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Molecular Devices GenePix 4100A User Manual

Microarray scanner
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GenePix
4100A Microarray Scanner
®
User Guide
5000449 D
October 2010

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Summary of Contents for Molecular Devices GenePix 4100A

  • Page 1 GenePix 4100A Microarray Scanner ® User Guide 5000449 D October 2010...
  • Page 2 Molecular Devices equipment, software, reagents, and consumables. This document is copyright protected and any reproduction of this document, in whole or any part, is strictly prohibited, except as Molecular Devices may authorize in writing. Software that may be described in this document is furnished under a license agreement.
  • Page 3 GenePix 4100A Microarray Scanner User Guide Licensing Notice Molecular Devices is not licensed under any patents owned by Oxford Gene Technology Limited (“OGT”), covering oligonucleotide arrays and methods of using them to analyze polynucleotides. The purchase of Molecular Devices products does not convey any license under any of OGT’s patent rights, including any right to make or use oligonucleotide...
  • Page 4 5000499 D...

  • Page 5: Table Of Contents

    Contents Foreword ........7 Who This Manual Is For .
  • Page 6 Contents Appendix C Warranty and Service ....33 Standard Warranty ......33 Out-of-Warranty Repair Service .

  • Page 7: Foreword

    Foreword The foreword describes the intended audience for the manual. It defines the typographical conventions used in the manual and lists the related documentation. Who This Manual Is For This manual is written for the GenePix 4100A Microarray Scanner user. ®...
  • Page 8 Foreword 5000499 D...

  • Page 9: Chapter 1 Introduction

    Introduction The GenePix 4100A Microarray Scanner uses a laser-excitation based ® fluorescence scanning and imaging system. The laser-based scanning system operates by slowly moving the slide in the Y–direction, while the slide is rapidly scanned in the X–direction. The design of the microarray scanner allows you to scan a 25 mm by 75 mm slide at up to two wavelengths: •...

  • Page 10: Scanner Components

    The main components of the 4100A Microarray Scanner are: • Protective enclosure • Optics • Lasers • Optical path • Emission filters • PMT (photo-multiplier tube) • Status lights Figure 1-1 GenePix 4100A Microarray Scanner For detailed information about each component, see Instrument Components on page 5000499 D...

  • Page 11: Scanner Specifications

    GenePix 4100A Microarray Scanner User Guide Scanner Specifications Table 1-1 Specifications Sample type Standard microscope slides (1 inch by 3 inches, 25 mm by 75 mm, or 26 mm by 76 mm; 0.9 to 1.2 mm thick) Maximum scan area...

  • Page 12: Site Requirements

    Introduction Site Requirements Table 1-2 Site Requirements Temperature 50 to 86ºF (15 to 30ºC) Humidity 5 to 95% non-condensing Power Universal input 50 to 60 Hz, 100 to 240 VAC, 2A max Space 25.6 inches deep by 16.9 inches wide by 13.4 inches high (65 cm by 43 cm by 34 cm).

  • Page 13: Chapter 2 Installation And Operation

    Installation and Operation The GenePix 4100A Microarray Scanner should be unpacked and in ® position on a flat level surface before performing any of the installation procedures. Perform the procedures in the following order. • Unpack the scanner and position it on the bench •...
  • Page 14 Installation and Operation To unpack the scanner and position it on the bench 1. Open the crate and remove any foam blocks used to protect the scanner from excessive shock and vibration during shipping. CAUTION! Do not touch or loosen any screws or parts other than those specifically described in the instructions.
  • Page 15 GenePix 4100A Microarray Scanner User Guide 3. Plug the USB cable into the USB type B port on the back of the scanner, and the USB type A port on the control computer. Figure 2-1 Connections on back of the scanner...

  • Page 16: Installing The Software

    Installation and Operation Installing the Software Before operating the scanner, you must install the GenePix Pro Software on a Windows-based control computer. To install the software 1. Locate the GenePix Pro Software CD. Note: You must be fully aware of the information contained in the GenePix Pro Software Reference Guide to ensure a ®...

  • Page 17: Turning On The Scanner

    1. Make sure the slide door is closed. 2. Turn on the scanner power switch. 3. Turn on the control computer. 4. Click Start > Programs > Molecular Devices > GenePix Pro, and then click the Report tab. 5. Click Functional Checkout in the Hardware Diagnostics Reports area, and follow the steps in the Wizard.
  • Page 18 Installation and Operation Note: Make sure the barcode on the slide is facing the front of the scanner. Figure 2-2 Slider holder Name Description Slide door In raised position Slide holder In load position Slide Place feature-side down Barcode Barcode is facing the front of the scanner 5000499 D...

  • Page 19: Shutting Down The Scanner

    GenePix 4100A Microarray Scanner User Guide 4. Lower the top of the slide holder. CAUTION! Make sure the top of the slide holder is lowered before closing the slide door. 5. Close the slide door. The slide holder moves into the scan position.
  • Page 20 Installation and Operation 5000499 D...

  • Page 21: Chapter 3 Maintenance And Troubleshooting

    Maintenance and Troubleshooting The GenePix 4100A Microarray Scanner requires very little ® maintenance. WARNING! Biohazardous Material. It is your responsibility to decontaminate the scanner, as well as any accessories, before requesting service, or before returning the scanner or any components. WARNING! Biohazardous Material.

  • Page 22: Moving The Scanner

    1. Remove any slide from the slide holder. 2. Close the GenePix Pro Software. 3. Click Start > Programs > Molecular Devices > GenePix Pro > GenePix Utilities. The GenePix Utilities window appears 4. Click Park Scanner for Shipping.

  • Page 23: Interlock Failure Symptoms

    GenePix 4100A Microarray Scanner User Guide 8. If the scanner is to be returned for service, pack the scanner in its original shipping crate. Otherwise, have two people lift the scanner or place it on a rolling cart to transport it to the new location.
  • Page 24 Maintenance and Troubleshooting 5000499 D...

  • Page 25: Appendix A Instrument Components

    Since the performance of such lasers is often sensitive to external temperature fluctuations, the scanner uses an active temperature stabilization design to minimize temperature-based laser fluctuations. The GenePix 4100A Microarray Scanner provides integrated output monitoring feedback for each laser to compensate for normal variations in laser intensity.

  • Page 26: Emission Filters

    Chroma Technology Corp: www.chroma.com Custom Filters The GenePix 4100A Microarray Scanner can be ordered with up to six pre-installed custom filters, in addition to the two standard filters. When choosing filters, it is important to match the optical characteristics of the filter, dye, and laser. The transmission band of the...

  • Page 27: Pmt

    GenePix 4100A Microarray Scanner User Guide The 4100A Microarray Scanner uses a high-sensitivity, low-noise PMT to detect the emitted fluorescent light. A PMT converts incident photons into electrons through the photoelectric effect. When an incident photon impinges on the active surface of the PMT (the photocathode), an electron is generated.

  • Page 28: Status Lights

    • Device standby • Scanning • Eject Figure A-1 Status lights – GenePix 4100A Microarray Scanner Item Name Description Device standby The scanner is powered up and ready to scan a slide Scanning The slide is in the load position and is being...

  • Page 29: Appendix B Instrument Performance Factors

    Instrument Performance Factors Spatial resolution, and dynamic range and detection limits are two key principles of the GenePix 4100A Microarray Scanner operation. ® Spatial Resolution In the 4100A Microarray Scanner, a single beam of light is rapidly scanned across the microarray, and a composite pixelated image is created from the digitized signals from the PMT.
  • Page 30 Instrument Performance Factors For a preview scan, the same 5 μm spots are scanned. However the Y-direction step size is increased to 40 μm, and each 40 μm preview scan pixel is an average of eight contiguous 5 μm spots in the X-direction.

  • Page 31: Dynamic Range And Detection Limit

    GenePix 4100A Microarray Scanner User Guide Dynamic Range and Detection Limit The dynamic range of an instrument is the range of signal values over which the instrument can accurately measure change. The 4100A Microarray Scanner has a dynamic range of 10 .
  • Page 32 Instrument Performance Factors 5000499 D...
  • Page 33 Warranty and Service Molecular Devices is committed to ensuring the highest quality of our products and customer service. If you have any problems with your GenePix 4100A Microarray ® Scanner, contact our Technical Support group. In the U.S., contact us at 1-800-635-5577.
  • Page 34 Once you register your name, you can then register your instrument. If you require advice on the use of your GenePix 4100A Microarray Scanner, do not hesitate to contact Molecular Devices Technical Support. Visit the website http://support.moleculardevices.com...

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