ClearScan™ USER MANUAL
Contents
1. Meaning of visual and audio signals Four LED pictograms on the front of the scanner and a buzzer keep the user informed about the scanner s status at all times See below for the meaning of the pictograms Meaning of icon power on connecting microarray read present gt Vac technical problem Version 1 1 4 March 2013 tel 44 0 1223 885905 e support cambridgebluegnome com 14 es BlueGnome Information displayed ClearScan USER MANUAL status LED on flashing slowly flashing rapidly beep scanner on powering up switching on power rs end of power up sequence scanner ready to connect short connecting dn connection sequence completed scanner ready to take a slide long disconnecting G GIGGGG short slide inserted scanner ready to read ech reading Les reading completed slide ready for removal W gt 3 short technical problem A 3 long In the event of a technical problem the scanner must be switched off and Technical Support contacted immediately Version 1 1 4 March 2013 tel 44 0 1223 885905 e support cambridgebluegnome com Oo BlueGnome ClearScan USER MANUAL Operating the scanner The ClearScan scanner is designed for use with BlueGnome s microarray slides only Only insert ISO 8037 1 compliant microscope slides into the de2. To display the information about the scanner you are working on click on the about the scanner option situated on the scanner tab of the main menu S mation on the scanner Majorities Scanner type bg710 Number of channels Serial number 712003 Version number Scan area x 20000m 24000pm pitch sum 40pm Oum gt 74000pm pitch Sum 40m Network configuration Clearscan IP Address 192 168 0 254 Blue snome MAC Address 00 50 c254b1 2d dog faa eral Broadcast 192 168 0 255 Gateway Dep Arm drData drSerie1 Hard Camino Laser 635 P Gm 1 Ori Laser 532 P Gm 1 Ori Information on the connected scanner including the version of the software currently used is displayed Slide detection in the autoloader ClearScan Auto If your scanner has an autoloader system you can load your slides in the autoloader s holder and the ClearScan software will automatically detect the position in which the slides are loaded slides needn t be loaded in sequential order Once the ClearScan Auto scanner is connected to the ClearScan software the auto loader zone appears on the right hand side of the user interface To detect slides and their location click on bd read loader icon Once slides have been detected they can be selected or deselected for subsequent processes using the check box adjacent to the slide name or by Select all or deselect all Version
3. powered up before use so that the lasers have time to achieve thermal stability which improves laser performance and improves the lasers lifespan e Placing a microscope slide in the insertion port located on the instrument front panel The barcode and microarray spots must be on the same face of the slide i e upwards as shown in the previous illustration Version 1 1 4 March 2013 tel 44 0 1223 885905 e support cambridgebluegnome com 17 3 BlueGnome ClearScan USER MANUAL Two rails guide the slide in by gripping it by the edges The insertion mechanism is designed not to damage the slide or the array spots deposited on it Gently insert the slide until you feel resistance The microarray presence detector identifies that a slide has been inserted and the microarray present LED comes on indicating that the scanner is ready to read the sample NOTE Any other use of the scanner may be dangerous or may harm the scanner Do not attempt to loosen screws or insert any object other than slides complying with ISO standard 8037 1 Operating the ClearScan Auto The ClearScan Auto is simple to operate The only direct user actions required without using the software are e Powering up switching off the scanner using the on off button located on the instrument rear panel When the scanner is powered up it performs a sequence of self tests and will indicate any malfunction via the Technical Problem LED The
4. 46 es BlueGnome ClearScan USER MANUAL The lasers are on when the scanner connects and are off when it disconnects from the ClearScan software To economize the lifetime of the lasers it is advisable to disconnect the scanner when it is not being used for long periods of time An automatic disconnection feature is available the default setting is to disconnect the scanner following a 30 minute period of inactivity A read of a 24sure or CytoChip Focus slide with the following parameters lasts 4 5 minutes e pixel size 10um e speed 20 lines s e read area preconfigured array area No speed is preset for optimal results with CytoChip and 24sure arrays No the pixel size is preconfigured for the BlueGnome slides that can be scanned for a 24sure or CytoChip Focus scan the pixel size is 10 um for a CytoChip Oligo slides the pixel size is 4 um median We use digital detection because it provides results with better signal to noise ratios due to very low background noise Detection is performed by fast extremely sensitive photomultipliers PMT Yes detection gain may be modified from 0 to 100 The gain variation is linear allowing the user to adjust this setting very precisely It may be useful to cancel out saturation or to equalize channels for instance The scanner features a high precision mechanical positioning system based on a patented real time control loop Absolute positioning is typically 10 um over the entire slide
5. Your breach of any term contained herein and You shall cease use of and destroy all copies of the Software The disclaimers of warranties and damages and limitations on liability shall survive termination ClearScan software uses F2D SAFIR software F2D SAFIR software was created by INRA and INRIA IRISA Rennes 2008 Some parts of ClearScan software are based on the Open source software programs listed below Each included Open source software program is displayed followed by the license he refers to Note that the terms software and program refer to the corresponding Open source software program i Text Version 2 1 4 subject to Mozilla Public License 1 1 JAI Java Advanced Imaging Version 1 1 subject to Binary Code License Agreement Jcommon Version 1 0 10 subject to GNU LESSER GENERAL PUBLIC LICENSE JFreeChart Version 1 0 6 subject to GNU LESSER GENERAL PUBLIC LICENSE jh Version 2 0 3 subject to GNU General Public License jhall Version 2 0 3 subject to GNU General Public License jhbasic Version 2 0 3 subject to GNU General Public License jsearch subject to GNU General Public License I2fprod common all Version 7 3 subject to Apache Public License 2 0 laf subject to Apache Public License org apache commons logging Version 1 0 4 subject to Apache Public License 2 0 PDFRenderer subject to GNU LESSER GENERAL PUBLIC LICENSE BlueGnome an Illumina company Version 1 1 4 March 2013 tel 44 0 1223 885905 e support cambri
6. scanner will then proceed with the scan and the image can be viewed in realtime as the scan proceeds The current status of the scanner the scan resolution and the scan time remaining are also displayed at the bottom of the screen Ky ClearScan no_Hame Image Window 1 n r Scanner J Wes To Imagi window IS B0 8 B208 I ALI EE 1220222 sal Fitto the width of the page Fitto the page A Real size 4 Zoom mode O Walk mode Mur Left ciek Murs Cin left click n D 3 J 171 scan resolution barcode time remaining Zoom in to a region of interest directly in the image window by using the mouse Click and drag to select area to view and zoom in Right click with the mouse reveals a context menu that also allows navigation around the image Version 1 1 4 March 2013 tel 44 0 1223 885905 e support cambridgebluegnome com 35 es BlueGnome ClearScan USER MANUAL The histogram Click on the P histogram icon on the main toolbar to display the histogram window The histogram provides the user with the signal intensities for each fluorescent channel and you visualize the number of saturating pixels in each channel Using the histogram you can assess whether the signals for each channel are well balanced if scanning in manual mode laser intensity and PMT gain can be modified in the scan parameters accordingly When both channels
7. window in the side pane where you can choose the image display options displayed values are those used in the last ClearScan session These options can be used to adjust image brightness contrast and to adjust the proportion of red or green in the ratio image by using balance control Display optio ns brightness contrast Brightness 40 Contrast 20 NOTE Changing these options only affect the way an image is displayed Display options have no effect on results or image data NOTE When an image is acquired by a ClearScan scanner pixel depth is 16 bits resulting in pixel values range from 0 to 65535 However the hardware limitations of standard graphics boards means that images are only displayed with an 8 bit pixel depth meaning that on screen pixel values range from 0 to 255 The software uses the 16 bit values for processing the images 8 bit images are only used for display purposes Image information Selecting the image information window on the side pane allows users to view the pixel intensity of selected areas of the scanned image By hovering over the image with the mouse a zoomed in image of the selected feature together with the signal intensity and the pixel coordinates are revealed Version 1 1 4 March 2013 tel 44 0 1223 885905 e support cambridgebluegnome com 38 es BlueGnome Image informations x Y po 4820 28930 Wavelength 635 P 12657
8. 013 New logo added computer hardware specs on p 20 included updated to include details of the updated ClearScan software version 2 0 Version 1 1 4 March 2013 tel 44 0 1223 885905 e support cambridgebluegnome com 52 es BlueGnome ClearScan USER MANUAL Software License agreement IMPORTANT PLEASE READ THE TERMS AND CONDITIONS OF THIS LICENSE AGREEMENT CAREFULLY BEFORE USING THE SOFTWARE BLUEGNOME AND OR ITS SUBSIDIARIES IS WILLING TO LICENSE THE SOFTWARE TO YOU AS THE INDIVIDUAL THE COMPANY OR THE LEGAL ENTITY THAT WILL BE UTILIZING THE SOFTWARE REFERENCED BELOW AS YOU OR YOUR ONLY ON THE CONDITION THAT YOU ACCEPT ALL OF THE TERMS OF THIS LICENSE AGREEMENT THIS IS A LEGAL AND ENFORCEABLE CONTRACT BETWEEN YOU AND BLUEGNOME BY OPENING THIS PACKAGE BREAKING THE SEAL CLICKING THE ACCEPT OR YES BUTTON OR OTHERWISE INDICATING ASSENT ELECTRONICALLY OR LOADING THE SOFTWARE YOU AGREE TO THE TERMS AND CONDITIONS OF THIS AGREEMENT IF YOU DO NOT AGREE TO THESE TERMS AND CONDITIONS CLICK THE I DO NOT ACCEPT OR NO BUTTON OR OTHERWISE INDICATE REFUSAL MAKE NO FURTHER USE OF THE SOFTWARE AND CONTACT BLUEGNOME CUSTOMER SERVICE FOR INFORMATION ON HOW TO OBTAIN A REFUND OF THE MONEY YOU PAID FOR THE SOFTWARE LESS SHIPPING HANDLING AND ANY APPLICABLE TAXES AT ANY TIME DURING THE SIXTY 60 DAY PERIOD FOLLOWING THE DATE OF PURCHASE 1 License The software and documentation that accompanies this li
9. 1 1 4 March 2013 tel 44 0 1223 885905 e support cambridgebluegnome com 29 es BlueGnome ClearScan USER MANUAL If the shutter of the auto loader is opened and closed again the will need to be selected again to re detect the slides ClearScan no_Hame Ca a n E 3 5 Ky Imagi rv vindow o Gm preview 41 LEE Rex read loader icon e Sie 1 e Ste 2 e Ste 3 Hl Side 4 Hl Side 5 Kl Side 6 Lal Sie 7 a Ste 8 Li Ste 9 Hl Side 12 Kl Side 13 Kl Side 14 kl Sie 15 e Sie 16 e Sie 17 Side 20 e Side 24 Side 22 Side 23 Side 24 It is possible to select a single slide for scanning by hovering the mouse over the slide name Scan or preview icons will then be revealed Slide 2 Start Scar Once the slides are selected the scanning processes for the ClearScan Auto proceed in the same way as the ClearScan NOTE To enable scanning of your slides you have to perform the detection step Only once the slides are detected will the Previews and Scan icons become visible Version 1 1 4 March 2013 tel 44 0 1223 885905 e support cambridgebluegnome com 30 es BlueGnome ClearScan USER MANUAL Scanning Upon insertion of the microarray slide the barcode is automatically read If it is not recognised scanning will not proceed If it is the scanning parameters scan areas speed resolution etc for th
10. 2013 tel 44 0 1223 885905 e support cambridgebluegnome com 4 es BlueGnome ClearScan USER MANUAL The following information is also present Attention laser radiation inside Attention dangerous voltage inside Attention read carefully instructions for use Separate collection for the electrical and electronic equipment 2012 04 712001 ClearScan BGOF1 Date of manufacture Serial number Scanner model with or without Autoloader system Version number of the instrument Version 1 1 4 March 2013 tel 44 0 1223 885905 e support cambridgebluegnome com Ge BlueGnome an Illumina company ClearScan USER MANUAL Pictograms are associated to each connector to explain its function DIAGNOSTIC RS232 port used for diagnostic issue Ethernet RJ45 port Mains power socket Current amp rating of fuse to be replaced Version 1 1 4 March 2013 tel 44 0 1223 885905 e support cambridgebluegnome com es BlueGnome ClearScan USER MANUAL Safety important information Only qualified personnel who know and understand the safety warnings and precautions described in this document may be authorised to use the ClearScan scanner Use for any purpose other than the purpose indicated in this manual exposes the user to serious hazards Caution use of controls or adjustments of procedures other than those specified herein may result in hazardous radiation exposure The following safet
11. 905 e support cambridgebluegnome com 42 es BlueGnome ClearScan USER MANUAL Scanner self tests and checks The scanner runs three levels of self tests and checks Initialization checks When the scanner is powered up the LEDs light up as indicated in the section Meaning of visual and audio signals Moving parts detectors laser power and the ethernet port are all checked If an error is detected three long beeps sound and the red LED indicating a technical problem lights up If this happens switch off the scanner immediately and contact Technical Support During slide scanning laser power and the autofocus are checked constantly The scanner will report if either of these controls did not function correctly as this can produce errors If such errors keep recurring refer to the Troubleshooting section ClearScan slide check You can also check the scanner more precisely if you so wish Insert the ClearScan Test slide provided with your scanner and run a check from the Scanner gt Check scanner menu in the ClearScan software The fluorescence signal image red green shift crosstalk and detection gain linearity are all checked The fluorescence signal and red green shift are compared to a reference value and to values obtained when the last check was run A data integrity check is also performed The scanner will indicate if any malfunction is detected In this case contact Technical Support The slide supplied with your scan
12. BlueG nome www cambridgebluegnome com an Illumina company ClearScan USER MANUAL For use with ClearScan 432401 PK ClearScan Auto 432402 PK FOR RESEARCH USE ONLY Not for Use in Diagnostic Procedures BlueGnome e CPC4 Capital Park Fulbourn Cambridge CB21 5XE UK e tel 44 0 1223 885905 www cambridgebluegnome com e support cambridgebluegnome com es BlueGnome ClearScan USER MANUAL Contents USER MANUAL ee E ooo 1 Identification and Certification Label 4 odlety important INformalloi sens cures enn sms dessus esse 7 LAS EF SAN CTY ee en cesmieueaie E E 7 ONNO Wale E 7 MOVING DANO sses renare EEEE ERR NEN 7 Safety SYSIEM ii 8 BE E EE 9 The ClearScan series iineeseereeseereeseeneennsne 10 Installing the scanner arri 11 List Of e Elei ee Re elen 11 ElecimicalcommunicaUon COMME GION ME 11 POSITION NS SCANNET ia 11 ClearScan network configuration sis 12 scanner check after installing th Scanner ne 13 IESIONAGTAGION ele E 14 Meaning of visual and audio signals e 14 operand TNS e ul CAR RR RR A 16 MIGFOSCODE SOCS TEE 16 KEEN Cl ET 17 Operating the ClearScan AUto iii ineesrrneeseenenns 18 Operating the ClearScan software iii 20 Hardware reQuirements ei 20 SOA ORDER 21 Starting the ClearScan SOftware cc cccccscsececcseccsceecesceeccsceeeescseeesceneesceeecc
13. F ible See Fm mR selecting ClearScan USER MANUAL attaches the image information window to the mouse so that the pixel intensities and coordinates can be viewed directly alongside the image Pixel values Slide coordinates pm A 4190 Y 25500 Image coordinates A 169 1700 Version 1 1 4 March 2013 tel 44 0 1223 885905 e support cambridgebluegnome com 39 es BlueGnome an Illumina company ClearScan USER MANUAL User preferences Using the Preferences menu you can Define the language and the appearance of ClearScan Choose a user as the account manager Choose a password to protect your account Click on the Users option to display the Preferences window Preferences 2 Users E Password General settings Use this section to define different ClearScan options Preferences General setting Folders Language English F Mutti access user OSingl access user UDo not show preventive messages Scanner Automatic scanner disconnection after minutes of inactivity Lei Enable Disable the scanner buzzer Update settings i Sutomatic check at startup Direct connection to the Internet D Manual proxy configuration Version 1 1 4 March 2013 tel 44 0 1223 885905 e support cambridgebluegnome com ro BlueGnome ClearScan USER MANUAL Item Description Language You can choose between French and English version
14. General tab 4 defines the scan parameters Manual mode Scan parameters P laser power and PMT gain or auto scanning mode Slide tab shows preconfigured scan area E Provides a fast low resolution scan of the whole Preview Scan slide area Scans the preconfigured area at high resolution don 10 or 4 uM median Is revealed once scanning preview scan Select Stop to stop the current scan With ClearScan Auto the whole run of slides to be scanned will be stopped Image Tool BO Toggle between mouse in zoom mode and drag image walk mode Image Image display ECO Image tools Select to display the preview image the red cy5 image or the green cy3 image or the combined cy5 and cy3 image respectively Version 1 1 4 March 2013 tel 44 0 1223 885905 e support cambridgebluegnome com 27 es BlueGnome Window ClearScan USER MANUAL These icons select which window to view ITEM ACTION E Return to main image view show hide the histogram window that displays histogram signal intensities for the images hi show hide the display options window allows ATA display brightness contrast and balance of the image to Se navigation Version 1 1 4 March 2013 be modified show hide the navigation window shows the area of the slide currently viewed tel 44 0 1223 885905 e support cambridgebluegnome com 28 es BlueGnome ClearScan USER MANUAL Scanner information
15. NUAL Symptom Diagnosis The image is dark or the measured signal is weak Make sure the detector gain is not too low set to 100 to check Make sure the laser power settings are not too low set to high to check Check the scanner using the BlueGnome supplied slide see Scanner self tests and checks The image is striped or the ClearScan software displays a Focus was not stable during the scan message Contact Technical Support to try to resolve the problem Otherwise you can deactivate the autofocus The image is distorted and spots are the wrong size Check that the problem isn t being caused by the direction in which the slide is inserted by turning it around 180 and then reinserting it If the defects are also rotated 180 the slide is causing the problem Otherwise contact Customer Support There is a spot in the same place on all images whatever slide you use Contact Customer Support Avoid using slides with liquids likely to run during scanning Version 1 1 4 March 2013 tel 44 0 1223 885905 e support cambridgebluegnome com 45 es BlueGnome ClearScan USER MANUAL FAQ Technical data The ClearScan is a confocal fluorescence scanner The imaging system consists of two laser sources that excite the chemifluorescent dyes 635nm and 532nm two detection photomultipliers and very high precision optical filters provide results with enhanced signal to noise rat
16. Scan has been designed to reduce all the above risks to zero when the equipment is used for its intended purpose and according to the supplied instructions When using the ClearScan the device housing and its mechanical shutter system protects you from all danger Never attempt to open the housing there are no user serviceable parts inside The user must call Technical Support if the machine exhibits any failure or malfunction The housing must only be opened by qualified personnel appointed by BlueGnome Once a slide is inserted into the ClearScan a protective shutter obstructing the slide insertion port closes If this shutter remains in the closed position for any reason whatsoever preventing you from inserting a slide or removing a previously inserted slide do not attempt to force it open contact Technical Support immediately Damage to this shutter may expose you to laser hazards The ClearScan Auto equipped with an autoloader system requires the user to close a sliding door after inserting slides into the autoloader system This door will be automatically locked during a scan Do not attempt to force it open during a scan Damage to this sliding door may expose you to laser hazards If for any reason the door is still locked after scanning or if you are able to open the door during a scan immediately switch off the machine and contact Technical Support If a slide is broken inside the scanner or cannot be easily extracted do not tr
17. age analysis Version 1 1 4 March 2013 tel 44 0 1223 885905 e support cambridgebluegnome com 25 es BlueGnome Image zoom toolbar ClearScan USER MANUAL ITEM ACTION zooms in on the entire image by 20 Zoom zooms out of the entire image by 20 Unzoom sul Page width gt Full image di Real size Undo 4 Redo Pi View spots Register images fits image width to the display window fits the entire image into the display window displays the image with a 100 zoom factor One pixel on the screen corresponds to one image pixel returns you to the previous zoom returns you to the zoom just cancelled Reveals the view spot window a floating version of image information that provides signal intensities on a pixel by pixel basis Can register the two images Should not be necessary but can correct if the lasers have become slightly misaligned Version 1 1 4 March 2013 tel 44 0 1223 885905 e support cambridgebluegnome com 26 es BlueGnome ClearScan USER MANUAL Scanner OWE Scanner ITEM ACTION Connects the software to the scanner the icon is d removed when connected to a scanner Connect O Is revealed once connected to the scanner Select to disconnect from the scanner Disconnect Searches connections to find available scanner s This icon disappears once connected to a df Locate scanner scanner Opens scan parameters window
18. are well balanced the plots should overlap as shown below Histogramm te ks 7920363 0 904579 25 10327936 1 t F min 2 0 KW F max 7928363 0 SI 1345 log scale Percentage bin size 100 153 54 Saturation Percentage 0 0556 zz 0 0359 Ge BOB ar AW ROT wi S Wa Den Li I i D D D 6550 0 13100 0 19650 0 26200 0 327500 39300 0 45650 0 52400 0 556950 0 65500 0 The histogram displays pixels on a graph The X axis represents pixel values from 0 to 65535 The Y axis represents the number of pixels which are equal to the value given by A axis On the left hand side of the graphic area the scale parameter may be manually adjusted To retrieve automatic scale just check the box at the left of the scale Log scale is available for each axis You can also display the Y axis in percentage Bin size may also be manually set The lower the bin size is the larger the number of dots will be displayed Thus it is better to work with high bin size to speed up display The saturation percentage is indicated for each of the wavelengths the red value correspond to the percentage of saturated pixels on the red channel 635nm while the green value indicates the percentage of saturated pixels on the green channel 532nm The histogram window can be removed by clicking the pel histogram icon again or selecting close In order to maximise the amount of information derived from the array th
19. at particular array will be applied Barcodes on BlueGnome s microarrays 24sure CytoChip Focus and CytoChip Oligo arrays will be automatically recognised Scanning in Auto mode This is the default and recommended mode Auto mode has been optimised for BlueGnome microarrays to give optimal results in terms of signal to noise and to give balanced red and green images with minimal saturation Scan reads the slide within the defined scan area using the currently defined scan settings Once the gt scan icon is selected the Select directory window appears here choose where you would like to save your scan images Note that it is not necessary to write a file name as this will be automatically created by ClearScan using the barcode and the scan area location _ TOP BOTTOM in the case of 24sure and Focus arrays or just Barcode tif for CytoChip Oligo arrays The format of the file name created by the ClearScan software is compatible with BlueFuse Multi 16bit multi Tiff format Images are saved automatically after the scan in the selected file directory We recommend that this is on the hard disk rather than on the network Look n Au 12april12 D File Mame Ci Weers Administrator Documents canst utoGaint est 2april 2 Files of Type All Files be Version 1 1 4 March 2013 tel 44 0 1223 885905 e support cambridgebluegnome com EN es BlueGnome ClearScan USER MANUAL NOTE Folder permissions If you use Win
20. ay type tel 44 0 1223 885905 e support cambridgebluegnome com 49 es BlueGnome ClearScan USER MANUAL ClearScan Description Specifications H Size 278 x 457 x 369 mm W x Dx H Weight 15 5 Kg Power consumption 100 240 V 220 V 110 V Initialization 41 W 30 W Standby 30 W 20 W Connected 32 W 24 W Barcode 35 W 26 W reading 33 W 25 W Scan ClearScan Auto Deseribilan Specifications H Size 333 x 595 x 422 mm W x D x H Weight 27Kg Power consumption 100 240 V 220 V 110V Initialization 37 W 20W Stand by 40 W 31 W Connected 35 W 27 W Barcode 35 W 26 W reading 33 W 25 W Scan Version 1 1 4 March 2013 tel 44 0 1223 885905 e support cambridgebluegnome com es BlueGnome company ClearScan USER MANUAL Declaration of conformity INNOPSYS i DECLARATION DE CONFORMITE Declaration of Conformity Nous INNOPSYS We ZA Activestre 31390 CARBONNE France D clarons que les produits Declare that the products Scanners de fluorescence de biopuces MicroArray Scanners Mod le ClearScan Range ClearScan Auto Satisfont aux exigences des directives Satisfy the requirements of the directives Equipement basse tension N 2006 95 CEE Low voltage equipment Compatibilit lectromagn tique N 2004 108 CEE Electromagnetic compatibility D chets d quipement lectrique et lectronique N 2002 96 CEE Waste Electrical a
21. cense collectively the Software is the property of BlueGnome or its licensors and is protected by copyright law While BlueGnome continues to own the Software You will have certain rights to use the Software after Your acceptance of this license This license governs any releases revisions or enhancements to the Software that BlueGnome may furnish to You Except as may be modified by an BlueGnome license certificate license coupon or license key that accompanies precedes or follows this license Your rights and obligations with respect to the use of this Software are as follows You may A use one copy of the Software on or in conjunction with a single computer that is owned or leased by You If a License Module accompanies precedes or follows this license You may make the number of copies of the Software licensed to You by BlueGnome as provided in Your License Module Your License Module shall constitute proof of Your right to make such copies B make one copy of the Software for archival purposes or copy the Software onto the hard disk of Your computer and retain the original for archival purposes C use the Software for internal business purposes only and may not use the Software on behalf of a client or customer D after written notice to BlueGnome transfer the Software on a permanent basis to another person or entity provided that You retain no copies of the Software and the transferee agrees to the terms of this l
22. ch 2 w dr Clearscan Network Manager v DM 7 e v Page v G Tools v e Oo BlueGnome Wel Ro salino Welcome Contact us You re on the embedded web site of a ClearScan Thanks to it you can change network settings o Internet Protected Mode Off Version 1 1 4 March 2013 tel 44 0 1223 885905 e support cambridgebluegnome com 12 ro BlueGnome ClearScan USER MANUAL Click the Network Settings link to view the current network parameter configuration e NanoScan Network Manager Windows Internet Explorer kalak G Cl be http 192 168 0 254 network cgi w NanoScan Network Manager o BlueGnome Wel es AI Network Settings Contact us Host Name clearscan Domain Name bluegnome IP Address 192 _168 Gateway A Netmask 255 _ 255 Broadcast 192 _ 168 Name Serveur 1 Name Serveur 2 Validate the configuration Reset a Ka Internet Protected Mode Off 100 Validate that the scanner is configured correctly Troubleshooting scanner network connectivity If you cannot browse to the scanner successfully check the following 1 Computer IP address and netmask are correctly set for preconfigured scanner 2 Confirm that the cable is actually a crossover cable 3 Scanner should be powered on 4 Try using the default scanner IP address 192 168 0 254 NOTE If you plan to connect your scanner to your networ
23. dgebluegnome com 56
24. dows and want to save your images or results in Windows folders named My documents My images you have to check first if those directories are read only which is the default of these folders ClearScan will check if directories are writable or not To modify read write attributes of folders right click on the folder then click on Properties and in the Attributes area uncheck the read only attribute Click Select directory to start the scan Click on the A Stop icon if you wish to stop the current image acquisition sequence Scan parameters reveals the configuration window Selecting the scan parameters icon on the main toolbar or on the scan image reveals the configuration window in the information side pane From here you can select Manual or Auto scanning modes Scanning in Manual mode NOTE It is recommended that Auto mode is used Auto mode has been preconfigured for BlueGnome microarrays to give optimal results In manual scanning mode it is possible to change the laser power and the PMT gain To work within manual scanning mode choose the Manual button on the scan configuration window Version 1 1 4 March 2013 tel 44 0 1223 885905 e support cambridgebluegnome com 32 J BlueGnome ClearScan USER MANUAL General E Automatic scrolling Manual Auto Laser power and PMT gain can be defined manually here alternatively the Auto settings can defi
25. e red and green distributions should be as close as possible to each other and the distributions tail off with a minimal amount of saturation around 0 05 saturated pixels Version 1 1 4 March 2013 tel 44 0 1223 885905 e support cambridgebluegnome com 36 es BlueGnome ClearScan USER MANUAL Image views and options To open images go to the File tab on the Main Menu Click on open image and search for the images you want to open Alternatively an image will automatically open if dragged into the main window Once the image is opened you can navigate through it by using the mouse To change the mouse mode from zoom to drag image walk mode use the icons on the tools window or right click in the Image display area The About image option on the Image tab of the main menu displays the information contained in the TIFF images such as the serial number of the scanner that acquired the image acquisition parameters etc as shown below genera imagel images property value image name 2940574 BOTTOM tif Comments Image 1 and image 2 tabs contain the information of laser power and PMT gain percentage of each wavelengths image 1 corresponding to red channel image 635 nm while image 2 to green channel image 532nm Version 1 1 4 March 2013 tel 44 0 1223 885905 e support cambridgebluegnome com 37 es BlueGnome ClearScan USER MANUAL Image display options tr A opens a
26. e scanner status and image display gt BlueGnome Delivering Decisions from DNA A Barcode fl Ip T Ip d When first connecting to the scanner you will need to search for an available scanner 2 Click on the sa search icon situated either on the Toolbar or in the scanner tab from the Main menu A window containing the available scanners is opened x search scanner found scanner scanner n 1 Mame Type State Version 1 1 4 March 2013 Clearscan IP Address 192 160 0254 are a MAC Address O0 S50 c2 54 b1 2d available Serial Number 712003 Search 7 Quit tel 44 0 1223 885905 e support cambridgebluegnome com 23 es BlueGnome ClearScan USER MANUAL If you work with multiple scanners connected to the same computer they will all be listed you can recognize a scanner by its IP address If you do not know this address you can use the beep icon to identify the scanner Click on the icon to connect to the selected scanner The connect to the scanner icon on the main toolbar connects to the scanner selected in the search scanner window or the scanner used in the last session as defined by its IP address If you have previously connected to a scanner the connect to the scanner icon will appear without having to locate a scanner File Scanner Image Preferences Window Help Scanner d File Image To Window eo Je Los The scanner user icons now become visib
27. eason please contact BlueGnome Customer Service for a refund of the money You paid for the Software less shipping handling and any applicable taxes at any time during the sixty 60 day period following the date of purchase Version 1 1 4 March 2013 tel 44 0 1223 885905 e support cambridgebluegnome com 54 es BlueGnome ClearScan USER MANUAL 5 Limited Warranty BlueGnome warrants that the media on which the Software is distributed will be free from defects for a period of sixty 60 days from the date of delivery of the Software to You Your sole remedy in the event of a breach of this warranty will be that BlueGnome will at its option replace any defective media returned to BlueGnome within the warranty period or refund the money You paid for the Software BlueGnome does not warrant that the Software will meet Your requirements or that operation of the Software will be uninterrupted or that the Software will be error free You acknowledge that the scientific and technical state of the art when the Software was distributed did not enable all possible uses to be tested and verified nor for the presence of possible defects to be detected You shall be responsible for verifying by any or all means the product s suitability for its requirements its good working order and for ensuring that it shall not cause damage to either persons or properties You acknowledge that the Software is supplied as is by BlueGnome without any other exp
28. enescaerescees 22 User workspace e 22 The software application main window e 23 CORRECHAOO INe scanne E 23 Toolbar icons explained alan ed en ad Re a date 25 Caner IMOM AOU PR TT TR EEEE EEE EE 29 Slide detection in the autoloader ClearScan Auto 29 SO eee eee 31 Scanning in Auto mode ii diiii ireeserreeseeneseeneeeenenns 31 Scan DAT AMOR ne do de desc diese ci 32 Version 1 1 4 March 2013 tel 44 0 1223 885905 e support cambridgebluegnome com 2 es BlueGnome ClearScan USER MANUAL Scanning in Manual mode is 32 DURI TNS SC AM PR n 39 ee une rara 35 The histogram i 36 Ju Le VIEWS and Mee de Lu ica 37 Open an existing Image 37 ADOULIMAGE zia een tt 37 Image display options eee 38 IMACS Tite td VE 38 EE EE 40 General settings iii 40 ele 42 Scanner self tests and CHECKS i 43 INI ANZA e La ee 43 Silber AR 43 ClearScan slide check is 43 Maintenance ene 44 Fan filter replaCeMEnti i 44 TOUDE POOU iror a see 45 FAQ Technical data 46 Bindels erg 48 D CORS eee eee 49 Declaration Of conformity ee 51 Se EE E elen E EE 53 Version 1 1 4 March 2013 tel 44 0 1223 885905 e support cambridgebluegnome com 3 es BlueGnome ClearScan USER MANUAL Identification and Certification Label Two labels are affixed at the rear of the ClearScan as show in the picture below i 000000 AX SAS 00040 Version 1 1 4 March
29. ent to configure this please ensure that you have administrator privileges so that we can configure it during installation Alternatively it is possible to connect the scanner directly to the network in which case the IP address needs to be changed to one supplied by local IT support to satisfy the network requirements Minimum Requirements e Processor Intel Core 13 2120 Processor 8M Cache 3 30 GHz e Microsoft Operating System English Genuine Windows 7 Professional 64Bit OS e Memory 4GB 1X4GB 1333 MHz DDR3 Non ECC e Hard Drive 500GB 3 5inch Serial ATA 7 200 Rom Hard Drive e Network Card Additional Broadcom 5722 10 100 1000 Mbits BASE TX network in terface card For example Dell Optiplex 790 specifying Win7 64 bit OS and additional network adaptor Version 1 1 4 March 2013 tel 44 0 1223 885905 e support cambridgebluegnome com 20 ro BlueGnome ClearScan USER MANUAL Recommended Requirements e Processor One Intel Xeon W3503 Dual Core 2 40 GHz 4MB Cache 4 80 GT s Intel QPI e Operating System English Genuine Windows 7 Professional 64Bit OS e Memory 4GB 2x2GB 1333MHz DDR3 ECC UDIMM e Hard Drive 1TB 3 5inch Serial ATA 7 200 Rom e Network Cards Additional Broadcom 5722 10 100 1000 BASE TX network inter face card PCle For example DELL Precision Fixed Workstation T3500 Base specifying Win7 64 bit OS and additional network adaptor Installation procedure P
30. es SOME STATES AND COUNTRIES INCLUDING MEMBER COUNTRIES OF THE EUROPEAN ECONOMIC AREA DO NOT ALLOW THE LIMITATION OR EXCLUSION OF LIABILITY FOR INCIDENTAL OR CONSEQUENTIAL DAMAGES SO THE BELOW LIMITATION OR EXCLUSION MAY NOT APPLY TO YOU TO THE MAXIMUM EXTENT PERMITTED BY APPLICABLE LAW AND REGARDLESS OF WHETHER ANY REMEDY SET FORTH HEREIN FAILS OF ITS ESSENTIAL PURPOSE IN NO EVENT WILL BLUEGNOME OR ITS LICENSORS BE LIABLE TO YOU FOR ANY SPECIAL CONSEQUENTIAL INDIRECT OR SIMILAR DAMAGES INCLUDING ANY LOST PROFITS OR LOST DATA ARISING OUT OF THE USE OR INABILITY TO USE THE SOFTWARE EVEN IF BLUEGNOME HAS BEEN ADVISED OF THE POSSIBILITY OF SUCH DAMAGES IN NO CASE SHALL BLUEGNOME S OR ITS LICENSORS LIABILITY EXCEED THE PURCHASE PRICE FOR THE SOFTWARE The Version 1 1 4 March 2013 tel 44 0 1223 885905 e support cambridgebluegnome com 55 es BlueGnome ClearScan USER MANUAL disclaimers and limitations set forth above will apply regardless of whether You accept the Software 7 General This Agreement and any related License Module is the entire agreement between You and BlueGnome relating to the Software and i supersedes all prior or contemporaneous oral or written communications proposals and representations with respect to its subject matter and Ii prevails over any conflicting or additional terms of any quote order acknowledgement or similar communications between the parties This Agreement shall terminate upon
31. ght to designate specified Content Updates as requiring purchase of a separate subscription at any time and without notice to You provided however that if You purchase maintenance hereunder that includes particular Content Updates on the date of purchase You will not have to pay an additional fee to continue receiving such Content Updates through the term of such maintenance even if BlueGnome designates such Content Updates as requiring separate purchase This License does not otherwise permit the licensee to obtain and use Content Updates 3 Product Installation and Required Activation There are technological measures in this Software that are designed to prevent unlicensed or illegal use of the Software You agree that BlueGnome may use these measures to protect BlueGnome against software piracy This License and the Software containing enforcement technology require activation key as further set forth in the documentation The Software will operate for an infinite period of time prior to Software activation by You During activation You will provide Your unique product key accompanying the Software and computer configuration in the form of an USB key If You do not complete the activation the Software will cease to function until activation is complete which will restore Software functionality 4 Sixty 60 Day Money Back Guarantee If You are the original licensee of this copy of the Software and are not completely satisfied with it for any r
32. icense and E use the Software in accordance with any additional permitted uses set forth below Version 1 1 4 March 2013 tel 44 0 1223 885905 e support cambridgebluegnome com 53 es BlueGnome ClearScan USER MANUAL You may not A copy the printed documentation that accompanies the Software B sublicense rent or lease any portion of the Software reverse engineer decompile disassemble modify translate make any attempt to discover the source code of the Software or create derivative works from the Software C use a previous version or copy of the Software after You have received and installed a disk replacement set or an upgraded version Upon upgrading the Software all copies of the prior version must be destroyed D use a later version of the Software than is provided herewith unless You have purchased upgrade insurance or have otherwise separately acquired the right to use such later version E use the Software in any manner not authorized by this license nor F use the Software in any manner that contradicts any additional restrictions set forth below 2 Content Updates You shall have the right to obtain Content Updates for any period for which You have purchased maintenance except for those Content Updates that BlueGnome elects to make available by separate paid subscription or for any period for which You have otherwise separately acquired the right to obtain Content Updates BlueGnome reserves the ri
33. ios Confocal means that fluorescence emitted from planes other than the plane on which the scanner s optical system is focussed is not measured thus cancelling out all extraneous fluorescence A photodetector e pi hole pinhole lens fluorescence from a closer plane best focalisation plane fluorescence from a farther plane The ClearScan s autofocus system achieves excellent measurement reproducibility irrespective of microscope slide quality CY3 CY5 Alexa647 Alexa 660 Alexa546 and Alexa555 dyes can be used Two laser sources are used one with a wavelength of 635nm for CY5 type chemifluorescent dyes and the second with a wavelength of 532nm for CY3 type chemifluorescent dyes The laser sources are temperature and current controlled to provide an extremely stable power output Power fluctuation does not exceed 2 of power output es it take for the lase To achieve the most accurate results you are advised to wait 10 minutes after the scanner has connected to the software The lasers will have reached their stable nominal operating temperature during this period Yes the power of both lasers can be set at two different levels high and low Low power is useful to decrease the bleaching of the fluorophores and to increase the lifetime of lasers High power is used to obtain the best sensitivity results when signal is low Version 1 1 4 March 2013 tel 44 0 1223 885905 e support cambridgebluegnome com
34. k then the crossover Ethernet cable should be replaced with a standard Ethernet cable otherwise continue to use the crossover cable Scanner check after installing the scanner This scanner check assesses fluorescence signal image red green shift crosstalk and detection gain linearity The scanner check takes 5 to 15 minutes once it has finished a window displays the checked parameters and indicates whether the scanner has passed the checks This checked list can be printed for your records and used to complete the ClearScan Check Protocol and the IQ OQ Protocol These checks will be performed by the BlueGnome support representative during scanner installation Once the scanner is switched on and connected to a PC workstation run the ClearScan software to connect to the scanner allow the lasers to warm up Version 1 1 4 March 2013 tel 44 0 1223 885905 e support cambridgebluegnome com 13 Gei BlueGnome umina company ClearScan USER MANUAL Insert the delivered Test slide Click on the check scanner button in the Scanner menu The scanner will perform the checks and produce a report see section Scanner checks and self tests for more details Restoring factory settings lf for any reason the IP address is badly configured or forgotten you can restore the machine s factory IP settings by holding down the reset button as shown in the illustration below while the scanner is powered up LULL P
35. lace the software installation CD in the PC s CD ROM drive and refer to the install txt file for installation details The current version of the ClearScan software may also be downloaded from www cambridgebluegnome com Version 1 1 4 March 2013 tel 44 0 1223 885905 e support cambridgebluegnome com 21 es BlueGnome ClearScan USER MANUAL Starting the ClearScan software User workspace When the program starts the following dialog box is displayed ClearScan starting Ge BlueGnome Delivering Decisions from DNA When using the software for the first time you need to create a user account by clicking on the Create button NOTE If this feature is irrelevant for your work environment a single user mode is available which does not ask you to log on whenever the program is run See section General settings Use the button Start to access the program from the workspace of the selected user Version 1 1 4 March 2013 tel 44 0 1223 885905 e support cambridgebluegnome com 22 es BlueGnome ClearScan USER MANUAL The software application main window Once a user s workspace is selected the user interface displays the Main Window on the monitor screen Main menu this menu provides access to all the software s features ClearScan Jess File Scanner Image Preferences Window Help Pixel size um Connecting the scanner dex Main toolbar These icons control th
36. le and the main window changes to include an image display area ClearScan no Hame Fie Scanner Image Preferences Window Help File Image Ton Imagi Window So Bo e azoa NOTE To get optimal scanner performance the lasers have to warm up for around 10 minutes after being connected to the ClearScan software prior to starting a scan It is possible to continue with a preview scan if the lasers are not at optimal temperature but not possible to continue with a high resolution scan Scanner Gee Use the disconnect from the scanner icon to disconnect the scanner alternatively the scanner will automatically disconnect from the software after a set period of time see General settings Version 1 1 4 March 2013 tel 44 0 1223 885905 e support cambridgeblueqnome com 24 es BlueGnome ClearScan USER MANUAL Image toolbar These icons control the scan settings and image zoom Gei ClearScan Jess ec dk File Scanner Image Preis es Window Help File Image To Imag Sege WC le es Image display area Navigation window Pixel size um 40 Toolbar icons explained The toolbars are separated according to function all functions can also be accessed from the main menu File ES Select to open an existing image or save the current image save the current image as a jpeg or other image file types This function is purely to save a picture and is not suitable for im
37. nd electronic equipment WEEE Restriction des substances dangereuses N 2002 95 CEE Restriction of Hazardous Substances RoHS Et sont conformes aux normes And are compliant with the standards Compatibilit lectromagn tique IEC 61326 1 Electromagnetic compatibility S curit lectrique IEC 61010 1 Electrical safety IEC 61010 2 081 S curit laser EN 60825 1 Laser safety normes aux versions en vigueur lors de la fabrication des scanners current version standards for scanners manufacturing Sous r serve d installation et d utilisation conformes aux instructions constructeur Subject to installation and use conforming to the manufacturer s instructions Ann e d apposition du marquage CE 2012 Year of CE marking Lieu et date d mission St phane LE BRUN Place and date of issue PDG Carbonne 16 04 2012 France CEO C line HARDY Qualit amp Affaires r glementaires Quality and Regulatory Affairs Ref D claration conformit Rev 00 ifi Version 1 1 4 March 2013 tel 44 0 1223 885905 e support cambridgebluegnome com 51 es BlueGnome ClearScan USER MANUAL Technical support BlueGnome an Illumina company BlueGnome an Illumina company CPC4 Capital Park Fulbourn Cambridge CB21 5XE UK Email support cambridgebluegnome com 44 0 1223 885905 Document history Version Date Comment 1 0 18 April 2012 First publication of ClearScan user manual 1 1 4 March 2
38. ne these parameters automatically on a per slide basis Laser power Glow high For more information about manual settings please refer to table below ITEM DESCRIPTION Scrolls automatically down the image window during the scanning Automatic scrolling process Sets a value for the gain percentage for each color channel Detection gain wavelength The default value is the value used in the last scan session Change gain to avoid saturation Two laser powers are available Low 5mW High 10mW Laser power p laser power Version 1 1 4 March 2013 tel 44 0 1223 885905 e support cambridgebluegnome com 33 es BlueGnome ClearScan USER MANUAL NOTE Scan parameters can only be adjusted during or after the preview scan Preview Scan A preview gives you a fast comprehensive image of the microarray when using Manual mode Use preview to adjust laser output and PMT gain to prevent saturation before initiating slide scanning Click on E preview icon to begin the preview scan of the whole slide The preview scan uses the following default parameters pixel size 40um speed 35 lines s area of Interest whole slide Version 1 1 4 March 2013 tel 44 0 1223 885905 e support cambridgebluegnome com 34 es BlueGnome ClearScan USER MANUAL During the scan The scan image During the preview or main scan the barcode will be scanned first and appear at the bottom of the user interface the
39. ner is valid for one year The software will no longer allow you to run checks with it beyond this date and you must procure a new one test slides can be purchased through Innopsys hitp www innopsys com The test slide must be stored in its box at room temperature and away from light when not being used You are advised to check the scanner once a month or each time you move it Only use the test slide with the scanner it was delivered with Version 1 1 4 March 2013 tel 44 0 1223 885905 e support cambridgebluegnome com 43 es BlueGnome ClearScan USER MANUAL Maintenance and Service Fan filter replacement For models equipped with a fan filter it is necessary to replace the filter with a new one every year In the event of fallure to meet the deadline for replacement of the filter the scanner warranty deed will be revoked The customer has to order a new filter through their distributor To replace the filter see picture remove the protection grid which is interlocked at the back of the scanner remove the old filter replace with the new filter and then interlock the protection grid by pressing each side No other user maintenance is required No other user service is allowed lf a problem occurs please contact BlueGnome Technical Support or your distributor Version 1 1 4 March 2013 tel 44 0 1223 885905 e support cambridgebluegnome com 44 es BlueGnome Troubleshooting ClearScan USER MA
40. o erase flash memory Version 1 1 4 March 2013 tel 44 0 1223 885905 e support cambridgebluegnome com 48 es BlueGnome Specifications ClearScan ClearScan Auto Specifications ClearScan USER MANUAL Description Excitation wavelength Compatible fluorophores Laser Power PMT Gain Autofocus Detection Dynamic Range Sensitivity Uniformity Sample Max Scanning Area Scan Speed Scanning Time Barcode Interface Operating condition Optical resolution Pixel Resolution Version 1 1 4 March 2013 635 nm and 532 nm Cy5 Alexa 647 Alexa 660 635 nm Cy3 Alexa 546 Alexa 555 532 nm Adjustable 2 laser power available Adjustable from 0 to 100 Dynamic real time Real confocal and high performances digital PMT Over than 10 0 05 fluor um Lower than 5 CV All standard microscope slide Width 25 26 mm Length 75 76 mm Thickness 0 9 1 2 mm 22 x 74 mm 10 or 20 lines per second depending on array type 3 5 minutes with a scan area of 22x74mm with a 10um pixel size for a 2 colour simultaneous acquisition Codabar code39 linterleaved 2 of 5 code93 code 2 of 5 lata code 2 of 5 matrix 2 of 5 code11 code128 telepen upcA E0 E1 eanJAN13 JAN8 UCC msi plessey rss 14 limited expanded china post code pdf417 Ethernet Temperature From 19 C to 26 C Humidity 15 95 HR Altitude 0 2000 m 2 um 635 nm spot diameter FWHM 4 or 10 um depending on arr
41. outlet 110V or 220V by using the mains power cable supplied Switch on using the rocker switch at the rear of the machine Version 1 1 4 March 2013 tel 44 0 1223 885905 e support cambridgebluegnome com 11 es BlueGnome ClearScan USER MANUAL ClearScan network configuration NOTE Your scanners network settings should have been preconfigured prior to shipment according to instructions received by BlueGnome from your IT department Please check with your IT department that they have provided this information Before connecting the ClearScan to your company network your IT department should verify that the network settings are correct This can be achieved using the scanner web interface as follows 1 Use a computer with IP settings configured to allow it to communicate with the pre configured scanner 2 Connect the computer to the scanner using the supplied crossover Ethernet cable 3 Opena web browser on the computer and browse to the URL http lt scannerlPaddress gt Replace lt scannerlPaddress gt with the IP address your IT department has allocated to the scanner Note if you have requested your scanner to receive its IP address via DHCP you can still browse to it using the de fault scanner IP address of 192 168 0 254 The browser should now display the scanner welcome page as shown below e ClearScan Network Manager Windows Internet Explorer EEE C e http 192 168 0 254 44 x Live Sear
42. ress or tacit warranty and in particular without any warranty as to its commercial value its secured safe innovative or relevant nature Specifically You do not warrant that the Software is free from any error that it will operate without interruption that it is compliant with its documentation that it will be compatible with the Your own equipment and software configuration nor that it will meet the Your requirements BlueGnome does not either expressly or tacitly warrant that the Software does not infringe any third party intellectual property right relating to a patent software or any other property right Therefore BlueGnome disclaims any and all liability towards You arising out of any or all proceedings for infringement that may be instituted in respect of the use of the Software BlueGnome disclaims any and all liability as regards Your use of the name of the Software No warranty is given as regards the existence of prior rights over the name of the Software or as regards the existence of a trademark TO THE MAXIMUM EXTENT PERMITTED BY APPLICABLE LAW THE ABOVE WARRANTY IS EXCLUSIVE AND IN LIEU OF ALL OTHER WARRANTIES WHETHER EXPRESS OR IMPLIED INCLUDING THE IMPLIED WARRANTIES OF MERCHANTABILITY FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT OF INTELLECTUAL PROPERTY RIGHTS THIS WARRANTY GIVES YOU SPECIFIC LEGAL RIGHTS YOU MAY HAVE OTHER RIGHTS WHICH VARY FROM STATE TO STATE AND COUNTRY TO COUNTRY 6 Disclaimer of Damag
43. s of ClearScan Do not show preventive messages Preventive messages are displayed when work or configuration has been created or modified without having been saved You can choose to turn this off or on Scanner In this panel you can define some parameters of the scanner connection including automatic disconnection You can handle users accounts by choosing between single access user and multi access user When Multi access user is selected each user must choose their own session when ClearScan starts from the user screen ClearScan starting Femove Exit Ge BlueGnome Delivering Decisions from DNA The user window allows users to create and delete users accounts Each user can protect their account by defining a password To change a password go to the Preference tab on the main menu and then click on Password to reveal this box Password New password Confirm password NOTE The password must consist of at least 6 characters Version 1 1 4 March 2013 tel 44 0 1223 885905 e support cambridgebluegnome com 41 BlueGnome ClearScan USER MANUAL In this section you can define the default folders for image results and work file storage rees General settings Folders Images C WsersiAdministrator Documents Scans scans C Users t dministrator Documents Scans m Contig CWserst amp dministratorbocuments Version 1 1 4 March 2013 tel 44 0 1223 885
44. test sequence lasts for approximately 30 seconds When the sequence has completed a short beep is emitted If the Technical Problem LED is off the scanner is ready for use It is advisable to wait 10 minutes after the scanner has connected as opposed to powered up before use so that the lasers have time to achieve thermal stability which improves laser performance and improves the lasers lifespan e Slide down the door until fully opened Insert slides horizontally in the loader slots numbered from 1 to 24 Gently push them until they reach the stop Version 1 1 4 March 2013 tel 44 0 1223 885905 e support cambridgebluegnome com 18 es BlueGnome ClearScan USER MANUAL The barcode and microarray spots must be on the same face of each of the slides i e upwards as shown in the previous illustration Gently slide the door up to close the autoloader system The microarray presence detector detects that a slide has been inserted and the microarray present LED comes on indicating that the scanner is ready to read the sample During a scan the door is automatically locked Do not attempt to force it open you may harm the scanner Wait for the end of the scans see section Meaning of visual and audio signals before sliding down the door and removing the slides Any other use of the scanner may be dangerous or may harm the scanner NOTE Do not attempt to loosen screws or insert any object other than slides complying
45. uto is a ClearScan scanner incorporating a 24 slide autoloader Version 1 1 4 March 2013 tel 44 0 1223 885905 e support cambridgebluegnome com 10 es BlueGnome ClearScan USER MANUAL Installing the scanner e scanner e mains power cable e ethernet crossover cable STP Shielded Twisted Pair e ClearScan user manual e software installation CD e ClearScan Test slide Electrical communication connection Before you connect the scanner to your electrical supply please ensure that e the wall socket is grounded e your electrical supply follows these specifications e Power supply 100 240 V 47 63 Hz e Plug fuse 1A at 110V 500mA at 220V e Electrical supply circuit breaker able to switch at least in 40ms NOTE Without a grounded socket and or if your electrical circuit does not comply with these specifications the equipment may be damaged and the user s safety may not be ensured Positioning the scanner The scanner must be located on a base or platform such that e it is not subject to strong vibrations not close to a centrifuge vortex etc e itis not exposed to direct sunlight e the housing does not come into any contact with chemicals especially acetone e it does not block scanner ventilation It must allow 5 cm of space behind the rear panel of the scanner e it does not move the scanner while it is functioning e it can support the weight of the scanner Connect the scanner to a grounded mains
46. vice These slides are 25 to 26 mm wide 75 to 76 mm long and 0 9 to 1 2 mm thick Make sure these slides are not damaged chipped edges for instance Take care with labels stuck on slides They must not stick up from the slide or come unstuck These precautions are of particular importance when using an autoloader system in association with ClearScan Verify that there is no sticky material on the slide otherwise the slide may not be removed from the scanner The total available scan area is shown below the specific scan areas of BlueGnome slides are preconfigured in the scanner software The slide is inserted in the direction indicated by the arrow Version 1 1 4 March 2013 tel 44 0 1223 885905 e support cambridgebluegnome com 16 Gei BlueGnome an Illumina company ClearScan USER MANUAL Operating the ClearScan The ClearScan is simple to operate The only direct user actions required without using the software are e Powering up switching off the scanner using the on off button located on the instrument rear panel TL When the scanner is powered up it performs a sequence of self tests and will indicate any malfunction via the Technical Problem LED The test sequence lasts for approximately 30 seconds When the sequence has completed a short beep is emitted If the Technical Problem LED is off the scanner is ready for use It is advisable to wait 10 minutes after the scanner has connected as opposed to
47. with ClearScan Version 1 1 4 March 2013 tel 44 0 1223 885905 e support cambridgebluegnome com 47 es BlueGnome ClearScan USER MANUAL Embedded firmware Source code of parts of the ClearScan embedded firmware This is the description for the source code of the parts of ClearScan firmware that fall under open source licenses GNU GPL v2 0 Parts of the firmware under GNU GPL v2 0 license are made available on demand at info cambridgebluegnome com BlueGnome makes no warranties whatsoever either express or implied including any warranties of merchantability or fitness for a particular purpose regarding this software BlueGnome offers no support for this software The preceding does not affect your warranties and statutory rights regarding any BlueGnome product s you purchased lt only applies to this source code made available to you All software listed below is under GNU GPL V2 0 open source license which is available at the following address http www gnu org licenses gpl 2 0 html u boot 1 2 0 and modifications This software is used to initialise and to launch the system noyau linux DENX ELDK based on kernel 2 4 25 and modifications This software is the kernel of the linux embedded operating system busybox 1 2 1 This software provides a fairly complete environment for any small or embedded system boa 0 94 14 0 5 rc21 This software is a http server eraseall 0 1 0 This software is used t
48. with ISO standard 8037 1 Be sure that inserted slides are pushed until the end stop Be sure that inserted slides are horizontal and not inserted on two different levels Version 1 1 4 March 2013 tel 44 0 1223 885905 e support cambridgebluegnome com 19 es BlueGnome ClearScan USER MANUAL Operating the ClearScan software The ClearScan software is required to control the ClearScan scanners and acquire the scan images for use in BlueFuse Multi Features of the software include e run and control ClearScan scanners ClearScan and ClearScan Auto e display images in real time during acquisition e control display parameters zoom image properties contrast balance e save acquired images in 16 bit TIFF format together with all acquisition parameters e g pixel size laser output etc and JPEG format e display any 16 20 bit TIFF image e manage multiple user accounts Hardware requirements A windows operating system computer i e Windows 7 is required to operate the scanner The memory requirements are relatively high as file sizes are large in high resolution mode we therefore stipulate 4GB RAM In standard configuration the scanner communicates with the computer via a network adaptor We therefore require two network adaptors a dedicated network adaptor for the scanner with a fixed IP address in the range of 192 168 0 1 253 and an additional adapter to network the PC If you are not able to get your IT departm
49. y and forcibly extract it do not attempt to open the housing contact Technical Support If the scanner housing is damaged do not use the equipment Contact Technical Support If any laser light is visible for any reason whatsoever immediately switch off the machine and contact Technical Support Warning replace the fuse with a fuse of the same type e T2AL 250V e Type 5 20 mm e Breaking capacity 150A Instructions to replace the fuse e Disconnect power cable and switch off the scanner e Turna 5 5 mm flat screwdriver from right to left inside the fuse holder to remove it e Replace the fuse and move back the fuse holder on the rear side of the scanner e Turn the screwdriver from left to right inside the fuse holder to lock it Version 1 1 4 March 2013 tel 44 0 1223 885905 e support cambridgebluegnome com 8 Oo BlueGnome ClearScan USER MANUAL Use terms The scanner is designed for use in research only It is not designed or certified for use in the diagnosis of human or animal diseases Version 1 1 4 March 2013 tel 44 0 1223 885905 e support cambridgebluegnome com es BlueGnome ClearScan USER MANUAL The ClearScan series ClearScan includes two different models ClearScan model number 432401 PK e ClearScan is able to scan 24sure 24sure and CytoChip Focus slides with a 10 um pixel size and CytoChip Oligo slides with a 4 um median scan setting ClearScan Auto model number 432402 PK e ClearScan A
50. y precautions are compulsory and must be stringently observed at all times Laser safety This device contains two laser sources These laser sources are harmless when the equipment is used for its intended purpose In all other cases the laser sources may cause bodily injury The technical specifications of the laser sources located in the machine are as follows e sourcet visible wavelength 635nm continuous wave maximum output 15mW divergence lt 1mrad Class Illb e source2 visible wavelength 532nm continuous wave maximum output 15mW divergence lt 1mrad Class Illb Do not attempt to gain access to the interior of the device High voltage Some electronic assemblies in the device require high voltages gt 1000V to operate normally These sources are harmless when the equipment is used for its intended purpose following the manufacturer s instructions In all other cases high voltage may cause severe or fatal bodily injury Do not attempt to gain access to the interior of the device The ClearScan contains moving parts These parts are harmless when the equipment is used for its intended purpose following the manufacturer s instructions In all other cases these parts may cause bodily injury Do not attempt to gain access to the interior of the device Version 1 1 4 March 2013 tel 44 0 1223 885905 e support cambridgebluegnome com es BlueGnome ClearScan USER MANUAL Safety system The Clear
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