Axon GenePix Personal 4100A, User Manual

Page 1: ...nts 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 Axon Instruments Molecular Devices Corp QUESTIONS See Axon s Knowledge Base http support axon com ...

Page 2: ......

Page 3: ...s equipment is not intended to be used and should not be used in human experimentation or applied to humans in any way COPYRIGHT The information in this Guide is copyrighted and must not be reproduced in any form whatsoever without written permission from Axon Instruments Molecular Devices Corp VERIFICATION This instrument is extensively tested and thoroughly calibrated before leaving the factory ...

Page 4: ......

Page 5: ...Pro Software 6 Connecting the GenePix Scanner to the Computer 6 Windows 2000 and Windows XP 7 Connecting the Security Key Dongle 7 Starting GenePix Pro 8 Troubleshooting Installation 9 SCSI Card Installation Problems 9 Chapter 3 Operation 11 Inserting a Slide 11 Proper Use of Slide Holder 11 Functional Checkout 12 Moving or Shipping the Scanner 13 Chapter 4 Imaging System Hardware 17 Discussion of...

Page 6: ... 22 Dynamic Range and Detection Limit 25 Specifications 26 Technical Assistance 27 Important Safety Information 29 Declaration of Conformity 49 Warranty and Service 51 Licensing Notice 53 Index 55 GenePix 4100A User s Guide Copyright 2005 Axon Instruments Molecular Devices Corp ...

Page 7: ...e This User s Guide focuses on the technical and theoretical aspects of the GenePix Personal 4100A hardware We recommend that you use this Guide in conjunction with the GenePix Pro Software User s Guide and the on line Help within GenePix Pro press F1 Chapter 1 ...

Page 8: ...tially at up to two wavelengths Has precisely controlled laser temperature and pixel by pixel laser correction to compensate for normal variation in laser intensity Uses 16 bit digitization Has a dynamic detection range of four orders of magnitude Has two standard filters and capacity for up to six custom filters Includes line averaging mode for enhanced signal to noise ratio Offers two scanning m...

Page 9: ... for the selection of a quality supplier and or components Preparing to Install your GenePix Scanner If you have purchased a GenePix Personal 4100A scanner without the optional host computer please follow all of the instructions below If you purchased your GenePix scanner with a bundled host computer the necessary hardware and software are already installed If so skip to Connecting the GenePix sca...

Page 10: ...a GenePix scanner without the optional host computer 1 Install the SCSI card 2 Turn on the computer 3 Install GenePix Pro For all users 4 Shut down the computer 5 Attach the GenePix scanner to the computer with the SCSI cable 6 Attach the power cord to the GenePix scanner 7 Turn on the GenePix scanner 8 Attach the security key dongle to the USB or parallel port of your computer 9 Turn on the compu...

Page 11: ...lot Do not force into place it should go in with a gentle push Screw the endplate to the chassis 4 Replace computer cover plug in power cord and turn on the computer Do not connect your GenePix scanner yet 5 Plug n Play operating systems such as Window 2000 and Windows XP will automatically recognize the Advansys SCSI card and install the correct driver For additional information please refer to t...

Page 12: ...se you have the autorun feature of Windows disabled you can manually start the installation by running the Setup exe program file on the CD ROM This file is found in the GenePix subdirectory on the CD ROM When the installer has finished you will be given the choice of restarting or shutting down your computer Select the Yes I want to shut down my computer now and install the hardware option Once y...

Page 13: ... the Add New Hardware Wizard This wizard starts any time a new Plug n Play device is detected Working through the wizard select the option to Search for the best driver for your device Press Next Select the CD ROM as one of the locations to search for the driver Press Next Windows will now find the correct driver for the GenePix scanner If you are connecting the GenePix scanner to a computer that ...

Page 14: ...Analysis Only version as the instrument is inactive in this mode and hence laser lifetime will be extended For image acquisition select GenePix Pro After the software has completed loading and the scanner has successfully initialized you will see a message in the bottom left corner of the software that indicates Eject position the slide may be removed This message indicates that the GenePix scanne...

Page 15: ...r technical support GenePix Pro automatically detects the GenePix Personal 4100A scanner If this does not occur please verify the following items The scanner power was turned on before booting the computer The SCSI cable between the computer and the scanner is securely connected The GenePix scanner has power the green power light at the front of the scanner will be glowing The SCSI card is properl...

Page 16: ......

Page 17: ...older The slide should be supported by the three sapphire balls on the frame A slight flick of the adjustment arm will ensure proper positioning of the slide Do not push the slide into position Gently close the slide holder lid until it snaps shut and close the door You are now ready to scan your sample See Image Acquisition in the Tutorial section of the GenePix Pro User s Guide for scanning inst...

Page 18: ...g to the specifications set by Axon Instruments Inc A similar but much more detailed procedure was performed at the factory prior to shipping this unit to you We recommend that you follow the procedure once upon receiving the scanner and then again any time you wish to check the performance of the scanner The GenePix 4100A microarray scanner has been designed to provide robust long lived microarra...

Page 19: ... it from damage prior to moving or shipping the scanner To park the scanner follow these instructions a Go to the Start Programs Axon Laboratory GenePix Pro folder and select GenePix Utilities as shown b When it opens you will see the following screen Select Park Scanner for Shipping Chapter 3 ...

Page 20: ...g the scanner please wait while the slide holder is being parked d When the slide holder is parked a new window will appear stating that the scanner has been parked Click OK GenePix 4100A User s Guide Copyright 2005 Axon Instruments Molecular Devices Corp ...

Page 21: ...these actions will automatically unpark the scanner The scanner is now ready to be moved If you are planning on shipping the scanner we also recommend the following a Wrap the scanner in a plastic bag for protection b Ship the scanner in its original packaging If you have insufficient packaging material it can be ordered from Axon for a nominal charge The Axon packaging materials have been tested ...

Page 22: ......

Page 23: ...m to its 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 photodetection The optical lens is located beneath the slideholder therefore the specimen must be placed feature side down into the slide hol...

Page 24: ...sons for this are quite simple conventional wide band light sources do not deliver high enough photon density at the appropriate wavelength to a sample in a scanning system In addition it is often difficult to use optical filters to obtain spectrally pure narrow band excitation light which is essential for having an optimal depth of field Optical Path Excitation laser light is directed onto the sl...

Page 25: ...7 nm and excluding light from the 635 nm laser and the Cy3 dye Likewise the Cy3 green filter is classified as 575DF35 The spectra for the emission filters in the GenePix scanner have very sharp cut on and cut off wavelengths so the transmission coefficient is close to 1 within the entire specified band and close to zero outside it You might have purchased additional filters for your scanner partic...

Page 26: ...specific fluorescence as well as increasing the electronic noise in the system The increase in noise can often be overcome by line averaging but the cost is decreased acquisition speed and increased photobleaching In general the signal to noise ratio is not improved by increasing the PMT voltage The output of a PMT is typically linear over a wide range of incident light intensities However there i...

Page 27: ... dual wavelength scan of a 26 mm 76 mm slide at 5 µm resolution in about 25 minutes When using such a mechanical device one must be able to monitor the variability in the performance of its mechanical components The GenePix scanner has been designed with a number of optimizations to ensure that variability in the mechanical performance is monitored in real time during acquisition and corrected The...

Page 28: ...s to the size of the pixel It determines the minimum distance that can be distinguished between two points of light In the GenePix scanner the highest spatial resolution is 5 microns It is possible to change the resolution of Data Scans by changing the pixel size setting in the Hardware Settings dialog of the GenePix Pro software It is important to note that this does not change the size of the sc...

Page 29: ...xel This is illustrated schematically in the figure below 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 For a P...

Page 30: ... On the left side of each image pair is the raw data scan from the GenePix Scanner Each square represents a 5 µm 5 µm spot as scanned by the 5 µm laser beam On the right are the resultant image pixels at various resolutions The shading indicates the spots that are scanned by the GenePix scanner as well as the corresponding pixels in the final image GenePix 4100A User s Guide Copyright 2005 Axon In...

Page 31: ... set below this range the probability that each impinging photon will be converted to an electron is diminished and the dynamic range will be limited on the low end Above this range noise begins to interfere with accurate signal measurement Both of these cases will limit the dynamic range The dynamic range of an instrument is often considered in conjunction with its detection limit The detection l...

Page 32: ...rder Detector Photomultiplier tube Digital resolution 16 bit Image format Single or multi image TIFF Computer Interface SCSI card included Scan time 6 5 minutes per channel for full size scan area at 10 µm resolution Dynamic range Four orders of magnitude Dimensions 36 cm 14 36 cm 14 29 cm 11 5 inches W D H Weight 18 kg 40 lbs Power supply 110 220V Universal power supply GenePix 4100A User s Guide...

Page 33: ...to resolve a problem there are several ways to contact Axon Instruments Molecular Devices Corp 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 ...

Page 34: ......

Page 35: ...eration Warning Indicates a possibility of severe or fatal injury to the user or other persons if the precautions or instructions are not observed Caution Using controls making adjustments or performing procedures other than those specified in the GenePix Personal 4100A User s Guide may result in hazardous exposure to laser light high voltage or moving parts Exposure to these hazards can cause sev...

Page 36: ...lides 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 Lasers CLASS 1 LASER PRODUCT Cautions Do not stick anything into the openings or vents of the GenePix 4100A other than loading the slide You may cause an interlock to fail Do not attempt to move any parts...

Page 37: ... Do not try to gain access to the interior of the instrument The moving parts inside the instrument can cause injury Fuses There are two 2A 250V fuses located adjacent to the power switch at the rear of the unit Hazardous Material Precautions Use standard laboratory procedures and cautions when working with chemicals Caution Always follow the manufacturer s precautions when working with chemicals ...

Page 38: ...utes 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 Symbol Explanations Green Device standby Ready to scan slide Stage waiting at the start position Blue Scanning Yellow Eject Slideholder ready to be unloaded GenePix 4100A User s Guide Copyright 2005 Axon Instruments Molecular Devic...

Page 39: ... Requirements The GenePix Personal 4100A is designed to operate optimally if the site 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...

Page 40: ...de fonctionnement normal Avertissement Indique un risque de dommage corporel sévère ou fatal pour l utilisateur ou d autres personnes si les précautions ou les instructions indiquées n étaient pas observées 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 informat...

Page 41: ... n entendez plus le bruit métallique caractéristique que provoque le verrouillage mécanique lorsqu il est enclenché Ce clic s entend normalement dès que la porte coulissante est ouverte d un quart de pouce environ 6 mm CLASS 1 LASER PRODUCT Sécurité concernant les Lasers Précautions à prendre Ne rien introduire dans les ouvertures ou aérations du GenePix 4100A à part une lame de microscope dans le...

Page 42: ...du scanner Avertissement Ne tentez pas d accéder à l intérieur de l instrument Il existe des pièces mobiles à l intérieur susceptibles de provoquer des dommages corporels Fusible Il y a deux fusibles 2A 250V situés à côté du commutateur d alimentation à l arrière de l appareil Précautions contre les substances dangereuses L utilisateur doit suivre les procédures standard de laboratoires et prendre...

Page 43: ... 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 Significations des Symboles Vert Appareil en attente Prêt à scanner une lame Attend en position de depart Bleu Balayage en cours Jaune Ejection Suppor...

Page 44: ... haute tension Danger Le GenePix 4100A est conçu pour fonctionner au mieux 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 c...

Page 45: ...cia Indica la posibilidad de lesión severa o fatal al usuario u otras personas si no se siguen las instrucciones y precauciones 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 del sistema Nota Identifica aspectos de int...

Page 46: ...ra donde se coloca la placa se abre aproximadamente 6 mm CLASS 1 LASER PRODUCT Seguridad del Láser Precauciones No inserte ningún objeto en las aperturas o respiraderos del GenePix 4100A diferente de la placa Puede ocasionar fallas en el circuito de seguridad No intente mover ningún componente debajo de la platina Usted puede causar fallas en el circuito de seguridad Clasificación y Potencia de lo...

Page 47: ...laboratorio estandarizados cuando trabaja con productos químicos Advertencia Utilice siempre las instrucciones de la fábrica cuando trabaje con productos químicos Axon Instruments no son responsables legalmente por daños o lesiones ocasionados como consecuencia del uso de materiales peligrosos Paneles Que No Forman Parte del Circuito de Seguridad Vista delas partes superior y posterior del GenePix...

Page 48: ...e los especificados aquí puede resultar en exposición peligrosa a la radiación del laser Explicaciones de los Símbolos Verde El equipo está a la espera Standby La platina está lista en posición de cargar la diapositiva y empezar Azul Registrando Scanning Amarillo Expulse Eject La platina está lista para descargar GenePix 4100A User s Guide Copyright 2005 Axon Instruments Molecular Devices Corp ...

Page 49: ...ción radiación del laser El GenePix 4100A está diseñado para 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...

Page 50: ...eit einer schweren oder tödlichen Verletzung hin wenn die Anweisungen oder Vorsichtsmassnahmen nicht beachtet werden 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 ...

Page 51: ...ffnet wird 8 Sie können keine Glasstreifen ablesen 9 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 Lasersicherheit CLASS 1 LASER PRODUCT Achtung Mit Ausnahme des Objektträgers dürfen unter keinen Umständen Gegenstände in die Öffnun...

Page 52: ...en Sie nicht das innere Teil des Gerätes zu öffnen Die darin enthaltenen beweglichen Teile können Verletzungen verursachen Sicherung Es gibt zwei Sicherungen 2A 250V die neben dem Schalter der Stromversorgung an der Rückseite des Gerätes gelegen sind Sicherheitsvorkehrungen Der Benutzer muss alle normalen Laboranweisungen und Sicherheitsvorkehrungen befolgen wenn Chemikalien verwendet werden Achtu...

Page 53: ...ebrauchsanweisung 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 Erklärung Der Symbole Grün Standby Modus Gerät ist bereit einen Objektträger zu lessen Führung des Objektträgers in Startposition Blau Scannin...

Page 54: ...ährlicher Stromkreis Örtliche Voraussetzungen Der GenePix 4100A arbeitet optimal wenn alle Umfeldvorrausetzungen 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 unkon...

Page 55: ...nded 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 EN 55011 1991 CISPR11 1992 Amd 1 2 1996 AS NZS 2064 1997 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 and ...

Page 56: ......

Page 57: ...ll 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 delays and additional expense to the customer The war...

Page 58: ...your instrument from Axon Instruments Molecular Devices contact our Technical Support Department If it is determined 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 t...

Page 59: ...ose arrays have 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 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 NOT SUGGEST ...

Page 60: ...S 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 No...

Page 61: ...lution 22 Help On Line 1 inserting a slide 11 installation scanner 4 6 SCSI card 4 5 software 4 6 troubleshooting 9 lasers temperature fluctuations 18 moving the scanner 13 14 15 oligonucleotide 53 optics 17 parking scanner 13 14 15 photo multiplier tube PMT 19 20 21 gain 21 voltage 20 21 pixel size 22 23 24 preview scan 2 23 24 scanning modes 2 SCSI cable 4 6 9 card 4 5 9 security key 7 signal to...