GenePix 4000B User Guide Rev. E
Contents
1. FORTRON SOURCE mu MODEL NO FSA110P32 S mm OUTPUT 110W MAX eee P1 5Vdc 10 0Amps 5 6 04 Max P2 5 7 0C COM 25 de 47 63Hz P3 4 15Vdc 4 0Amps a P6 15Vdc 1 0Amps tr Axon Part Number 3420 014 High Voltage Hazard High voltage electronics can be found in the GenePix 4000B Array Scanner instrument Under normal operating conditions you are protected from high voltage within the instrument Warning Do not try to gain access to the interior of the instrument Exposure to high voltage electronics 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 Electrical Ratings Moving Parts The GenePix 4000B Array Scanner instrument contains moving parts that can cause injury Under normal operating conditions the instrument is designed to protect you from the moving parts The interlock and protective housing are designed so that you cannot access the moving parts during a scan Warning Do not try to gain access to the interior of the instrument The moving parts inside the instrument can cause injury Fuses There are no fuses in the GenePix 4000B Hazardous Material Precautions Use standard laboratory procedures and cautions when working with chemicals Caution Always follow the man2. ada 1 Ehecklistok Parts dica it IA 1 Computer Required ai 2 Preparing to Install Gene Pixs aid ete letter 3 Quick Overview of GenePix Hardware and Software Installation 3 Installation orde LA o ein nn 4 Installation of GenePix Pro 3 0 cccccccnessssvsecccccescesssevcecceeceevsevseccecceassnvsescescessceesnccessacs 5 Connecting the GenePix 4000B to the Computer ss 5 Windows 98 Windows Millennium and Windows 2000 6 AVIIdOWS N Terr er AEEA IEEE A es EE ae 6 Connecting the Security Dongle ss 6 Starting GenePix Pro O cien sehe 7 Table of Contents xxii Troubleshooting Installation a a aan 7 SCSI Card Installation Problems sus 7 Hardware Problems eneore 220 e eE EEEE ERNER 8 Software Problems No ae Ran LIE 8 Chapter 2 Introduction to GenePix 4000B oooooonnoonnconnconococonoconcconocono nono nonnnnnn cono nonnconn nono noo 9 Chapter 3 Functional Checkout naco nacanannns 11 Chapter 4 Imaging System Hardware nono 13 Ov rall F atures ii An M ne 13 Discussion of Hardware Components ss 13 0 oi Suecia a ee ai 13 EEX CICA GION ai ta tasca 14 Mirrors Lenses and Et dais 14 Phote Detection una An ae aera ane 15 Mechanical iuris e bannen 16 Ele CHONO een er A A E A A A AA a 16 General Items Ob Interest ara a dd iia 17 Spatial Resolutio
3. rdida o invalid z de la informaci n obtenida si el usuario no obedece las instrucciones provistas Importante Resalta informaci n fundamental para el funcionamiento ptimo del sistema Nota Identifica aspectos de inter s general Cubierta Protectora La cubierta protectora y el circuito de seguridad del instrumento est n dise ados para protegerlo a usted de exposici n a la radiaci n l ser alto voltaje o a partes m viles Usted no necesita acceder al interior del instrumento En el interior no hay partes que requieran su servicio Advertencia No fuerce el circuito de seguridad ni abra la cubierta protectora o intente acceder al interior del instrumento a trav s de cualquiera de sus aperturas Abrir la cubierta protectora puede ocasionar da o en los componentes del instrumento y producir exposici n accidental a la radiaci n l ser al alto voltaje o a partes m viles El GenePix 4000B es un equipo de l ser de Clase 1 Adentro se localizan l seres de alta potencia fuera del alcance del usuario Las placas pueden colocarse sin peligro en la regi n del area de barrido del l ser porque la entrada de las placas tiene circuitos de seguridad redundantes que bloquean los rayos de luz Hay dos paneles en el equipo que no son parte del circuito de seguridad pero que est n asegurados con tornillos que requieren una herramienta para sacarlos Estos est n indicados mas adelante No remueva ning n tornillo para abrir l
4. Click the Hardware Diagnostic Reports link Click the Functional Checkout link Follow the Functional Checkout procedure Chapter 3 Imaging System Hardware e 13 Chapter 4 Imaging System Hardware The GenePix 4000B scanner is one of the fastest and most sensitive scanners currently available This chapter introduces some of the fundamental hardware concepts needed to understand the operation of the GenePix 4000B Overall Features The GenePix 4000B is designed for simultaneous scanning of two wavelengths of excitation laser light Axon s patent pending design eliminates the image alignment problems associated with sequential scanning systems while also abolishing channel crosstalk problems associated with multi wavelength designs permitting high precision real time acquisition and display of ratio images Discussion of Hardware Components When discussing the hardware components of the GenePix 4000B it is convenient to reduce the system to its optical mechanical and electrical components Optics Fundamentally the GenePix 4000B uses a laser excitation based epifluorescence scanning system The optical system can be considered in terms of excitation light mirrors lenses filters and photo detection Chapter 4 14 e Imaging System Hardware Excitation In the GenePix 4000B laser excitation is provided by individual 635 nm and 532 nm lasers These wavelengths correspond to the ideal wavelengths used to excite the fluoropho
5. Tiir ungef hr 6 mm ge ffnet ist Lasersicherheit CLASS 1 LASER PRODUCT Achtung Mit Ausnahme des Objekttr gers diirfen unter keinen Umst nden Gegenstiinde in die Offnungen oder Ausg nge des GenePix 4000B gesteckt werden da sonst ein Versagen der elektrischen Verriegelung verursacht werden k nnte Unterhalb des Objekttr gers diirfen keine Teile bewegt werden auch dies k nnte ein Versagen der elektrischen Verriegelung verursachen GenePix 4000B Users Guide Copyright 1999 2001 Axon Instruments Inc Klassifizierung und Intensitat der benutzten Laser Wellenl nge St rke Divergenz Betriebsart Klassifizierung Warnung Verletzungen k nnen enstehen wenn man Laserstrahlen ausgesetzt wird Direkter Kontakt mit den Strahlen kann zu Blindheit f hren Stromversorgung Klassifikation C FORTRON SOURCE mm MODEL NO FSA110P32 S mm OUTPUT 110W MAX INPUT _ P1 5Vdc 10 0Amps 100 240V P2 5 7 DC COM 6 0A MAX 53 4 15Vde 4 0Amps 47 63Hz BEN P6 15Vdc 1 0Amps Axon Teil Nr 3420 014 Hochspannungsgefahr Der GenePix 4000B Array Scanner enth lt Hochspannungselektronik Unter normalen Gebrauchskonditionen sind Sie vor diesen Spannungen gesch tzt Warnung Versuchen Sie nicht an das innere Teil des Scanners heranzukommen Kontakt mit der Hochspannungselektronik kann schwere oder t dliche Verletzungen verursachen Hochspannungselektronik befindet sich auch im Ko
6. au faisceau laser de hautes tensions ou des pi ces mobiles Le GenePix 4000B est un instrument laser de Classe 1 Il incorpore des lasers de puissance auxquels l utilisateur ne peut pas acc der Les lames peuvent tre plac es en toute s curit dans la zone de balayage des lasers la porte coulissante bloque automatiquement l mission des rayons lors de son ouverture Il y a deux acc s potentiels sous l appareil qui ne poss dent pas cette protection ils sont ferm s par des vis et requi rent donc l usage d outils pour leur ouverture voir les figures ci dessous N enlevez aucune vis pour tenter d ouvrir le bo tier ou pour aucune autre raison Les lasers internes peuvent endommager vos yeux avant que vous n ayez le temps de les fermer Attention Pr sence de hautes tensions l int rieur L utilisateur ne doit proc der 4 aucune intervention l int rieur du bo tier L appareil peut tre endommag par une simple tentative d ouverture du boitier Sympt mes Li s aux Probl mes de Verrouillage Il est dangereux de continuer utiliser le GenePix 4000B si seul l un des deux verrouillages de s curit fonctionne Pri re de contacter le fabricant et ou le fournisseur imm diatement l un des num ros indiqu s l arriere du GenePix 4000B L apparition de l un des sympt mes suivants d signe un probl me avec la double protection 1 L ensemble miro
7. complies with Axon Instruments 21 CFR 1040 10 amp 1040 11 E 320 WHIPPLE ROAD UNION CITY CA 94587 AXON LABEL PART NUMBER 2400 330 REV B DANGER Laser radiation when open AVOID DIRECT EXPOSURE TO BEAM Figura 2 Etiqueta de Identificaci n y Certificaci n La etiqueta est fijada a la parte posterior del GenePix 4000B en la mitad inferior de la cubierta protectora ner is PATENTS PENDING Power Supply PWR 4 Axon Part No 2300 419 SERVICE CONTACTS U S Office Axon Instruments Inc 3280 WHIPPLE ROAD UNION CITY CALIFORNIA USA 94587 Tel 650 675 6200 AXON LABEL PART NUMBER 2400 331 REV B Figura 3 Etiqueta de la Unidad de Poder La etiqueta esta fijada en la base de la unidad de poder xi Explicaciones de los Simbolos El equipo esta ala espera Standby La platina est lista en posici n de cargar la diapositiva y empezar Registrando Scanning Expulse Eject La platina esta lista para descargar GenePix 40008 Axon Instruments PATENTS PENDING DANGER Laser radiation when open AVOID DIRECT EXPOSURE TO BEAM MANUFACTURE DATE SERIAL NUMBER FOSTER CITY CA This device complies with 21 CFR 1040 10 amp Q 2220 WHIPPLE ROAD UNION CITY CA 24587 AXON LABEL PART NUMBER 2400 330 REV B Atenci n vea Atenci n voltajes Atenci n radiaci n instrucciones peligrosos del l s
8. which eliminates the need for image alignment after acquisition e has precisely controlled laser temperature and pixel by pixel laser correction for constant power output e uses 16 bit digitization e has a dynamic detection range of four orders of magnitude Chapter 2 10 e Introduction to GenePix 4000B e possesses extra high signal to noise scan mode e offers two scanning modes a Preview Scan at 40 um resolution and a Data Scan at 5 um resolution GenePix 4000B User s Guide Copyright 1999 2001 Axon Instruments Inc Functional Checkout e 11 Chapter 3 GenePix 4000B Functional Checkout The Functional Checkout procedure is to help you confirm that your GenePix 4000B array scanner is performing according 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 instrument and then any time after that if you wish to check the performance of the instrument The GenePix 4000B array scanner has been designed to provide robust long lived array scanning for years of normal use However if the images you acquire on the GenePix 4000B scanner do not appear correct and if you believe there is a problem with the scanner it is important to follow these instructions before contacting Technical Support 1 2 Start the GenePix software and click the Report tab
9. 97 Immunity EN 61010 1 1993 A A2 1995 EN 60825 1 1994 A 11 1996 I the undersigned hereby declare that the equipment specified above conforms to the above Directives and Standards Authorized Signature and Date _ signature on file Title of Signatory Declaration of Conformity xvii Customer License Agreement Customer License Agreement for Single User of GenePix Pro 3 0 This software is licensed by Axon Instruments Inc Axon to you for use on the terms set forth below By opening the sealed software package and or by using the software you agree to be bound by the terms of this agreement AXON hereby agrees to grant you a non exclusive license to use the enclosed AXON software the SOFTWARE subject to the terms and restrictions set forth in this License Agreement Copyright The SOFTWARE and its documentation are owned by AXON and are protected by United States copyright laws and international treaty provisions This SOFTWARE may not be copied for resale or for bundling with other products without prior written permission from AXON Restrictions on Use and Transfer You may not reverse engineer decompile disassemble or create derivative works from the SOFTWARE Export of Software You agree not to export the SOFTWARE in violation of any United States statute or regulation Ownership of Software and Media CD ROM You own the media CD ROM on which the SOFTWARE is recorded but AXON owns the SOF
10. GenePix 4000B ARRAY SCANNER User s Guide Part Number 2500 136 RevE July 2001 Printed in USA The GenePix 4000B Array Scanner is for research purposes only It is not intended or approved for diagnosis of disease in humans or animals Copyright 1999 2001 Axon Instruments Inc No part of this Guide 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 Inc For Technical Assistance If you need help to resolve a problem there are several ways to contact Axon Instruments World Wide Web www axon com Phone 1 510 675 6200 Fax 1 510 675 6300 E mail tech axon com Technical Support Important Safety Information for the GenePix 4000B The operator of the GenePix 4000B Array Scanner The lasers inside can cause eye damage before you instrument is assumed to be trained in the correct operation have a chance to blink of the instrument and the safety issues Throughout the GenePix 4000B Array Scanner User s Guide the word There are high voltages inside you refers to this trained operator There are no user serviceable parts inside Using controls making adjustments or performing The unit will be damaged if you attempt to open the procedures other than those specified in the GenePix protective housing 4000B User s Guide may result in
11. N SOURCE mu MODEL NO FSA110P32 S mm OUTPUT 110W MAX o alla P1 5Vdc 10 0Amps 3 i P2 5 7 DC COM ri 6 0A MAX los a 15Vdc 4 0A 47 63Hz 4 c 4 0Amps P6 15Vdc 1 0Amps R f rence Axon 3420 014 Danger de haute tension Des circuits haute tension se trouvent l int rieur de l instrument laser Array Scanner GenePix 4000B Dans des conditions d utilisation normales vous tes prot g e des hautes tensions l int rieur de l instrument Avertissement Ne tentez pas d acc der l int rieur de l instrument L exposition des circuits haute tension peut provoquer des dommages corporels s v res ou fatals Il existe galement des circuits haute tension dans l ordinateur contr lant le scanner Reportez vous la documentation du fabricant de l ordinateur sur les risques li s ces hautes tensions Suivez les instructions concernant les pr cautions d utilisation de l ordinateur Entr e courant continu Maximum Pi ces mobiles L instrument laser Array Scanner GenePix 4000B contient des pi ces mobiles pouvant entra ner des risques de dommages corporels Dans des conditions d utilisation normales cet instrument est con u pour vous viter tout risque li aux pi ces mobiles Le syst me de s curit et le bo tier de protection sont con ues pour pr venir tout acc s aux pi ces mobiles durant l utilisation du scanner Avertissemen
12. PLE ROAD UNION CITY CALIFORNIA USA 94587 Tel 650 675 6200 Abbildung 1 Kundendienst und Warnetiketten Das Etikett ist auf der R ckseite des GenePix 4000B auf dem oberen Teil des Schutzgeh uses befestigt PATENTS PENDING DANGER Laser radiation when open AVOID DIRECT EXPOSURE TO BEAM Erkl rung Der Symbole Standby Modus Ger t ist bereit einen Objekttr ger zu lesen F hrung des Objekttr gers in Startposition Scanning Eject Ger t ist bereit zur Ausgabe des Objekttr gers GenePix 40008 Axon Instruments PATENTS PENDING DANGER Laser radiation when open AVOID DIRECT EXPOSURE TO BEAM MANUFACTURE DATE SERIAL NUMBER FOSTER CITY CA This device complies with 21 CFR 1040 10 amp 1040 11 3280 WHIPPLE ROAD UNION CITY CA 24587 AXON LABEL PART NUMBER 2400 330 REV B MANUFACTURE DATE SERIAL NUMBER FOSTER CITY CA This device complies with Axon Instruments 21 CFR 1040 10 amp 1040 11 J 5290 WHIPPLE ROAD UNION GITY GA 94587 AXON LABEL PART NUMBER 2400 330 REV B Abbildung 2 Identifikations und Beglaubigungsetikett Das Etikett ist auf der R ckseite des GenePix 4000B Vor Benutzung unbedingt die Gebrauchsanweisung Achtung Achtung Gefahrlicher Laserbestrahlung Stromkreis an der unteren H lfte des Schutzgeh uses befestigt GenePix 40006 Axon Instruments PATENTS PENDING Power S
13. SERVICEABLE COMPONENTS ARE CONTAINED WITHIN THIS UNIT CONSULT THE FACTORY FOR REPAIR RETURN INSTRUCTIONS USE ONLY AXON POWER SUPPLY APN 2300 419 FAILURE TO DO SO MAY CAUSE ELECTRONIC DAMAGE WITHIN THE UNIT SERVICE CONTACTS MADE IN U S A U S Office Axon Instruments Inc 3280 WHIPPLE ROAD UNION CITY CALIFORNIA USA 94587 Tel 650 675 6200 AXON LABEL PART NUMBER 2400 329 REV B GenePix 40008 Figure 1 Service Contacts and Warning Label Axon Instruments Label is affixed at the rear of the GenePix 40008 on the upper half of the PATENTS PENDING protective housing A DANGER Laser radiation when open VOID DIRECT EXPOSURE TO BEAM MANUFACTURE DATE SERIAL NUMBER FOSTER a CA Gene Pix 40008 Axon Instruments PATENTS PENDING DANGER Laser radiation when open AVOID DIRECT EXPOSURE TO BEAM MANUFACTURE DATE SERIAL NUMBER This device complies with A 21 CFR 1040 10 amp 1040 11 29 WHIPPLE ROAD UNION CITY CA 54587 AXON LABEL PART NUMBER 2400 330 REV B FOSTER CITY CA s 2 Attention see Attention Attention laser This device complies with Axon Instruments i j y 21 CFR 1040 10 8 1040 11 HA be s for dangerous voltage radiation AXON LABEL PART NUMBER 2400 330 REV B Figure 2 Identification and Certification Label Label is affixed at he rear of the GenePix 4000B on the lower half of the a b Site Requirements prot
14. TWARE and all copies of the SOFTWARE Product Improvements AXON reserves the right to make corrections or improvements to the SOFTWARE and its documentation and to the related media at any time without notice and with no responsibility to provide these changes to purchasers of earlier versions of such products Customer License Agreement xviii Term This license is effective until terminated You may terminate it by destroying the SOFTWARE and its documentation and all copies thereof This License will also terminate if you fail to comply with any term or condition of this Agreement You agree upon such termination to destroy all copies of the SOFTWARE and its documentation Limited Warranty and Disclaimer of Liability AXON warrants that the media on which the SOFTWARE is recorded and the documentation provided with the SOFTWARE are free from defects in materials and workmanship under normal use For 90 days from the date of receipt AXON will repair or replace without cost to you any defective products returned to the factory properly packaged with transportation charges prepaid AXON will pay for the return of the product to you but if the return shipment is to a location outside the United States you will be responsible for paying all duties and taxes Before returning defective products to the factory you must contact AXON to obtain a Return Merchandise Authorization RMA number and shipping instructions Failure to do so will cau
15. a cubierta e Los l seres interiores pueden da ar sus ojos antes de que pueda pesta ear e Interiormente hay altos voltajes e Enel interior no hay partes que requieran servicio por parte del usuario e a unidad se da ar si usted intenta abrir la cubierta protectora S ntomas de Da os en el Circuito de Seguridad Si usted encuentra cualquiera de los siguientes s ntomas el circuito de seguridad podr a estar da ado Es peligroso continuar usando el GenePix 4000B cuando hay s lo un circuito de seguridad funcionando Comun quese al mantenimiento t cnico a cualquiera de los n meros telef nicos indicados en la parte posterior del GenePix 4000B 1 El espejo y el montaje de los lentes siguen movi ndose por debajo de la placa despu s de abrir la puerta 2 La luz azul emitida por el diodo LED con etiqueta Scanning localizado en la parte superior del GenePix 4000B no se extingue cuando la puerta esta abierta 3 Usted no puede registrar ninguna placa 4 No se puede escuchar el sonido caracteristico del contacto entre metales producido por el circuito de seguridad cuando se ajusta en su lugar Este ocurre normalmente cuando la apertura donde se coloca la placa se abre aproximadamente 6 mm CLASS 1 LASER PRODUCT Seguridad del Laser Precauciones e No inserte ning n objeto en las aperturas o respiraderos del GenePix 4000B diferente de la placa Puede ocasionar fallas en el circuito de segurid
16. ad e No intente mover ning n componente debajo de la platina Usted puede causar fallas en el circuito de seguridad Informaci n sobre la Seguridad Clasificacion y Potencia de los Laseres Incluidos Longitud de Onda Potencia Divergencia Duraci n Tipo de Laser_ Advertencia Exposici n a la radiaci n l ser puede ocasionar lesiones Por ejemplo mirar directamente a la luz del l ser puede causar ceguera Clasificaci n de la Unidad de Poder C FORTRON SOURCE mu MODEL NO FSA110P32 S mm OUTPUT 110W MAX INPUT P1 5Vdc 10 0Amps 100 240V g es 6 0A MAX P2 5 7 DC COM N 47 63Hz P3 4 15Vdc 4 0Amps S e P6 15Vdc 1 0Amps 3 Y El n mero de Parte de Axon Instruments es 3420 014 Peligro de Alto Voltaje El GenePix 4000B Array Scanner contiene electr nica de alto voltaje Bajo condiciones normales de operaci n usted est protegido del alto voltaje del instrumento Advertencia No intente acceder al interior del instrumento Exposici n a alto voltaje puede causar lesiones severas o fatales Electr nica de alto voltaje se encuentra en el computador que controla el esc ner Revise la documentaci n del fabricante sobre las advertencias al respecto Cerciorese de seguir cuidadosamente las instrucciones sobre la utilizaci n apropiada del computador ENTRADA CORRIENTE CONTINUA M xima Partes M viles El GenePix 4000B Array Scanner contiene partes m viles qu
17. ass slide with a total depth of focus of 64 um equally distributed on both sides of the focal plane depth of focus is defined as the range over which the signal is within 50 of the maximum signal The GenePix software allows the focal point to change from 50 um to 200 um relative to the zero position Photo Detection The GenePix 4000B uses a pair of high sensitivity low noise photo multiplier tubes PMTs to detect the emitted fluorescent light Loosely defined PMTs are optical components that convert incident photons into electrons via the photoelectric effect When an incident photon impinges on the active surface of the PMT the photocathode an electron is generated This electron flows through a series of electron multipliers dynodes to the anode The amount of current that flows from the anode is directly proportional to the amount of incident light at the photocathode The amount of amplification that a PMT can produce depends on the number of dynodes in the PMT and the voltage that is applied to the PMT With PMTs it is possible to achieve a gain of 10 When you increase the PMT voltage setting in the GenePix 4000B software you are increasing the gain of the PMTs Note It is important to realize that when you increase the gain of the system you are also increasing the sensitivity to non specific fluorescence thus increasing any electronic noise in the system This increase in noise can often be overcome by line averagin
18. dentification et tiquette de certification Cette tiquette est coll e l arri re du GenePix 4000B sur la partie inf rieure du boitier GenePix 40005 Axon Instruments PATENTS PENDING Power Supply PWR 4 Axon Part No 2300 419 SERVICE CONTACTS U S Office Axon Instruments Inc 3280 WHIPPLE ROAD UNION CITY CALIFORNIA USA 94587 Tel 650 675 6200 AXON LABEL PART NUMBER 2400 331 REV B Figure 3 Etiquette de l alimentation Cette tiquette est fix e sur le bas du l alimentation Significations des Symboles Appareil en attente Pr t a scanner une lame Attend en position de d part Balayage en cours Ejection Support de lame accessible GenePix 40005 Axon Instruments PATENTS PENDING DANGER Laser radiation when open AVOID DIRECT EXPOSURE TO BEAM MANUFACTURE bare SERIAL NUMBER Bei CITY CA This device complies with 21 CFR 1040 10 amp 1040 11 3230 WHIPPLE ROAD UNION CITY GA 34507 AXON LABEL PART NUMBER 2400 330 REV B Attention voir les Attention haute Attention instructions tension rayonnement d utilisation Danger Laser Conditions n cessaires sur le site Le GenePix 4000B est congu pour fonctionner au mieux de ses performances si les conditions n cessaires sur le site sont satisfaites Comme pour tout autre instrument optique de pr cision il ne doit pas tre expos la poussi re
19. e Parallel port security dongle APN 6190 014 GenePix cover letter APN 9320 090 GenePix Test Slides APN GP 2 GP 4 Bundled host computer optional Computer Requirements Minimum System Requirements IBM AT compatible computer with a Pentium 400 MHz or faster processor Windows 98 or ME operating system dual boot systems are not recommended 512 MB RAM Hard disk with 20 GB free for image storage CD ROM drive 1024x768 display system with 65K colors Parallel port Internet Explorer 5 0 GenePix 4000B User s Guide Copyright 1999 2001 Axon Instruments Inc Installing GenePix e 3 Recommended System Requirements e IBM AT compatible computer with a Pentium III 800 MHz or faster processor e Windows NT 4 0 or Windows 2000 operating system dual boot systems are not recommended e 768 MB RAM or more e Hard disk with 30 GB or more free for image storage e Recordable Rewriteable CD ROM or Jaz drive e 1280x1024 display system with 16M colors e Parallel port e Internet Explorer 5 0 or higher Preparing to Install GenePix If you have purchased GenePix without the optional host computer please follow the instructions below If you purchased GenePix with a bundled host computer the necessary hardware and software are already installed If so skip to Connecting the GenePix 4000B to the Computer Quick Overview of GenePix Hardware and Software Installation For users who require a minimal level of detail the fol
20. e pueden causar lesiones El instrumento est dise ado para protegerlo a usted de las partes en movimiento en condiciones normales de funcionamiento El circuito de seguridad y la cubierta protectora impiden el acceso al interior del instrumento durante un escan Advertencia No intente acceder al interior del instrumento Las partes m viles pueden causar lesiones Fusibles El GenePix 4000B no contiene fusibles Precaucions con Materiales Peligrosos El usuario debe utilizar procedimientos y precauciones de laboratorio estandarizados cuando trabaja con productos qu micos Advertencia Utilice siempre las instrucciones de la f brica cuando trabaje con productos qu micos El fabricante y o el proveedor no son responsables A legalmente por da os o lesiones ocasionados como consecuencia del uso de materiales peligrosos Paneles Que No Forman Parte del Circuito de Seguridad Vista de la base del GenePix mostrando los tornillos que aseguran la parte superior de la cubierta protectora NO REMUEVA ESTOS CINCO TORNILLOS PELIGRO Radiacion con laser si se abre EVITE EXPOSICION DIRECTA AL RAYO LASER Mantenimiento y Reparaci n No se requiere ning n mantenimiento por parte del usuario Este no est autorizado para ejecutar ninguna reparaci n Si hay alg n problema por favor comun quese al mantenimiento t cnico a cualquiera de los n meros telef nicos indicados en la etiqueta Lista de Controles Este gu a prov
21. ect your printer to the dongle GenePix 4000B User s Guide Copyright 1999 2001 Axon Instruments Inc Installing GenePix e 7 Starting GenePix Pro 3 0 After the successful installation of the software you will find the entry Axon Laboratory in your list of Programs in the Start menu and there will be two new icons your desktop There are GenePix Pro 3 0 and GenePix Pro 3 0 demo entries in your Axon Laboratory group and icons for these on your desktop Both of these shortcuts will start GenePix Pro The only difference between the demo version and the non demo version is that the demo version does not interact with the scanner Typically if you are only analyzing data and are not doing any image acquisition you would select the demo version For acquisition select GenePix Pro 3 0 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 4000B had been initialized and you can load your first slide Note for Windows 2000 Users Due to security changes in the Windows 2000 operating system a user must belong to the Administrator or Power User group also known as Standard user in order to run Internet Explorer IE scripts from the Reports Tab in GenePix Pro 3 0 If a user does not have Standard user access
22. ective housing x The GenePix 4000B is designed to operate optimally if the site requirements are met As with any precision optical moy instrument care should be taken to maintain a low dust GenePix 400065 ade PERE de low vibration environment Temperature and humidity Axon Instruments extremes may compromise performance PATENTS PENDING Power Supply PWR 4 Environmental Temperature 50 86 F 10 30 C SR AP Environmental Humidity 5 95 non condensing oe Power Requirements Input 100 240V 6A max 47 63 Axon Instruments Inc Hz 3280 WHIPPLE ROAD UNION CITY CALIFORNIA USA 94587 Space Requirements 18 in deep x 13 in wide x 7 in high Tel 650 675 6200 AXON LABEL PART NUMBER 200 351 REV 44 1 cm x 33 1 cm x 17 8 cm Figure 3 Power Supply Label Weight Requirements Sufficient to support 35 8 Ib 16 2 Label is affixed to the bottom of the power supply kg with minimal vibration Safety Information vi Informations de s curit importantes sur le GenePix 4000B L utilisateur de l instrument laser Array Scanner GenePix 4000B est suppos avoir regu la formation ad quate sur Putilisation de cet instrument et les consignes de s curit associ es Le GenePix 4000B Array Scanner User s Guide s adresse un op rateur qualifi L utilisation de commandes et l ex amp cution de r glages ou de proc dures autres que ceux sp cifi s dans le GenePix 4000B User s Guide entrain
23. ee una lista de controles Precauci n el uso de los controles el ajuste o la ejecuci n de procedimientos diferentes de los especificados aqu puede resultar en exposici n peligrosa a la radiaci n del laser GenePix 4000B Users Guide Copyright 1999 2001 Axon Instruments Inc Etiquetas de Seguridad Si una etiqueta se hace ilegible o se pierde por algun motivo por favor contacte el servicio t cnico del sistema para obtener etiquetas sin costo alguno Mientras espera por las etiquetas de reemplazo copie las que aparecen en esta secci n y pegue una copia en el instrumento Simbolos de Advertencia GenePix 40005 Axon Instruments PATENTS PENDING TO PREVENT ELECTRICAL SHOCK AND DAMAGE TO THE INSTRUMENT DO NOT ATTEMPTTO OPEN UNIT NO CUSTOMER SERVICEABLE COMPONENTS ARE CONTAINED WITHIN THIS UNIT CONSULT THE FACTORY FOR REPAIR RETURN INSTRUCTIONS USE ONLY AXON POWER SUPPLY APN 2300 419 FAILURE TO DO SO MAY CAUSE ELECTRONIC DAMAGE WITHIN THE UNIT SERVICE CONTACTS MADE IN U S A U S Office Axon Instruments Inc 3280 WHIPPLE ROAD UNION CITY CALIFORNIA USA 94587 Tel 650 675 6200 AXON LABEL PART NUMBER 2400 329 REV B Figura 1 Etiqueta con Advertencias y Contactos para Reparaci n La etiqueta est fijada a la parte posterior del GenePix 4000B en la mitad superior de la cubierta protectora GenePix 40008 Axon Instruments PATENTS PENDING MANUFACTURE DATE SERIAL NUMBER This device
24. er para su uso Requerimientos del Lugar de Instalaci n El GenePix 4000B est dise ado para operar ptimamente si el lugar de instalaci n cumple con los requerimientos Como con cualquier instrumento ptico de precisi n debe tener cuidado de manterlo en un lugar bajo en polvo y de poca vibraci n Temperaturas extremas y humedad pueden comprometer su funcionamiento Temperatura ambiental 50 86 F 10 30 C Humedad ambiental 5 95 sin condensaci n Energ a requerida Entrada 100 240V 6 A m ximo 47 63 Hz Espacio requerido 18 profundidad x 13 amplitud x 7 altura 44 1 cm x 33 0 cm x 17 8 cm Peso requerido Suficiente para sostener 35 8 lb 16 2 kg con m nima vibraci n Informaci n sobre la Seguridad xii Wichtige Sicherheitsmassnahmen fiir GenePix 4000B Es wird vorausgesetzt dass der Benutzer des GenePix 4000B qualifiziert ist das Ger t richtig und sicher zu verwenden Innerhalb der gesamten Beschreibung fiir den GenePix 4000B Array Scanner bezieht sich das Wort Sie auf diesen qualifizierten Benutzer Die Benutzung der Kontrollvorrichtungen Anderungen oder das Ausfiihren anderer Handlungen ausser denen die in der Gebrauchsanweisung des GenePix 4000B erklart sind k nnen zu gef hrlichen Strahlungen hoher Voltzahl oder losen Teilen f hren Kontakt mit diesen Gefahren kann zu schweren oder t dlichen Verletzungen f hren Sicherheitstext der in dieser Gebrauchanwe
25. eraient de graves dangers d exposition au faisceau laser des hautes tensions ou des pi ces mobiles Ces dangers peuvent tre l origine de dommages corporels s v res ou fatals Informations de s curit utilis es dans ce Guide Veillez 4 prendre les pr cautions indiqu es dans ce guide Avertissement Indique un risque de dommage corporel s v re ou fatal pour l utilisateur ou d autres personnes si les pr cautions ou les instructions indiqu es n taient pas observ es Attention Indique un risque de dommage pour l instrument de perte de donn es ou de donn es invalides si Putilisateur ne suit pas les recommandations de ce manuel Important D signe des informations vitales pour le fonctionnement optimal du syst me Note Identifie des informations d int r t g n ral Le bo tier de protection Le bo tier et les verrouillages de s curit de l instrument sont congus pour vous prot ger du danger d exposition au faisceau laser des hautes tensions ou des pi ces mobiles Il n est pas n cessaire que vous acc diez l int rieur de l instrument o aucune intervention n est n cessaire Avertissement Ne d sactivez pas les verrouillages de s curit n ouvrez pas le boitier et ne tentez pas d acc der a l int rieur de l instrument par aucune autre ouverture L ouverture du boitier pourrait endommager les composants de l instrument et entrainer un danger d exposition
26. et aux vibrations Des conditions extr mes de temp rature et d humidit peuvent compromettre ses performances Temp rature 10 30 C Humidit 5 95 sans condensation Alimentation 100 240V 6A max 47 63 Hz Espace n cessaire 44 1 cm x 33 0 cm x 17 8 cm Poids Structure suffisante pour supporter un poids de 16 2 kg pratiquement sans vibration GenePix 4000B User s Guide Copyright 1999 2001 Axon Instruments Inc Informacion Importante sobre la Seguridad del GenePix 4000B Se asume que el operador del GenePix 4000B Array Scanner esta entrenado en las precauciones de seguridad a seguir y en la utilizaci n correcta del instrumento La palabra usted como se utiliza en esta gu a del usuario del GenePix 4000B Array Scanner se refiere a este operador entrenado Utilizaci n o ajuste de los controles y la ejecuci n de procedimientos diferentes a los especificados en la gu a del usuario del GenePix 4000B puede resultar en exposici n peligrosa a radiaci n l ser alto voltaje o a partes m viles Exposici n a estos peligros pueden producir lesiones severas o fatales Declaraciones de Seguridad Utilizadas en esta Gu a Cercior se de observar las declaraciones de seguridad que se presentan en esta gu a Advertencia Indica la posibilidad de lesi n severa o fatal al usuario u otras personas si no se siguen las instrucciones y precauciones Precauci n Indica que puede ocurrir da o del intrumento p
27. f the NASA Supplement to the FAR as applicable Manufacturer is Axon Instruments Inc 3280 Whipple Road Union City CA 94587 Governing Body This Agreement is governed by the laws of the State of California GenePix 4000B User s Guide Copyright 1999 2001 Axon Instruments Inc XIX COPYRIGHT The information in this Guide is copyrighted and must not be reproduced in any form whatsoever without written permission from Axon Instruments Inc VERIFICATION This instrument is extensively tested and thoroughly calibrated before leaving the factory Nevertheless researchers should independently verify the basic accuracy of the instrument using suitable test samples Copyright Verification Caution Table of Contents For Technical Assistance 00 ccccccccccccscccccsssssssescescescsssssssessescesssesscsseessssseseesseessesseseeeeeeeees i Important Safety Information for the GenePix 4000B iii Informations de s curit importantes sur le GenePix 4000B vi Informaci n Importante sobre la Seguridad del GenePix 4000B e 1x Wichtige Sicherheitsmassnahmen f r GenePix 4000B xii Declaration of Conformity ss XV Customer License Agreement sus xvil Chapter 1 Installing GenePix 1 About his User s Gude 3
28. g but the cost is decreased acquisition speed 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 However there is a very non linear relationship between the gain of the PMT and the applied Chapter 4 16 e Imaging System Hardware PMT voltage Therefore a slide scanned at a PMT voltage of 800 V will not be twice as bright as the same slide scanned at 400 V The PMTs in the GenePix 4000B meet 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 arrays Second the PMTs have been further selected for their reliability and optimal signal to noise performance Mechanical The GenePix 4000B is a mechanical device Its laser based scanning system uses a patent pending mechanical design The GenePix 4000B operates by slowly scanning the slide in the y direction and rapidly scanning in the x direction The design of the GenePix 4000B allows a scan of a 25 mm x 75 mm slide at 5 um resolution in about 12 minutes When using such a mechanical device one must be able to monitor the variability in the performance of its mechanical components The GenePix 4000B has been designed with a number of optimizations to ensure that variabi
29. hazardous exposure to laser light high voltage or moving parts Exposure to Interlock Failure Symptoms these hazards can cause severe or fatal injury Tf you experience any of the following symptoms you may have an interlock failure It is unsafe to continue to use Safety Text Used In This Guide the GenePix 4000B with only one interlock functioning Make sure you follow the precautionary statements Please contact Technical Support immediately at either of presented in this guide the numbers indicated on the rear panel of the GenePix Warning Indicates a possibility of severe or fatal injury 40008 to the user or other persons if the precautions or 1 Mirror and lens assembly keeps moving below the instructions are not observed slide after the door is opened Caution Indicates that damage to the instrument loss of 2 The blue Scanning LED on top of GenePix 4000B data or invalid data could occur if the user fails to comply doesn t extinguish when the door is open with the advice given You cannot scan any slides Important Highlights information that is critical for 4 5 a You can no longer hear the distinctive metal on metal optimal performance of the system sound that the mechanical interlock makes when it Note Identifies items of general interest falls into place This normally happens when the slide loading door has opened about 4 The Protective Housing The protective housing and instrument interlocks are de
30. he Setup exe program file on the CD ROM This file is found in the GenePix subdirectory on the CD ROM To start the setup program manually from the Start menu select Run and type x GenePix setup exe where x is the drive letter of your CD ROM drive 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 your computer has shut down proceed below to Connecting the GenePix 4000B to the Computer section Connecting the GenePix 4000B to the Computer Caution Failure to follow these instructions in the correct order can lead to damage to your instrument Before connecting the GenePix 4000B to your SCSI connector please ensure that your computer has been turned off and that the GenePix power supply 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 hardware The SCSI connector and power connector are located at the back of the GenePix 4000B Chapter 1 6 e Installing GenePix Once the SCSI connection has been made check that the power supply is turned off then connect the power cord to GenePix Turn on the power supply and then turn on your computer Windows 98 Windows Millennium and Windows 2000 If the connections have been made correctly when you restart your computer Windows wi
31. i e if they have guest or restricted user access the Windows 2000 environment does not allow such users access to the scripting library required by IE and therefore will encounter a Library not registered error when running scripts in GenePix Pro 3 0 Troubleshooting Installation SCSI Card Installation Problems If you encounter any problems with the installation of the included SCSI card please refer to the instructions that came with the card If you require further assistance on installation of the included SCSI card contact Technical Support If you are using a SCSI card that was not provided with your GenePix scanner you should contact the supplier of that SCSI card for technical support Chapter 1 8 e Installing GenePix Hardware Problems GenePix Pro 3 0 automatically detects the GenePix 4000B If this does not occur please verify the following items The data cable between the computer and GenePix 4000B is securely connected The GenePix 4000B has power the green power light on the top of the scanner will be glowing The SCSI card is operational see above 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 Software Problems If you have purchased your GenePix with a bundled host computer the software has already been installed If you are using a previously purchased computer please consider the fol
32. ion The GenePix 4000B is a scanning instrument This means that a single point of light is rapidly scanned across the array and a composite image is created from the digitized signals from the PMT The spatial resolution of the system refers to the size of this single scanning point In the GenePix 4000B the spatial resolution is 5 um for a Data Scan and 40 um for a Preview Scan During the Preview Scan the same 5 um spot is scanned however the slow y direction scanning operates eight times faster and only one eighth of the samples in the x direction are used It is possible to change the resolution of Data Scans Using the software you can specify a resolution that is a multiple of 5 When the slide is scanned the appropriate number of pixels are averaged to create a single pixel representation For example if you set the resolution to 10 um 4 raw data pixels are averaged to produce each pixel in the final image This option is often 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 MB However keep in mind that you need to acquire enough pixels for each feature in order to make accurate measurements Finally reducing the scanner resolution in software does not reduce the scan time it only reduces the final image file size It also increases signal to noise by the square root of the number of pixels averaged Dynamic Range and Sens
33. irected onto the slide If the laser light impinges on an appropriate fluorophore bound on the slide emission light of a different wavelength is emitted These emission photons are directed back through the optical system where they pass through another set of filters before reaching the dual photodetectors One of the problems faced by a dual scanning system is crosstalk where the two different wavelengths of light are not sufficiently separated in the scanning system For example emission light from one fluorophore can be recorded by the detector for the second fluorophore or spurious excitation light for the first fluorophore can bleed back into the detector for the second fluorophore Crosstalk is often a concern when GenePix 4000B User s Guide Copyright 1999 2001 Axon Instruments Inc Imaging System Hardware e 15 one is using a pair of fluorophores that have similar spectral properties The result can be an erroneous contribution of fluorescence from one optical channel to the other The GenePix 4000B employs two approaches to reduce crosstalk to negligible levels First the filter sets and excitation lasers have been carefully chosen to ensure that crosstalk between the two fluorophores is minimized Second and more importantly the patent pending optical design guarantees that spectral overlap is zero User controlled focusing is a new feature in the GenePix 4000B The focal point at the zero position is at the surface of the gl
34. irs lentilles continue se d placer sous la lame apr s l ouverture de la porte coulissante 2 La DEL Scanning voyant bleu sur le dessus du GenePix 4000B ne s teint pas quand la porte est ouverte Il vous est impossible de scanner une lame 4 Vous n entendez plus le bruit m tallique caract ristique que provoque le verrouillage m canique lorsqu il est enclench Ce clic s entend normalement d s que la porte coulissante est ouverte d un quart de pouce environ 6 mm S curit concernant les Lasers CLASS 1 LASER PRODUCT Pr cautions prendre Ne rien introduire dans les ouvertures ou a rations du GenePix 4000B part une lame de microscope dans le compartiment pr vu pour son chargement Vous pourriez provoquer une d faillance des syst mes de s curit syst mes double verrouillage Ne pas tenter de d placer un composant derri re le support des lames Ceci risquerait de provoquer une d faillance des syst mes de s curit syst mes double verrouillage GenePix 4000B Users Guide Copyright 1999 2001 Axon Instruments Inc A A Puissance et Classification des Lasers Utilis s Longueur Divergence Classe des lasers d onde embarqu s Classe Ib Classe Ib Avertissement L exposition au faisceau laser peut entrainer des dommages corporels Par exemple fixer directement le laser entraine un risque de c cit Classification de l alimentation CP FORTRO
35. isung verwendet wird Versichern Sie sich bitte dass Sie alle Vorsichtsmassnahmen beachten Warnung Weist auf die M glichkeit einer schweren oder t dlichen Verletzung hin wenn die Anweisungen oder Vorsichtsmassnahmen nicht beachtet werden Achtung Weist darauf hin dass bei Nichtbeachtung der Vorschriften Schaden am Ger t entstehen kann und Datenausfall oder m glicherweise ung ltige Daten resultieren k nnen Wichtig Weist auf Information hin die wichtig ist um die optimale Leistung des Ger tes sicherzustellen Anmerkung Deutet auf Themen von generellem Interesse hin Das Schutzgeh use Das Schutzgeh use und die elektrische Verriegelung sind so konstruiert dass Sie vor Laserstrahlen Hochspannung und beweglichen Teilen gesch tzt sind Sie brauchen das innere Teil des Ger tes nicht zu ffnen weil keine f r den Nutzer justierbaren Teile vorhanden sind Warnung Ver ndern Sie nicht die elektrische Verriegelung ffnen Sie nicht das Schutzgeh use oder versuchen Sie gleichermassen nicht das Innere des Ger tes durch andere ffnungen zu erreichen Der GenePix 4000B ist ein Laserprodukt der Klasse 1 Auf den Bereich der im Ger t entstehenden st rkeren Laserstrahlen hat der Benutzer kein Zugriff Glasstreifen k nnen sicher in den Laserrasterbereich eingef hrt werden weil die ladende T r mehrere Verriegelungen hat die Laserstrahlen blockieren Es gibt zwei ffnungen die nicht elektrisch verriegelt sonde
36. itivity The dynamic range of an instrument is the signal width that can be resolved above the noise the instrument produces The dynamic range depends on all the components in a given system For example if you use a PMT with a dynamic range of 10 but process the signals through a sub standard 8 bit analog to digital converter you will end up with an instrument with a poor dynamic range Furthermore while an instrument may have a large dynamic range one may not be able to use the whole range reliably if the response is non linear Therefore when rating Chapter 4 18 e Imaging System Hardware an instrument one must consider the range over which its response remains linear For the GenePix 4000B the dynamic range is 10 The dynamic range of an instrument is often considered in conjunction with its sensitivity The sensitivity is defined as the minimum detectable signal above background noise Although you may be able to see features below this level the minimum signal that can be accurately quantified is the dye concentration for which the signal is three times the background noise For the GenePix 4000B the sensitivity is on the order of 0 1 fluorophores um for Cy3 and Cy5 Limitations GenePix 4000B is an acquisition and first pass data analysis system for array experiments It has been designed to fulfill all your primary acquisition and analysis needs extracting data from arrays and exporting it to advanced data analysis and p
37. lity in the mechanical performance is monitored in real time during acquisition and corrected The utmost attention has been given to selecting and implementing components to create a highly reliable high performance instrument Electronic While the optical components of the GenePix 4000B are indispensable for generating the electrical current from PMTs the electronic components are just as important They govern the operation of the PMTs and the conversion of their analog current signals into a digital signal that can be processed by the host computer Axon Instruments is the world leader in the design and construction of low noise amplifiers Our amplifiers are used around the world by researchers in the neuroscience community We have worked hard for over a decade to create low noise amplifiers and high performance computer hardware to digitize these signals Our expertise in this area has been applied to the GenePix 4000B Integrated with the GenePix 4000B 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 are linear GenePix 4000B User s Guide Copyright 1999 2001 Axon Instruments Inc Imaging System Hardware e 17 over a wide dynamic range and that the signal to noise level exceeds all other currently available array scanners General Items of Interest Spatial Resolut
38. ll show a message that indicates that New Hardware has been detected Windows will automatically install the necessary driver for the GenePix 4000B scanner If Windows does not automatically find the driver you can manually select the driver using 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 4000B If you are connecting the GenePix 4000B to a computer that was purchased with the GenePix the driver is already installed Windows NT You will be able to verify that the GenePix scanner has been successfully installed when you start GenePix Pro 3 0 This is outlined further below Connecting the Security Dongle GenePix Pro 3 0 requires a security dongle to operate If the dongle is absent you will be able to open images in GenePix Pro but you will not be able to save your settings files or save your analysis results In addition you can analyze only 100 features without a dongle Installation of the dongle is straightforward Simply connect it to the parallel port of your computer If you have a printer already installed do not worry The dongle is a pass through device and you simply connect the dongle to the parallel port then conn
39. lowing GenePix Pro 3 0 requires a minimum of 256 MB of RAM to acquire images GenePix Pro is capable of analyzing data when less than 256 MB of RAM is present but the maximum image size is reduced and performance will be non optimal GenePix Pro 3 0 requires a security dongle to enable saving of results or settings files If the dongle is not found the software operates with limited file saving functionality GenePix Pro 3 0 requires Internet Explorer 4 0 or later to be installed for its Report tab and on line Help to function correctly GenePix 4000B User s Guide Copyright 1999 2001 Axon Instruments Inc Introduction to GenePix 4000B e 9 Chapter 2 Introduction to GenePix 4000B The GenePix 4000B is the latest array scanner from Axon Instruments Inc succeeding the GenePix 4000A scanner The 4000B has the same basic design as the 4000A but with the following new features e Data Scan resolution has been increased from 10 um to 5 um e User attenuatable laser power e User adjustable focus e Pixel by pixel laser power correction Axon Instruments has consulted widely among the scientific pioneers of array techniques to produce an instrument that fulfills all their image acquisition and primary analysis needs GenePix 4000B Features The GenePix 4000B scanner e simultaneously scans array slides at two wavelengths using a dual laser scanning system which dramatically reduces scan time 5 minutes for full scan and
40. lowing outlines the steps necessary to install GenePix hardware and software Caution If you do not follow the instructions in the order specified below you may damage your instrument Important Initially do not attach the GenePix 4000B to your computer 1 Optional Install the SCSI card This step is not required if the scanner is shipped with a computer Chapter 1 gt e Installing GenePix 2 Optional Start the computer This step is not required if the scanner is shipped with a computer 3 Optional Install GenePix Pro 3 0 This step is not required if the scanner is shipped with a computer 4 Shutdown the computer 5 Attach the GenePix 4000B to the computer with the SCSI cable 6 Attach the power supply to the GenePix 4000B making sure the power supply is turned off while you are doing this 7 Turn on the power supply 8 Attach the security dongle to parallel port 9 Turn on the computer 10 Windows will automatically find the scanner and install the appropriate driver 11 Start GenePix Pro 3 0 using the GenePix Pro icon on the desktop 12 Start scanning Installation of the SCSI card Included with your GenePix 4000B is a SCSI adapter card for your host computer This card is used to transfer data and instructions between the host computer and the GenePix 4000B hardware The SCSI card that is included with GenePix 4000B is a PCI based Plug n Play card that will install easily on most compu
41. n iio ie a RR 17 Dynamic Range and Sensitivity 17 Limitations sei neti rn nee iia a aaa es 18 SUMMATY a ee una aan 18 Acknowledgments cit it dd dr ne tee cdi 19 Index ii A TE AA eee 21 GenePix 4000B User s Guide Copyright 1999 2001 Axon Instruments Inc About This User s Guide This User s Guide focuses on the technical and theoretical aspects of the GenePix 4000B hardware We recommend that you use this Guide in conjunction with the GenePix Pro 3 0 User s Guide and the on line Help within GenePix Pro 3 0 press F1 For information on setting up your GenePix 4000B scanner and software please refer to Chapter 1 For a guided tutorial on scanning your first slide see Chapter 4 of the GenePix Pro 3 0 User s Guide Checklist of Parts The following items are included in your GenePix package GenePix 4000B bench top instrument PCI SCSI adapter for host computer Driver diskette for SCSI card SCSI data transfer cable Power supply unit power cord Power cord for power supply GenePix 4000B User s Guide Installing GenePix e 1 Chapter 1 Installing GenePix APN APN APN APN APN APN 2300 343 6130 004 2700 089 2100 408 3420 014 3010 011 013 014 or 015 Chapter 1 2 e Installing GenePix Three copies of GenePix Pro 3 0 software for Windows 95 98 or NT Each copy contains e GenePix Pro 3 0 Installation CD ROM APN 2700 090 e GenePix Pro 3 0 User s Guide APN 2500 137
42. ntrollrechner des Ger tes Lesen Sie sich bitte die Gebrauchsanweisung ber die Hochspannungsgefahr durch Befolgen Sie alle Anweisungen ber die Sicherheitsmassnahmen beim Gebrauch des Rechners Eingabe Gleichstrom Maxim Bewegliche Teile Der GenePix 4000B Array Scanner enh lt bewegliche Teile die Verletzungen verursachen k nnen Unter normalen Umst nden ist das Ger t so konstruiert um Sie vor den beweglichen Teilen zu sch tzen Die Verrieglung und das Sch tzgeh use sind da damit ein Zugriff auf die beweglichen Teile w hrend einer Ablesung nicht m glich ist Warnung Versuchen Sie nicht das innere Teil des Ger tes zu ffnen Die darin enthaltenen beweglichen Teile k nnen Verletzungen verursachen Sicherung Es befinden sich im GenePix 4000B keine Sicherungen xiii Sicherheitsvorkehrungen Der Benutzer muss alle normalen Laboranweisungen und Sicherheitsvorkehrungen befolgen wenn Chemikalien verwendet werden Achtung Befolgen Sie immer die Anweisungen der Hersteller wenn Sie mit Chemikalien arbeiten Der Hersteller und oder der Lieferant bernehmen keine Verantwortung f r Sch den die durch den Missbrauch von gef hrlichen Chemikalien verursacht werden Ger te ffnungen Ohne Elektrische Verriegelung Die untere Ansicht des GenePix zeigt die Schrauben welche den oberen Teil des Schutzgeh uses zusammenhalten ENTFERNEN SIE DIESE FUNF SCHRAUBEN UNTER KEINEN UMST NDEN VORSICHT Laserbest
43. rahlung wenn ge ffnet VERMEIDEN SIE DIREKTEN KONTAKT MIT DEM LASERSTRAHL Instandhaltung und Vorsorge Es ist keine Vorsorge durch den Benutzer n tig Jede eigenm chtige Reparatur durch den Benutzer ist untersagt Wenn ein Problem auftritt dann rufen Sie bitte den Technischen Hilfsdienst an Liste von Kontrollvorrichtungen Diese Gebrauchsanweisung enth lt eine Liste der Kontrollvorrichtungen Achtung Der Gebrauch von Kontrollvorrichtungen oder Einstellungen bzw die Ausf hrung von Handlungen au er denen die in dieser Anweisung beschrieben sind k nnen zu gef hrlichen Strahlungen f hren Sicherheitsmassnahmen xiv Sicherheitsetiketten Sollte ein Etikett unlesbar werden oder aus unbekannten Gr nden fehlen setzen Sie sich bitte mit dem Technischen Hilfsdienst f r einen kostenlosen Ersatz des Etiketts in Verbindung W hrend Sie auf das Etikett warten kopieren Sie die Etiketten am Ende dieses Abschnitts und befestigen Sie eine Kopie des Etiketts am Ger t Abbildungen mit Sicherheitshinweisen GenePix 40008 Axon Instruments PATENTS PENDING TO PREVENT ELECTRICAL SHOCK AND DAMAGE TO THE INSTRUMENT DO NOT ATTEMPT TO OPEN UNIT NO CUSTOMER SERVICEABLE COMPONENTS ARE CONTAINED WITHIN THIS UNIT CONSULT THE FACTORY FOR REPAIR RETURN INSTRUCTIONS USE ONLY AXON POWER SUPPLY APN 2300 419 FAILURE TO DO SO MAY CAUSE ELECTRONIC DAMAGE WITHIN THE UNIT U S Office Axon Instruments Inc 3280 WHIP
44. res Cy3 and Cy5 Amersham Pharmacia Biotech which are currently the most widely used fluorescent probes for array imaging The individual lasers have been selected because of their superior optical performance and reliability Since the performance of such lasers is often sensitive to external temperature fluctuations the GenePix 4000B uses an active temperature stabilization design to minimize temperature based laser fluctuations Furthermore each laser has stabilized feedback output to ensure that photon output is constant User attenuatable laser power is a new feature in the GenePix 4000B The software allows you to scan at 10 30 or 100 of the full laser power Laser power cannot be attenuated during scanning Laser excitation sources are often used in scanning systems instead of conventional wide band white light sources such as a xenon or mercury light source The reasons 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 Mirrors Lenses and Filters Excitation laser light is directed onto the slide after passing through a series of filters and mirrors While laser light is by definition very narrow band the GenePix 4000B employs additional optical filters to ensure that no spurious excitation light is d
45. resentation software The data extracted and displayed by GenePix 4000B can only be as good as the preparation of the slides the better the slides the better the data that GenePix will return to you Summary The GenePix 4000B is a high performance instrument that has been designed to maximize the quality of data that it generates The utmost attention has been given to creating a fast low noise high sensitivity instrument GenePix 4000B User s Guide Copyright 1999 2001 Axon Instruments Inc Acknowledgments e 19 Acknowledgments Axon Instruments Inc would like to extend its thanks to the numerous academic and corporate scientists who provided critical input during the planning evaluation and testing of the GenePix 4000B system In particular Drs Stephen J Smith and Michael B Eisen of the Stanford University School of Medicine and Dr Joseph L DeRisi of the University of California at San Francisco were instrumental in the development of the GenePix scanner and software helping to make the GenePix 4000B an instrument designed for the research community Acknowledgments acknowledgments 19 amplifiers 16 Copyright i crosstalk 14 Cy3 Cy5 14 Data Scan 17 digitization 9 dynamic range 9 fluorophore 14 See Cy3 Cy5 GenePix installation 1 hardware 13 amplifiers 16 laser excitation 14 quantum efficiency 16 spatial resolution 17 Help on line 1 image size 17 Index e 21 Index laser
46. rn mit Schrauben befestigt sind Diese k nnen nur mit Hilfe eines Werkzeuges entfernt werden Sie sind unten abgebildet Entfernen Sie niemals die Schrauben um das Geh use zu ffnen e Die im Ger t enstehenden Laserstrahlen k nnen Ihre Augen besch digen bevor Sie Gelegenheit haben sich zu schiitzen Im Ger t entstehen hohe Spannungen e Es befinden sich im Ger t keine fiir den Nutzer justierbaren Teile Wenn Sie versuchen das Schutzgeh use zu ffnen kann dies eine Besch digung des Ger tes zur Folge haben Hinweise auf ein Versagen der elektrischen Verriegelung Wenn eines der nachfolgenden Probleme auftritt hat wahrscheinlich eine Verriegelung versagt Es ist sehr gef hrlich weiterhin den GenePix 4000B zu benutzen wenn nur eine elektrische Verriegelung funktioniert Bitte rufen Sie sofort den Technischen Hilfsdienst an sobald eines der unten beschriebenen Symptome auftritt Die Service Nummern befinden sich auf der hinteren Seite des Ger tes 1 Spiegel und Linsensysteme bewegen sich weiterhin unter dem Objekttr ger nachdem die T r ge ffnet wurde 2 Die blaue Scanning Lichtdiode oben auf dem GenePix 4000B erl scht nicht wenn die T r ge ffnet wird 3 Sie k nnen keine Glasstreifen ablesen 4 Der Benutzer h rt nicht mehr das metallene Ger usch welches bei normaler Funktion durch das Einrasten der mechanischen Verriegelung ausgel st wird Dies passiert normalerweise wenn die
47. s temperature fluctuations 14 limitations software 18 on line Help 1 photo multiplier tube gain 15 Preview Scan 17 scanning modes 10 spatial resolution 17 temperature fluctuations 14 Index 22 e Imaging System Hardware GenePix 4000B User s Guide Copyright 1999 2001 Axon Instruments Inc Index
48. se long delays and additional expense to you AXON has no control over your use of the SOFTWARE Therefore AXON does not and cannot warrant the results or performance that may be obtained by its use The entire risk as to the results and performance of the SOFTWARE is assumed by you Should the SOFTWARE or its documentation prove defective you assume the entire cost of all necessary servicing repair or correction Neither AXON nor anyone else who has been involved in the creation production or delivery of this SOFTWARE and its documentation shall be liable for any direct indirect consequential or incidental damages arising out of the use or inability to use such products even if AXON has been advised of the possibility of such damages or claim This warranty is in lieu of all other warranties expressed or implied Some states do not allow the exclusion or limitation of implied warranties or liability for incidental or consequential damages so the above limitations or exclusions may not apply to you U S Government Restricted Rights The SOFTWARE and its documentation are provided with RESTRICTED RIGHTS Use duplication or disclosure by the U S Government is subject to restrictions as set forth in subparagraph c 1 ii of The Rights in Technical Data and Computer Software clause at DFARS 252 227 7013 or subparagraphs c 1 and 2 of the Commercial Computer Software Restricted Rights at 48 CFR 52 227 19 or clause 18 52 227 86 d o
49. signed to protect you from exposure to the laser light Lasers high voltage or moving parts You do not need to access the interior of the instrument There are no serviceable parts inside Do not stick anything into the openings or vents of the GenePix 4000B other than loading the slide You may cause an interlock to fail Cautions Warning Do not defeat the interlock open the protective housing or try to gain access to the interior of the instrument through any other openings Opening the Do not attempt to move any parts below the housing can damage the instrument components and result slideholder You may cause an interlock to fail in hazardous exposure to laser light high voltage or moving parts Embedded Laser Classification and Power The GenePix 4000B is a Class I laser device There are pe PP higher power lasers embedded inside it but the user can Laser s Class not access these Slides can be placed safely in the laser s scanning area because the slide loading door has redundant interlocks that block the beams There are two panels on the device that are not interlocked but these are fastened Warning Exposure to laser light can cause injury For with screws and require a tool to remove them They are example viewing the laser light directly can cause shown in the Non Interlocked Panels section below Do blindness not remove any screws to open the housing Safety Information Power Supply Classification
50. sus peut entra ner un risque d exposition dangereuse des rayonnements Informations de s curit viii Etiquettes de s curit Si une tiquette devient illisible ou manque pour une raison quelconque contactez le service Support du Array System pour obtenir gratuitement une tiquette de remplacement En attendant copiez les tiquettes illustr es dans ce manuel et attachez cette copie l instrument Symboles d alerte Signal tique GenePix 40005 Axon Instruments PATENTS PENDING TO PREVENT ELECTRICAL SHOCK AND DAMAGE TO THE INSTRUMENT DO NOT ATTEMPT TO OPEN UNIT NO CUSTOMER SERVICEABLE COMPONENTS ARE CONTAINED WITHIN THIS UNIT CONSULT THE FACTORY FOR REPAIR RETURN INSTRUCTIONS USE ONLY AXON POWER SUPPLY APN 2300 419 FAILURE TO DO SO MAY CAUSE ELECTRONIC DAMAGE WITHIN THE UNIT U S Office Axon Instruments Inc 3280 WHIPPLE ROAD UNION CITY CALIFORNIA USA 94587 Tel 650 675 6200 AXON LABEL PART NUMBER 2400 329 REV B Figure 1 Adresse et avertissements Cette tiquette est coll e l arri re du GenePix 4000B sur la partie sup rieure du boitier PATENTS PENDING DANGER Laser radiation when open AVOID DIRECT EXPOSURE TO BEAM MANUFACTURE DATE SERIAL NUMBER FOSTER CITY CA This device complies with Axon Instruments 21 CFR 1040 10 amp 1040 11 3 5290 WHIPPLE ROAD UNION GITY CA 94587 AXON LABEL PART NUMBER 2400 330 REV B Figure 2 I
51. t Ne tentez pas d acc der l int rieur de l instrument Il existe des pi ces mobiles l int rieur susceptibles de provoquer des dommages corporels vii Fusible Il n existe pas de fusible l int rieur du GenePix 4000B Pr cautions contre les substances dangereuses L utilisateur doit suivre les proc dures standard de laboratoires et prendre les pr cautions appropri es la manipulation de produits chimiques Attention Veillez toujours suivre les consignes de s curit du fabricant lors de la manipulation de produits chimiques Le fabricant et ou le fournisseur ne peuvent tre tenues pour responsables de dommages ventuels directs ou indirects caus s par l utilisation de substances dangereuses Acc s non verrouill s par la Double Protection Vue de dessous du GenePix montrant les vis qui maintiennent la partie sup rieure du bo tier NE PAS RETIRER CES CINQ VIS DANGER Radiation laser lorsque ouvert EVITER IMPERATIVEMENT L EXPOSITION DIRECTE AUX RAYONS Maintenance et Service des acc s non verrouill s par la Double Protection Aucune maintenance de la part de l utilisateur n est n cessaire De plus auun service de maintenance n est autoris de la part d un tiers Liste des Contr les Ce guide constitue une liste des contr les 4 effectuer r guli rement Attention Tout contr le r glage ou ex cution de proc dures autres que celles sp cifi es ci des
52. ters We recommend that you use the included SCSI card Please follow the instructions included with the adapter for the proper installation of the card If you already have a SCSI card installed on your host computer and do not want to replace it with the included SCSI card you must verify that it is a SCSI 2 device that is Win ASPI compliant You must also ensure that you have the proper cabling to connect the SCSI card to the GenePix 4000B While it is possible that an existing SCSI card may work with the GenePix 4000B technical support is provided only for the SCSI card that is bundled with the GenePix 4000B If you are using the GenePix 4000B on a computer with multiple SCSI devices please ensure that there are no SCSI ID conflicts At the factory the GenePix SCSI ID GenePix 4000B User s Guide Copyright 1999 2001 Axon Instruments Inc Installing GenePix e 5 is set to 4 but the ID can be easily changed using the SCSI ID switch found at the back of the GenePix 4000B Installation of GenePix Pro 3 0 First to be able to install GenePix 3 0 under Windows NT 4 0 or Windows 2000 a user must be logged in as an Administrator GenePix Pro 3 0 is on the included CD ROM Simply insert the CD ROM into your computer and the installation program automatically starts If the installation program does not start automatically perhaps because you have the auto start feature of Windows disabled you can manually start the installation by running t
53. ufacturer s precautions when working with chemicals The manufacturer and or supplier is not responsible or liable for any damages caused by or as a consequence of the use of any hazardous material Non Interlocked Panels View of the bottom of the GenePix showing the screws which hold the top part of the protective housing DO NOT REMOVE THESE FIVE SCREWS DANGER Laser radiation when open AVOID DIRECT EXPOSURE TO BEAM Maintenance and Service No user maintenance is required No user service is allowed If there is a problem 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 GenePix 4000B User s Guide Copyright 1999 2001 Axon Instruments Inc Safety Labels Symbol Explanations If a label becomes illegible or is missing for any reason please contact Array System Technical Support for a free Device standby replacement label While waiting for the replacement label E A Ready to scan slide Stage copy the labels shown in this section and attach the copy of waiting at the start position the label to the instrument wim Eject Slideholder ready to be unloaded GenePIx 40005 Axon Instruments PATENTS PENDING TO PREVENT ELECTRICAL SHOCK AND DAMAGE TO THE INSTRUMENT DO NOT ATTEMPT TO OPEN UNIT NO CUSTOMER
54. upply PWR 4 Axon Part No 2300 419 SERVICE CONTACTS U S Office Axon Instruments Inc 3280 WHIPPLE ROAD UNION CITY CALIFORNIA USA 94587 Tel 650 675 6200 AXON LABEL PART NUMBER 2400 331 REV B Abbildung 3 Stromversorgungetikett Das Etikett befindet sich am boden der Stromversorgung Ortliche Voraussetzungen Der GenePix 4000B arbeitet optimal wenn alle Umfeldvorrausetzungen gegeben sind Genau wie bei anderen optischen Ger ten sollte auch hier ein staub und schwingungsfreies Umfeld existieren Extreme Temperaturen und Luftfeuchtigkeit k nnen die optimalen Funktionen des Ger tes beeintr chtigen Umgebungstemperatur 10 30 C Umgebungsluftfeuchtigkeit 5 95 unkondensiert Stromvoraussetzung Zufuhr 100 240 V 6 A max 47 63 Hz Platzvoraussetzung 44 1 cm x 33 0 cm x 17 8 cm Gewichtsvoraussetzung Genug um 16 2 kg zu unterstiitzen mit minimalen Schwingungen GenePix 4000B User s Guide Copyright 1999 2001 Axon Instruments Inc XV Declaration of Conformity Manufacturer Axon Instruments Inc 3280 Whipple Road Union City CA 94587 USA Type of Equipment Array Scanner Model Number GenePix 4000B Serial Number Year of Manufacture 2000 Application of Council Directives EC Low Voltage Directive 73 23 EEC as amended EC EMC Directive 89 336 EEC as amended Harmonized Standards to which Conformity is Declared EN 61326 04 1997 Emmisions EN 61326 04 19
Download Pdf Manuals
Related Search