102 regulatory information acoustic noise 102 electromagnetic interference 102 recycling and disposal 102 removing scanner covers 72 removing slides 33 Report Log 41 S safety guidelines 16 regulations 103 symbols for scanner 15 safety symbols 15 scan dimensions 98 Scan Progress dialog box 39 scan region area 49 changing for non Agilent slides 61 creating for non Agilent slides 59 definition 59 Scan Region Editor 54 59 creating new scan regions 59 60 editing existing scan regions 61 starti
65. ner System Scan Control Software 8 5 User Guide 13 1 Introduction Scanner rear view Air vent Power fuses holder Line voltage indicator window Line voltage setting ower plug socket USB Connection Laser fuse holder Figure 4 Microarray Scanner Rear View Site preparation Make sure the environment meets the Microarray scanner specifications on page 96 of Chapter 6 If you have any questions contact your local Agilent sales and support center or www agilent com chem dnasupport 14 Make sure the access lid has sufficient clearance Place on sturdy lab bench or table Agilent G2565CA Microarray Scanner System Scan Control Software 8 5 User Guide 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 G2565CA Microarray Scanner System Scan Control Software 8 5 User Guide 15 1 16 Introduction Safety guidelines
66. ng 59 scan regions 54 creating 60 editing 61 scan report 41 scan resolution 49 scan settings automatic file naming 56 change 44 changing in scan table 38 split and rotate image 58 scan slot 39 scan table settings changing 44 changing individual 46 changing through profiles 45 dye channels 49 output path 51 red and green PMT gain 51 resetting to current profile values 47 scan region 49 scan resolution 49 sensitivity level PMT 51 slide description 52 slide ID 48 TIFF file dynamic range 50 XDR ratio 51 scan time 40 97 scan definition 32 scanner electromagnetic interference 102 initializing 22 maintenance tasks 68 to 70 moving 72 specifications 96 stopping during scan 41 turning on 22 warning on removing covers 72 scanner lid opening 76 scanning 17 scanning slides 32 36 selecting a profile 37 setting slot locations 36 starting the carousel run 39 scans storage space and scan time table 50 selecting a profile 37 sensitivity level PMT setting 51 serial number scanner 74 75 setting slot locations 36 signal to noise performance 17 site preparation 14 slide ID 48 slide positioning 17 slide specifications glass slide 98 scan dimensions 98 slides description for scanning 52 inserting into carousel 24 inserting into slide holders 24 jammed 77 removing 33 scanning 32 specifications 98 software icon 22 main window 23 maintenance 68 not re
67. ntering Slide ID manually Manualentry You must enter IDs for non barcoded slides or slides with unsupported barcode formats using the keyboard or an appropriate external barcode reader Agilent G2565CA Microarray Scanner System Scan Control Software 8 5 User Guide Changing scan settings 3 If you enter the ID through the keyboard double click the Slide ID cell first before typing in the barcode or a unique text identifier Check for Agilent supported barcodes and empty slots To view the Agilent supported barcodes and check for empty slots in the Slide ID column you click Tools gt Carousel Check The program first checks the carousel for empty slots and places No chip in each Slide ID cell with no slide Then the program reads the barcodes for all the slides and places them in the Slide ID cells 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 does reduce file size up to a factor of 2 Scanregion 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 barcode or other non transparent border areas of the slide and affecting the scanner s ability to autofocus properly Minimizing the scan region wil
68. on Agilent HD 2 color gene expression microarrays Agilent HD 1 color gene expression microarrays Agilent HD CGH CNV ChIP microarrays Agilent HD miRNA microarrays Agilent G3 CGH CNV ChIP microarrays You can also create new profiles from existing ones You may need to scan microarray regions not installed by default To create new ones you use the Scan Region Editor To extend the lifetime of the lasers you set up times for the system to automatically turn the lasers on and off with this dialog box Agilent G2565CA Microarray Scanner System Scan Control Software 8 5 User Guide UsingTools 4 Creating Editing profiles using the Profile Editor Edit an existing profile You can edit and save an existing profile Or you can edit an existing profile and save the edits to a new profile name See Create a new profile on page 56 1 Select Tools gt Profile Editor from the menu bar Figure 28 Profile Editor Note that you can never remove 2 Select a profile to edit the lt default gt profile from the list 3 You can remove all others including any profiles you create from the lt default gt profile 4 Click Save Figure 27 Profile Editor Current Profile lt Default gt 8 Description a Dye channel Scan region Scan resolution Tiff File dynamic range Red PMT gain Green PMT gain XDR Ratio Output path Slide description Naming prefix 1 Naming prefix 2 Compress Tiff Split rotate image Import
69. on may be unstable Using last known PMT setting PMT calibration lost Using factory default settings Slide skipped because it is outside the allowable thickness range or the selected scan region contains an obstruction to the initial focus positions The autoloader loading arm is in an unknown location It is unclear if it is safe to move the carousel The chip carousel is not present Please place the carousel in the scanner and try again 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 If you 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 Go to the Scan Control main menu and set the output directory to another directory on another hard drive Delete or transfer files from the current hard drive See Step 5 Transfer files and archive data on page 42 You can reset this warning using the Reset Calibration Warnings tool See Additional Tools on page 65 If this warning persists or reoccurs contact your local Agilent sales and support center
70. on selections will now be available 20 Agilent G2565CA Microarray Scanner System Scan Control Software 8 5 User Guide Getting Started 2 Non Agilent Barcode Licensing If you need to scan non Agilent barcodes in 2 or 3 micron resolution contact Agilent for a special no charge license for accessing this capability Without this license if a slide barcode is not present or not recognized by the scanner as an Agilent array and the array is to be scanned in either 2 or 3 micron resolution the scanner will skip the slide and report the following message Scan settings or slide is not supported by the current scanner license Contact Agilent via pdl non_ag_barcode agilent com to obtain license to scan non Agilent barcodes in high resolution Obtaining and installing a non Agilent barcode license 1 Send an e mail to PDL non_ag_barcode agilent com with your scanner serial number in the body of the e mail and one will promptly be sent to you This license will need to be renewed annually 2 Once you receive your license place the license in the following directory C ProgramFiles Agilent Microarray directory 3 Close and re open the Scan Control software The scanner will recognize the new license Agilent G2565CA Microarray Scanner System Scan Control Software 8 5 User Guide 21 2 Getting Started Operating the Scanner Step 1 Turn on the Agilent Microarray Scanner 4 Turn on the Microarray Scanner using th
71. ons lt 1 pixel at 5 micron resolution 5 CV global non uniformity average local non uniformity is typically 1 based upon 100um features Table5 Scan Time for Single and Double Pass Scans for Agilent HD Scan Region 61 x 21 6 mm Resolution Scan Time min 2 micron single pass 20 3 micron single pass 15 5 micron single pass 8 10 micron single pass 8 2 micron double pass 40 3 micron double pass 30 5 micron double pass 16 Single scan 16 bit dynamic range gt 104 Single scan 20 bit dynamic range gt 10 Dual scan extended dynamic range XDR gt 10 Agilent G2565CA Microarray Scanner System Scan Control Software 8 5 User Guide 97 mensions are iece of glass 1 9 A 21 6 AA the lower right side int is ed in Figure 40 All d fi ion is speci ters and the reference po The scan reg in millime of the glass 76 2 0 25 1 4 imensions RR STi Scan d jeqe7 epooeg lp in nomina insic fluorescence 1NS1C 61 0 d out of the carousel These slide holders 60 0 No mirrored slides Index of refraction from 1 510 to 1 515 microarrays in an e 3 inches long 76 2 mm 0 25 mm or 1 4 mm e inch wide 25 4 mm 0 45 mm or 0 7 mm e 1 mm thick 0 1 mm e High quality with low intr The microarray scanner uses slide holders to move the The detailed specifications of the glass are as follows are designed to accept a 1 in x 3
72. ooting 87 Microarray Scanner Error Messages 88 This chapter provides maintenance and troubleshooting information for the Agilent G2565CA Microarray Scanner System ee Agilent Technologies 5 Maintaining and Troubleshooting Your System Maintaining your system 68 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 These sections describe the software and hardware maintenance maintenance tasks that you need to perform on a regular tasks basis to keep the microarray scanner operating efficiently Tips to prevent This section presents hints on the operation and care of the problems microarray scanner to help you avoid problems Scheduled software 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 Agilent G2565CA Microarray Scanner System Scan Control Software 8 5 User Guide Maintaining and Troubleshooting Your System 5 Scheduled hardware maintenance Perform these tasks to help maintain the performance of you
73. or you may damage the instrument 5 Optional Place the carousel cover onto the carousel until the two side tabs snap into place Home slot Figure 17 Carousel cover 6 Close the scanner lid Agilent G2565CA Microarray Scanner System Scan Control Software 8 5 User Guide Getting Started 2 You cannot do any of the following tasks until you close the lid Initialize the scanner Check the carousel for empty slots gt Read barcodes before the carousel run Start a carousel run Stationary alignment pins Stationary alignment pin slots Movable alignment pin Movable alignment pin slot Figure 18 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 G2565CA Microarray Scanner System Scan Control Software 8 5 User Guide 31 2 Getting Started Step 4 Scan your slides A scan refers to creating animage of Follow the steps below to prepare your slides for scanning the probes ona single slide A carousel and start the carousel run See the next section Scanning run refers to scans of allofthe Your Slides for more detailed instructions specified slides in the carousel Step 1 Set slot locations on page 36 Step 2 Set a profile for changing all settings in the scan table on page 37
74. ot solve the problem contact your local Agilent sales and support center 94 Agilent G2565CA Microarray Scanner System Scan Control Software 8 5 User Guide Microarray scanner specifications Slide specifications Regulatory information Input voltage check Agilent G2565CA Microarray Scanner System Scan Control Software 8 5 User Guide 6 Reference Microarray scanner specifications 96 Slide specifications 98 Regulatory information 102 Input voltage check 105 This chapter includes specifications regulatory information and instructions for checking the voltage if you move the instrument 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 barcode 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 In this section you can make sure the input voltage is correct after a move ee Agilent Technologies 95 6 Reference Microarray scanner specifications Approximate dimensions Weight Power input Fuses Temperature range Humidity Altitude Usage Laser information 96 Agilent G2565CA Microarray Scanner System Scan Control Software 8 5 User Guide The microarray scanner
75. r 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 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 34 Opening and removing the air filter access door 3 Remove the air filter from the door housing and inspect the air filter visually Agilent G2565CA Microarray Scanner System Scan Control Software 8 5 User Guide 69 5 Maintaining and Troubleshooting Your System Air filter access door Figure 35 Removing the air filter Cleaning the 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 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
76. rray scanner The power supply fuses are directly above the power cord plug The laser fuse is located in a circular fuse holder to the left of the power cord plug The fuses can be ordered directly from Agilent Technologies Always disconnect the power cord before checking or replacing the fuses CAUTION 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 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 3 Pull out the fuse holder and check the fuse integrity 4 If a fuse is blown replace the fuse with a T4A 250 VAC rated fuse Part 2110 1309 5 Push the fuse holder back in until it clicks into place 6 Plug in the power cord 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 G2565CA Microarray Scanner System Scan Control Software 8 5 User Guide Maintaining and Troubleshooting Your System 5 Power supply fuse holder Figure 37 Removing the fuse holder for the power supply Checking and replacing the red laser fuse If the microarray scanner can be powered on but the red laser is no
77. sponding 76 starting 22 system requirements 12 specifications 15 barcodes 99 Microarray Scanner 96 split and rotate tiff image 58 splitting rotating image 58 110 Agilent G2565CA Microarray Scanner System Scan Control Software 8 5 User Guide Index starting software 22 status indicator lights 13 78 79 status in Scan Progress dialog box 39 stopping the scan 41 support technical 74 system features 10 T technical support 74 changing URL to reach 74 technical support calling 74 temperature considerations 71 TIFF file dynamic range 50 tiff image split and rotate 58 top view of scanner 13 transferring files 42 troubleshooting autoloader arm extended into carousel 82 capturing diagnostic data 83 error messages 88 to 94 FAQs 76 hardware 78 to 81 replacing fuses 80 to 81 technical support 74 using recovery CD 87 with status indicator lights 78 V version information finding 75 view report 41 voltage check 105 voltage setting input 105 X XDR ratio 51 Agilent G2565CA Microarray Scanner System Scan Control Software 8 5 User Guide 111 www agilent com Information descriptions and specifications are subject to change without notice For updated information on Agilent products please go to http genomics agilent com Agilent Technologies Inc 2010 June 2010 G2505 90021 Revision A opie Agilent Technologies
78. t G2565CA Microarray Scanner System Scan Control Software 8 5 User Guide Maintaining and Troubleshooting Your System 5 Please make a note of the serial number of your Agilent Microarray Scanner the software version 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 Scanner information Model Serial Installation Date Software Version Software Update Version Date Software Update Version Date Find the version information for scanner software 1 Select Help gt About from the menu bar to find version information 2 To close the program click OK Agilent G2565CA Microarray Scanner System Scan Control Software 8 5 User Guide 75 5 Maintaining and Troubleshooting Your System Frequently Asked Questions FAQs Table2 FAQs The following are frequently asked questions FAQs and the corresponding answers that can help you operate and maintain the Agilent Microarray Scanner System and troubleshoot issues that occur FAQ Answer want to move the microarray scanner to another area Can I save files over the network while scanning Where do I find support information such as drivers guides and troubleshooting solutions for my PC workstation cannot open the top lid to access the carousel The Scan Control program does not respond Scanner performance could be adversely affect
79. t on you can easily check and replace the laser fuse from the rear of the unit 1 Disconnect the power cord 2 Use a small flat edge screwdriver to unscrew the small plastic circular cap until it releases Agilent G2565CA Microarray Scanner System Scan Control Software 8 5 User Guide 81 5 Maintaining and Troubleshooting Your System CAUTION Laser fuse holder Figure 38 Laser fuse holder location 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 Part 2110 0458 5 Push the fuse holder back into place and screw on the cap Troubleshooting an autoloader arm extended into the carousel 1 Turn off the scanner 2 Rotate the carousel and push the arm back into position If this does not work call your local Agilent sales and support center for instructions Removing the carousel when the slide holder autoloader arm is extended into the carousel will cause serious damage to the microarray scanner 82 Agilent G2565CA Microarray Scanner System Scan Control Software 8 5 User Guide Maintaining and Troubleshooting Your System 5 Using HyperTerminal to Capture Diagnostic Data Agilent service personnel and users can capture information for troubleshooting the scanner by setting up a HyperTerminal session These instructions apply to Windows XP systems For instructions on capturing diagnostic data for scanners operating on Windows Vista
80. the like that if not 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 G2565CA Microarray Scanner System Scan Control Software 8 5 User Guide 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 and preparation for its operation 2 Getting Started In this chapter learn how to safely operate the Microarray Scanner and learn how to set up and then scan slides with the Agilent Scan Control program 3 Changing Scan Settings Learn what the scan settings do and when and how to change them 4 Using Tools In this chapter learn how to set up profiles groups of scan settings scan regions and laser auto On Off times 5 Maintaining and Troubleshooting Your System This chapter describes maintenance procedures and tips as well as error messages for troubleshooting your system 6 Reference This chapter presents slide specifications and regulatory compliance information Agilent G2565CA Microarray Scanner System Scan Control Software 8 5 User Guide 3 Agilent G2565CA Microarray Scanner System Scan Control Software 8 5 User Guide Contents 1 Introduction 9 A powerful tool for microarray analysis 10 System
81. thin 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 Error Message Description or Solution Application Is Already Running Autofocus error Did not detect two reflective surfaces during home You cannot run two copies of the Scan Control program at the same time 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 24 or try another slide holder 2 Verify that the slide meets the Agilent specifications See Slide specifications on page 98 3 If the problem persists with one slide then something might be wrong with that slide 4 If needed select or create an appropriate 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 Create a new scan region with the Scan Region Editor on page 60 5 Contact your local Agilent sales and support center Agilent G2565CA Microarray Scanner System Scan Control Software 8 5 User Guide 89 5 Maintaining and Troubleshooting Your System Table 4 Error Messages continued Error Message Description or Solution Autofocus error No PSD signal is Do the following detected Make sure there is a slide i
82. thin the warm up period If this occurs the system sets the warning and recalibrates the lasers at 80 of their specified power The Scan Control program scales the TIFF file to compensate for the lower laser power You can reset these warnings by selecting Tools gt Reset Calibration Warnings If the next calibration is again unsuccessful and the warnings reappear you should contact your local Agilent sales and support center Agilent G2565CA Microarray Scanner System Scan Control Software 8 5 User Guide 65 4 66 Using Tools Extended Laser Calibration Normal calibration of the lasers does not measure the maximum power output The extended laser calibration tool performs a more comprehensive check of the laser subsystem If you are receiving repeated laser calibration warnings Agilent support may request that you use the extended laser calibration tool then e mail the log files containing the results Agilent G2565CA Microarray Scanner System Scan Control Software 8 5 User Guide Agilent G2565CA Microarray Scanner System Scan Control Software 8 5 User Guide 5 Maintaining and Troubleshooting Your System Maintaining your system 68 Scheduled software maintenance 68 Scheduled hardware maintenance 69 Tips to prevent problems 71 Troubleshooting your system 73 Technical Support 74 Frequently Asked Questions FAQs 76 Hardware Troubleshooting 78 Using HyperTerminal to Capture Diagnostic Data 83 Software Troublesh
83. ting Your System 5 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 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 Use operation HyperTerminal to capture diagnostic information See Using HyperTerminal to Capture Diagnostic Data on page 83 Off Flashing Off Attempting to connect to PC Install Scan Control Software 8 0 if 20 sec off 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 up and Wait Maximum warm up time is 30 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 and support center Agilent G2565CA Microarray Scanner System Scan Control Software 8 5 User Guide 79 5 80 Maintaining and Troubleshooting Your System 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 microa
84. try again Figure 39 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 74 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 Scan your slides on page 32 of Chapter 2 e Errors before the scan starts are shown in message boxes e Some errors during the scan are shown in the Status message in the Scan Progress dialog box Agilent G2565CA Microarray Scanner System Scan Control Software 8 5 User Guide Table4 Error Messages Maintaining and Troubleshooting Your System 5 e Error messages are logged in the Carousel Report Log as the carousel run progresses See View the Carousel Report Log during the run on page 41 of Chapter 2 We recommend that you check the Report Log at least after the first scan and when the carousel run is completed The report is automatically generated at the end of a carousel run Troubleshooting with error messages The Agilent Microarray Scanner System creates error messages to help you solve issues that may arise Many of the error messages include a solution wi
85. uding Amendment 1 1992 and Amendment 2 1995 Agilent G2565CA Microarray Scanner System Scan Control Software 8 5 User Guide 103 6 104 Reference Barcode and barcode label specifications Pollution Degree 2 Installation Category II e Class 1 Equipment requires a grounding system e Class 1 Laser Product e UL CSA Approved Product Agilent G2565CA Microarray Scanner System Scan Control Software 8 5 User Guide Reference 6 Input voltage check Verify input voltage Before turning on the microarray scanner for the first time or after it has been moved to another site verify that the 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 e 100 VAC e 120 VAC e 220 VAC e 240 VAC 1 Go to the rear of the microarray scanner 2 View the input voltage setting through the small window Input voltage setting view window Figure 43 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 change the voltage setting Agilent G2565CA Microarray Scanner System Scan Control Software 8 5 User Guide 105 6 Reference Change the voltage setting 1 Disconnect the power cord WARNING Always disconnect the power cord before changing the input voltage setting 2 Use a small flat e
86. um scan region the longer the scan time Scan region of 71 mm x 21 6 mm The new region appears as a regions vary because of factors suchas selection in the scan table and in the Profile Editor barcode label placement and size and areas with frosted glass Start the Scan Region Editor From the Scan Control main window e Select Tools gt Scan Region Editor from the menu bar Figure 27 Agilent Technologies Scan Region Editor JA e x File Help QIE Xx 2 Scanner G2505C been ee ee nee WIDTH I Scan Region H 3 10 1 90 E Min upper left comer G 5 H Max lower right comer Ti 74 20 23 50 11 E Slide Ne Slide Holder Fast 61 x 2 mm 11 00 2 00 FastMiddle 11 00 10 90 61 00 2 00 Fast 1mm 3 10 1 90 71 00 2 00 PGWTest1 11 00 1 90 61 00 2 00 PGWTest2 11 00 1 90 61 00 2 00 fad Figure 29 Scan Region Editor Agilent G2565CA Microarray Scanner System Scan Control Software 8 5 User Guide 59 4 60 Using Tools From the Start menu e Select Start gt Programs gt Agilent Life Sciences gt Scan Region Editor on the taskbar You cannot access the Scan Region Editor 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 Create a new scan region with the Scan Region Editor When creating a new scan region or using existing scan regions make
87. upport folder create a new folder and call it HyperTerminal Capture Files In the HyperTerminal Capture Files folder type the filename Capture yymmdd in the filename text box where yymmdd represents today s date and represents the number of the capture session for that day Click Save Click Start in the Capture Text dialog box ajx Folder C Documents and Settings david_baker My File final Capture Fies Capture 060105 1 TXT Browse F 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 Start a HyperTerminal capture session after initial set up If the lasers are warmed up skip to step 3 1 Turn on the scanner to start initialization 2 Start the Scan Control program to warm up the lasers 3 Double click on the Desktop Scanner ht icon Agilent G2565CA Microarray Scanner System Scan Control Software 8 5 User Guide Maintaining and Troubleshooting Your System 5 4 From the HyperTerminal Transfer drop down menu click Capture Text 5 In the Capture Text dialog a Change the filename in the File text box to reflect today s date and capture session b Click Start Folder C Documents and Settings david_baker My File final Capture Fies Capture 06010 TXT Browse cma You can also click Browse to open the Select Capture File dialog box
88. urface Ledge of slide holder Figure 10 Proper placement of slide on ledge Agilent G2565CA Microarray Scanner System Scan Control Software 8 5 User Guide 25 2 Getting Started 5 Align the slide with the slide holder following these two rules The end without the barcode 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 barcodes one on each side of the glass See Figure 11 Typically non Agilent slides have only one barcode Place the active microarray side of the slide facing toward the slide holder cover See Barcode and barcode label If you have a slide whose spotted array is on the opposite specifications on page 99 to apply side of the slide as the barcode the scanner cannot read a second readable barcode the barcode CAUTION An improperly inserted slide can damage the Microarray Scanner Double barcoded slide example Inactive Glass Surface SIDE 1 cn Sum s EE Sm N oa Active Active Microarray Microarray Surface Surface SIDE 2 Figure 11 Slide orientation 26 Agilent G2565CA Microarray Scanner System Scan Control Software 8 5 User Guide Getting Started 2 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

Agilent G2565CA Microarray Scanner System (Scan Control Software 8.5) User Guide

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