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Installation

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Chapter 2

Installation

About This User’s Guide

This User’s Guide focuses on the technical and theoretical aspects of the GenePix
Autoloader 4200AL scanner. We recommend that you use this Guide in
conjunction with the GenePix Pro Software User’s Guide, and the on-line Help in
GenePix Pro (press <F1>).

For information on setting up your GenePix Autoloader 4200AL scanner and
software, please refer to this chapter.

For a guided tutorial on scanning your first slide, see Chapter 3 of this manual, and
Chapter 4 of the GenePix Pro Software User’s Guide.

Computer Requirements

Please refer to the Axon Instruments web site for up-to-date information.

Should you choose to purchase your own computer, Axon recommends that due
consideration be made for the selection of a quality supplier and/or components.

Chapter 2

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Содержание GenePix Autoloader 4200AL

Страница 1: ...n Instruments Molecular Devices Corp No part of this manual may be reproduced stored in a retrieval system or transmitted in any form or by any means electronic mechanical photocopying microfilming recording or otherwise without written permission from Molecular Devices Corp QUESTIONS See Axon s Knowledge Base http support axon com ...

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Страница 3: ...oroughly calibrated before leaving the factory Nevertheless researchers should independently verify the basic accuracy of the instrument using suitable test samples WARNING If this equipment is used in a manner not specified by the manufacturer the protection provided by the equipment may be impaired DISCLAIMER This equipment is not intended to be used and should not be used in human experimentati...

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Страница 5: ...g the GenePix Pro Software 7 Connecting the GenePix Scanner to the Computer 7 Windows 2000 and Windows XP Installation 7 Connecting the Security Key 8 Troubleshooting Installation 8 SCSI Card Installation Problems 8 Chapter 3 Operation 11 The Shipping lock Slide Carrier 11 Loading the Slide Carrier 12 Inserting the Slide Carrier 13 Single slide Scanning 13 Batch Scanning 14 Configuring a Batch Sca...

Страница 6: ...ing System Hardware 25 Discussion of Hardware Components 25 Optics 25 Mechanical 30 Electronic 31 General Items of Interest 31 Spatial Resolution 31 Dynamic Range and Detection Limit 32 Specifications 33 Technical Assistance 35 Warranty and Repair Service 37 Licensing Notice 41 Declaration of Conformity 43 Important Safety Information 45 Index 65 GenePix 4200AL User s Guide Copyright 2005 Axon Ins...

Страница 7: ...yzes up to 36 slides Convenient all in one scan stack and store slide carrier Line by line dynamic autofocusing for unprecedented field uniformity Up to four internally installed laser excitation sources Gradient neutral density wheel permitting 5 100 laser transmission Data Scan resolution from 5 µm to 100 µm Fast Preview Scan at 40 µm Uses 16 bit ultra low noise digitization Dynamic range of 104...

Страница 8: ...array Informatics software Axon Instruments has consulted widely among the scientific pioneers of microarray techniques to produce an instrument that fulfills all their image acquisition and primary analysis needs GenePix 4200AL User s Guide Copyright 2005 Axon Instruments Molecular Devices Corp ...

Страница 9: ... F1 For information on setting up your GenePix Autoloader 4200AL scanner and software please refer to this chapter For a guided tutorial on scanning your first slide see Chapter 3 of this manual and Chapter 4 of the GenePix Pro Software User s Guide Computer Requirements Please refer to the Axon Instruments web site for up to date information Should you choose to purchase your own computer Axon re...

Страница 10: ... this slide carrier for routine scanning but save it as it must be in the scanner whenever the scanner is moved Always use the Park Scanner utility prior to moving the scanner whether making a short move to another location or shipping the scanner a long distance Open the Park Scanner utility from the GenePix Utilities program which can be found in the Start Menu Axon Laboratory GenePix Pro group ...

Страница 11: ...ion Here is a brief outline of how to get started with your GenePix scanner Detailed instructions follow immediately below If you have purchased a GenePix scanner without the optional host computer 1 Install the SCSI card see below 2 Install GenePix Pro and attach the security key to parallel or USB port For all users 3 Attach the GenePix scanner to the computer with the SCSI cable 4 Attach the po...

Страница 12: ...the computer Do not connect GenePix scanner yet 6 Plug and Play operating systems such as Window 2000 and Windows XP will automatically recognize the Iomega SCSI adapter and install the correct driver 7 Install GenePix Pro software see below 8 Close Windows and turn off the computer Attach the SCSI cable to the SCSI adapter and the GenePix scanner the scanner should also be powered off see below 9...

Страница 13: ...anner to your SCSI connector please ensure that your computer has been turned off and that the GenePix scanner power is turned off Once the computer has been turned off connect the 50 pin data cable between the SCSI adapter of your computer and the GenePix scanner hardware The SCSI connector and power connector are located at the back of the GenePix scanner Once the SCSI connection has been made c...

Страница 14: ...ou will not be able to save your settings files or save your analysis results In addition you can analyze only 1000 features without a key To install the GenePix Pro key please consult the instructions in the GenePix Pro manual Troubleshooting Installation SCSI Card Installation Problems If you followed the above instructions and still require further assistance on installation of the included SCS...

Страница 15: ...on 9 The GenePix SCSI ID 4 does not conflict with any other SCSI devices that you may have already installed on your computer e g a Jaz drive The scanner power was turned on before booting the computer Chapter 2 ...

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Страница 17: ...astic slide Do not use this slide carrier for routine scanning but save it as it must be in the scanner whenever the scanner is moved See Setting Up and Moving the GenePix Scanner in Chapter 2 To begin scanning you must first remove the shipping lock slide carrier Open GenePix Pro and wait for the scanner to initialize When the Status Bar reads Ready click the Eject Slide Carrier button After the ...

Страница 18: ...are between 0 9 mm and 1 1 mm thick including any labels Thicker slides will get stuck in the slide carrier and will cause slide handling failures due to the excessive force required to extract the slide from the carrier When in doubt check to make sure that the slides move freely in the slide carrier when they are seated Note You can scan a single slide using the Single scan type in GenePix Pro f...

Страница 19: ...irm stop The carrier should be all the way inside the instrument Do not force it Close the door The status bar will read Mapping Slide Carrier as GenePix Pro automatically maps the positions of the slides in the carrier A map of the slides in the carrier is displayed Before a scan the slide positions are colored as follows Blue slide is present and will be scanned White no slide is present Gray sl...

Страница 20: ...ts position on the Batch Scan tab Set laser filter and PMT parameters in the Hardware Settings dialog box Click Preview Scan or Data Scan to scan the slide When you are finished scanning click the Eject Slide Carrier button on the right hand side of the GenePix Pro main window To begin a Batch Scan after using Single Scan mode you must first Eject and reinsert the slide carrier Batch Scanning When...

Страница 21: ...the Copy Row and Paste Row buttons Settings To set individual hardware settings select the slide and then navigate to the appropriate GPS file Overr de PMT Gain with Auto PMT Gain i For each slide in the batch you can use the PMT gain as specified in the settings above either initial or from a GPS file or you can override and use the gain calculated by the Set PMT Gain Automatically algorithm To u...

Страница 22: ...he current position in the slide carrier select Continue To cancel the batch or to restart a batch from a position that has already been scanned press Stop The slide carrier ejects and you must remove it and then reinsert it to start scanning again Setting PMT Gain Automatically GenePix Pro and the GenePix Autoloader scanner support automatic setting of PMT gain when scanning The algorithm require...

Страница 23: ...is saved by default in the Axon Data directory but you can specify where it is saved in the Options Folders dialog box Functional Checkout The Functional Checkout procedure is to help you confirm that your GenePix Autoloader 4200AL microarray scanner is performing according the specifications set by Axon Instruments A similar but much more detailed procedure was performed at the factory prior to s...

Страница 24: ...remaining filter positions The installation process involves two steps 1 Install the filters in the scanner 2 Record the information for the new filters in GenePix Pro 1 Install the filter s in the scanner Turn off power to the instrument before opening the filter wheel compartment 1 Use a 5 32 hex wrench provided with the optional filter kit to access the filter wheel compartment on the front of ...

Страница 25: ...le filters by the edges only The rim of the filter is marked with an arrow indicating the direction of light propagation through the filter Drop the filter into the hole with the arrow pointing down If you have a separate Emission ND filter and Laser Rejection Filter the Emission ND filter goes in first followed by the Laser Rejection Filter which goes on top Arrow Indicator Figure 4 Filter with a...

Страница 26: ...the hex key clockwise to secure the latch 2 Record the information for the new filters in GenePix Pro 1 Turn on the scanner and computer If GenePix Pro is running shut it down 2 From the Windows Start menu go to Programs Axon Laboratory GenePix Pro Filter Tool Figure 6 Filter tool editor GenePix 4200AL User s Guide Copyright 2005 Axon Instruments Molecular Devices Corp ...

Страница 27: ...te name e g Alexa 488 or Blue Filter Enter both names here so that each user can choose their preferred nomenclature in GenePix Pro Under Formal name enter the midpoint of the wavelength range that is transmitted by the filter followed by the total wavelength range For example a filter that is centered at 530 nm and transmits a 30 nm band of light i e it transmits 515 545 nm will be named 530DF30 ...

Страница 28: ...sed before opening GenePix Utilities You cannot run GenePix Utilities in Analysis Only mode Figure 8 GenePix Utilities Park Scanner For Shipping See Setting Up and Moving the GenePix Scanner in Chapter 2 Release Magazine Lock Important The Release Magazine Lock utility should only be used under the supervision of Axon Technical Support Improper use of this utility may cause damage to your scanner ...

Страница 29: ...ner and or slides Calibrate Focus Focus calibration works with the GenePix 4000B only Save EEPROM Image Click the Save EEPROM Image button to save the scanner s internal configuration to a file On clicking the button the location of the file is reported in a dialog box You may be asked to save an EEPROM image file by Technical Support when they are troubleshooting a scanner problem for you Chapter...

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Страница 31: ... optical mechanical and electrical components Optics Fundamentally the GenePix scanner uses a laser excitation based fluorescence scanning and imaging system The optical system can be considered in terms of excitation light mirrors lenses filters and photo detection The optical lens is located beneath the slide scanning area Slides must be placed into the slide carrier with the arrayed surface fac...

Страница 32: ...blue laser with 488 nm excitation can be used with fluorescein and similar dyes and a yellow laser with 594 nm excitation can be used with Texas Red and similar dyes The Alexa Fluor dyes from Molecular Probes offers a number of dyes compatible with all four lasers excitation sources available in the GenePix 4200AL scanner Laser excitation sources are often used in scanning systems instead of conve...

Страница 33: ... autofluorescence reagent background etc The GenePix scanner comes with standard emission filters installed one for each laser installed at the time of purchase Each standard emission filter is optimized for the emission spectrum of the respective dye The factory installed Cy5 red filter is a bandpass filter with cut on frequency at a wavelength of 655 nm and cut off frequency at 695 nm This is id...

Страница 34: ...ssion peak of the chosen dye and must be narrow enough to exclude light from the laser other dyes etc but not so narrow that too many emission photons are excluded otherwise sensitivity will be lost We also strongly recommend that a reject filter of OD 8 be employed to eliminate laser excitation Installing Filters Before installing filters turn the scanner power off To gain access to the filter wh...

Страница 35: ...procedure in reverse order The filter information is stored in the PC board of the scanner not the computer After each filter installation or change is made turn on the scanner and open the Filter Tool program located in the Axon Laboratory GenePix Pro 5 folder of the start menu Activate the filter position by pressing on the check box and enter a description that will help you identify the filter...

Страница 36: ...t two essential criteria for high quality imaging First since different photocathodes have varying sensitivities to specific wavelengths of light quantum efficiency the PMTs have been optimized for the typical wavelengths of fluorescence emission light produced by microarrays Second the PMTs have been further selected for their reliability and optimal signal to noise performance Mechanical The Gen...

Страница 37: ...nce computer hardware to digitize these signals Our expertise in this area has been applied to the GenePix scanner Integrated with the GenePix scanner is not only our high performance analog digital converter but also the experience and knowledge to create low noise high performance amplifiers We have employed a unique design to ensure that the PMTs in GenePix scanner are linear over a wide dynami...

Страница 38: ...ection line as the value of a 20 µm pixel Changing the resolution of a Data Scan may often be useful if you have large features and you do not need to scan at maximum resolution As you decrease the resolution you will decrease the final image size in megabytes However keep in mind that you need to acquire enough pixels for each feature in order to make accurate measurements Note too that increasin...

Страница 39: ...hes significantly Specifications Sample type Standard microscope slides 1 3 25 75 mm 26 76 mm 0 9 1 1 mm thick Maximum scan area 22 69 mm Maximum resolution 5 µm Scan mode and order Sequential fully user configurable scan order Detector Photomultiplier tube PMT Digital resolution 16 bit Image format Single image or multi image TIFF Computer interface SCSI adapter included Scan time Four minutes pe...

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Страница 41: ...p to resolve a problem there are several ways to contact Axon Instruments Molecular Devices World Wide Web www axon com Phone 800 635 5577 Fax 1 510 675 6300 E mail axontech axon com Questions See Axon s Knowledge Base http support axon com Technical Assistance ...

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Страница 43: ...rges prepaid Axon Instruments Molecular Devices will pay for the return shipping of the product to the customer If the shipment is to a location outside the United States the customer will be responsible for paying all duties taxes and freight clearance charges if applicable To obtain warranty service follow the procedure described in the Repair Service section Failure to do so will cause long del...

Страница 44: ...ed your instrument must return to the factory for repair the Technical Support Representative will issue a Service Request SR number Our Logistic Coordinator will contact you with specific instructions Out of Warranty Repair Service Out of warranty repair service is available Contact the supplier for current rates or see our web site at www axon com Optional Service Agreement Purchasing an optiona...

Страница 45: ...ve a means to adequately package it Axon Instruments Molecular Devices can ship the proper packaging material to you for a small fee This may seem an expense you would like to avoid but it is inexpensive compared to the cost of repairing an instrument that has sustained shipping damage It is your responsibility to package the instrument properly before shipping If the packaging is inadequate and t...

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Страница 47: ...either been purchased from OGT s licensed suppliers or have been made by the customer under a license from OGT Please contact OGT to enquire about a license under OGT s patents at licensing ogt co uk mailto licensing ogt co uk USE OF THIS INSTRUMENT WITH MICROARRAYS MAY REQUIRE A LICENSE FROM ONE OR MORE THIRD PARTIES THAT HAVE PATENTS RELEVANT TO SUCH USE AXON INSTRUMENTS MOLECULAR DEVICES DOES N...

Страница 48: ... SEPARATELY LICENSED BY AFFYMETRIX NO LICENSE IS CONVEYED BY IMPLICATION ESTOPPEL OR OTHERWISE TO USE THIS INSTRUMENT WITH MICROARRAYS MADE USING IN SITU OR PHOTOLITHOGRAPHIC SYNTHESIS NO OTHER LICENSE IS CONVEYED BY IMPLICATION ESTOPPEL OR OTHERWISE UNDER ANY AFFYMETRIX PATENT OR OTHER INTELLECTUAL PROPERTY RIGHT This instrument is licensed by Affymetrix under the following patents U S Patent Nos...

Страница 49: ...tion of Council Directives EC EMC Directive 89 336 EEC as amended EC Low Voltage Directive 73 23 EEC as amended Harmonized Standards to which Conformity is Declared EMC EN 61326 04 1997 Emissions EN 61326 04 1997 Immunity Low Voltage EN 61010 1 1993 A1 A2 1995 EN 60825 1 1994 A11 1996 Laser Safety I the undersigned hereby declare that the equipment specified above conforms to the above Directives ...

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Страница 51: ...se hazards can cause severe or fatal injury Caution Indicates that damage to the instrument loss of data or invalid data could occur if the user fails to comply with the advice given Important Highlights information that is critical for optimal performance of the system Note Identifies items of general interest The Protective Housing The protective housing and instrument interlocks are designed to...

Страница 52: ...ont of the GenePix 4200AL doesn t extinguish when the door is open 3 You cannot scan any slides 4 You can no longer hear the distinctive metal on metal sound that the mechanical interlock makes when it falls into place This normally happens when the slide loading door has opened about Lifting Hazard Warning The GenePix Autoloader 4200 scanner weighs approximately 99 lbs 45 kg and requires two pers...

Страница 53: ... can cause severe or fatal injury High voltage electronics can also be found in the scanner s controlling computer See the computer manufacturer documentation on the high voltage hazard warnings Make sure you follow the instructions on the safe operation of the computer Moving Parts The GenePix 4200AL Microarray Scanner instrument contains moving parts that can cause injury Under normal operating ...

Страница 54: ...please contact Technical Support List of Controls This Guide constitutes a list of controls Caution Use of controls or adjustments or performance of procedures other than those specified herein may result in hazardous radiation exposure Safety Labels If a label becomes illegible or is missing for any reason please contact Microarray System Technical Support for a free replacement label While waiti...

Страница 55: ...te requirements are met As with any precision optical instrument care should be taken to maintain a low dust low vibration environment Temperature and humidity extremes may compromise performance Environmental Temperature 50 86º F 10 30º C Environmental Humidity 5 95 non condensing Power Requirements Universal Input 50 60 Hz 100 240V AC 2A max Space Requirements 25 6 in deep 16 9 in wide 13 4 in h...

Страница 56: ... laser à des hautes tensions ou à des pièces mobiles Ces dangers peuvent être à l origine de dommages corporels sévères ou fatals Attention Indique un risque de dommage pour l instrument de perte de données ou de données invalides si l utilisateur ne suit pas les recommandations de ce manuel Important Désigne des informations vitales pour le fonctionnement optimal du système Note Identifie des inf...

Страница 57: ...ensemble miroirs lentilles continue à se déplacer sous la lame après l ouverture de la porte coulissante 2 La DEL Scanning voyant bleu à l avant du GenePix 4200AL ne s éteint pas quand la porte est ouverte 3 Il vous est impossible de scanner une lame 4 Vous n entendez plus le bruit métallique caractéristique que provoque le verrouillage mécanique lorsqu il est enclenché Ce clic s entend normalemen...

Страница 58: ...ères ou fatals Il existe également des circuits à haute tension dans l ordinateur contrôlant le scanner Reportez vous à la documentation du fabricant de l ordinateur sur les risques liés à ces hautes tensions Suivez les instructions concernant les précautions d utilisation de l ordinateur Pièces mobiles L instrument à laser Microarray Scanner GenePix 4200AL contient des pièces mobiles pouvant entr...

Страница 59: ...e plus auun service de maintenance n est autorisé de la part d un tiers Liste des Contrôles Ce guide constitue une liste des contrôles à effectuer régulièrement Attention Tout contrôle réglage ou exécution de procédures autres que celles spécifiées ci dessus peut entraîner un risque d exposition dangereuse à des rayonnements Etiquettes de sécurité Si une étiquette devient illisible ou manque pour ...

Страница 60: ...eux de ses performances si les conditions nécessaires sur le site sont satisfaites Comme pour tout autre instrument optique de précision il ne doit pas être exposé à la poussière et aux vibrations Des conditions extrêmes de température et d humidité peuvent compromettre ses performances Température 10 30º C Humidité 5 95 sans condensation Alimentation 100 240V 6A max 47 63 Hz Espace nécessaire 65 ...

Страница 61: ...ix 4200AL puede resultar en exposición peligrosa a radiación láser alto voltaje o a partes móviles Exposición a estos peligros pueden producir lesiones severas o fatales Precaución Indica que puede ocurrir daño del intrumento pérdida o invalidéz de la información obtenida si el usuario no obedece las instrucciones provistas Importante Resalta información fundamental para el funcionamiento óptimo d...

Страница 62: ...el montaje de los lentes siguen moviéndose por debajo de la placa después de abrir la puerta 2 La luz azul emitida por el diodo LED con etiqueta Scanning localizado en la parte delantera del GenePix 4200AL no se extingue cuando la puerta está abierta 3 Usted no puede registrar ninguna placa 4 No se puede escuchar el sonido característico del contacto entre metales producido por el circuito de segu...

Страница 63: ...ón a alto voltaje puede causar lesiones severas o fatales Electrónica de alto voltaje se encuentra en el computador que controla el escáner Revise la documentación del fabricante sobre las advertencias al respecto Cerciorese de seguir cuidadosamente las instrucciones sobre la utilización apropiada del computador Partes Móviles El GenePix 4200AL Microarray Scanner contiene partes móviles que pueden...

Страница 64: ...vor comuníquese al mantenimiento técnico a cualquiera de los números telefónicos indicados en la etiqueta Lista de Controles Este guía provee una lista de controles Precaución el uso de los controles el ajuste o la ejecución de procedimientos diferentes de los especificados aquí puede resultar en exposición peligrosa a la radiación del laser Etiquetas de Seguridad Si una etiqueta se hace ilegible ...

Страница 65: ... operar óptimamente si el lugar de instalación cumple con los requerimientos Como con cualquier instrumento óptico de precisión debe tener cuidado de manterlo en un lugar bajo en polvo y de poca vibración Temperaturas extremas y humedad pueden comprometer su funcionamiento Temperatura ambiental 50 86 ºF 10 30 ºC Humedad ambiental 5 95 sin condensación Energía requerida Entrada 100 240V 6 A máximo ...

Страница 66: ... zu schweren oder tödlichen Verletzungen führen Achtung Weist darauf hin dass bei Nichtbeachtung der Vorschriften Schaden am Gerät entstehen kann und Datenausfall oder möglicherweise ungültige Daten resultieren können Wichtig Weist auf Information hin die wichtig ist um die optimale Leistung des Gerätes sicherzustellen Anmerkung Deutet auf Themen von generellem Interesse hin Das Schutzgehäuse Das ...

Страница 67: ...2 Die blaue Scanning Lichtdiode an der Vorderseite des GenePix 4200AL erlöscht nicht wenn die Tür geöffnet wird 3 Sie können keine Glasstreifen ablesen 4 Der Benutzer hört nicht mehr das metallene Geräusch welches bei normaler Funktion durch das Einrasten der mechanischen Verriegelung ausgelöst wird Dies passiert normalerweise wenn die Tür ungefähr 6 mm geöffnet ist Warnung Gefahr bei Anhebung Der...

Страница 68: ...ch im Kontrollrechner des Gerätes Lesen Sie sich bitte die Gebrauchsanweisung über die Hochspannungsgefahr durch Befolgen Sie alle Anweisungen über die Sicherheitsmassnahmen beim Gebrauch des Rechners Bewegliche Teile Der GenePix 4200AL Microarray Scanner enhält bewegliche Teile die Verletzungen verursachen können Unter normalen Umständen ist das Gerät so konstruiert um Sie vor den beweglichen Tei...

Страница 69: ...nn rufen Sie bitte den Technischen Hilfsdienst an Liste von Kontrollvorrichtungen Diese Gebrauchsanweisung enthält eine Liste der Kontrollvorrichtungen Achtung Der Gebrauch von Kontrollvorrichtungen oder Einstellungen bzw die Ausführung von Handlungen außer denen die in dieser Anweisung beschrieben sind können zu gefährlichen Strahlungen führen Sicherheitsetiketten Sollte ein Etikett unlesbar werd...

Страница 70: ...setzungen gegeben sind Genau wie bei anderen optischen Geräten sollte auch hier ein staub und schwingungsfreies Umfeld existieren Extreme Temperaturen und Luftfeuchtigkeit können die optimalen Funktionen des Gerätes beeinträchtigen Umgebungstemperatur 10 30 ºC Umgebungsluftfeuchtigkeit 5 95 unkondensiert Stromvoraussetzung Zufuhr 100 240 V 6 A max 47 63 Hz Platzvoraussetzung 65 cm 43 cm 34 cm Bitt...

Страница 71: ...orophore 27 See Cy3 Cy5 GenePix Installation 3 Genepix Utilities 22 Hardware 25 Amplifiers 31 Laser Excitation 26 Quantum Efficiency 30 Spatial Resolution 31 Help On Line 3 Image Size 32 Lasers Temperature Fluctuations 26 On line Help 3 Photo Multiplier Tube Gain 30 Preview Scan 31 Spatial Resolution 31 Stokes Shift 27 Temperature Fluctuations 26 Index ...

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