1. Manuals
  2. Brands
  3. Molecular Devices Manuals
  4. Scanner
  5. GenePix 4000B
  6. User manual

Molecular Devices GenePix 4000B User Manual

Hide thumbs
Table of Contents

Advertisement

Quick Links

Download this manual
GenePix
4000B Microarray Scanner
®
User Guide
5000450 D
October 2010

Advertisement

Table of Contents
loading
Need help?

Need help?

Do you have a question about the GenePix 4000B and is the answer not in the manual?

Questions and answers

Subscribe to Our Youtube Channel

Related Manuals for Molecular Devices GenePix 4000B

Summary of Contents for Molecular Devices GenePix 4000B

  • Page 1 GenePix 4000B Microarray Scanner ® User Guide 5000450 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 4000B 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 5000450 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

    Note: Provides essential information for the completion of a procedure. Related Documentation The customer documentation for the GenePix 4000B Microarray Scanner includes the GenePix Pro Software Reference Guide, Safety ®...
  • Page 8 Foreword 5000450 D...

  • Page 9: Chapter 1 Principles Of Operation

    Principles of Operation The GenePix 4000B 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 scanner allows you to scan a 25 mm by 75 mm slide at up to two wavelengths: •...

  • Page 10: Scanner Components

    Principles of Operation Scanner Components The main components of the GenePix 4000B Microarray Scanner are: • Protective enclosure • Optics • Lasers • Optical path • Emission filters • PMTs (photo-multiplier tubes) • Status lights • External power supply Figure 1-1 GenePix 4000B Microarray Scanner ®...

  • Page 11: Scanner Specifications

    GenePix 4000B 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

    Principles of Operation 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

    Insert a slide Unpacking the scanner and positioning it on the bench The GenePix 4000B Microarray Scanner is packed in a specially designed crate. Retain the crate and the packing materials. If the scanner requires repair, you must return it in the original packaging. If the crate has been damaged in transit, you must retain it for inspection by the carrier.
  • 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 4000B Microarray Scanner User Guide 4. Plug the round connector of the cable leading from the external power supply into the matching power port on the back of the scanner. Plug the main power supply cable into the external power supply, and the lab’s power outlet.

  • 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

    GenePix 4000B Microarray Scanner User Guide Turning on the Scanner Proper startup of the GenePix 4000B Microarray Scanner includes a functional checkout procedure to confirm that the scanner is performing according to the specifications established during commissioning before the scanner left the factory.
  • Page 18 Installation and Operation 3. With the slide held between your thumb and finger, carefully place the slide, feature-side down into the slide holder. Note: Make sure the barcode on the slide is facing the front of the scanner. Figure 2-3 Slider holder Name Description Slide door...

  • Page 19: Shutting Down The Scanner

    5. Move the slide door to the right. The slide holder moves into the scan position. Shutting Down the Scanner Proper shutdown of the GenePix 4000B Microarray Scanner ensures the scanner or software are not damaged. To shut down the scanner 1.
  • Page 20 Installation and Operation 5000450 D...

  • Page 21: Chapter 3 Maintenance & Troubleshooting

    Maintenance & Troubleshooting The GenePix 4000B 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

    Maintenance & Troubleshooting Moving the Scanner If the GenePix 4000B Microarray Scanner must be moved within the lab, or returned to the factory for service, the scanner must be prepared for transport. If you do not have the original shipping crate, contact us and a new crate can be provided for an additional charge.

  • Page 23: Interlock Failure Symptoms

    GenePix 4000B Microarray Scanner User Guide 7. Unplug the USB cable from the back of the scanner and the control computer. CAUTION! Do not tilt or stand the scanner on its end when moving it within the lab, or transferring it from the bench to the shipping crate.

  • Page 24: Fuses

    Maintenance & Troubleshooting Fuses If the GenePix 4000B Microarray Scanner does not start up, a fuse might no longer be functioning. If you suspect a fuse has stopped functioning, contact Technical Support. 5000450 D...

  • Page 25: Appendix A Instrument Components

    4000B Microarray Scanner automatically corrects fluorescent intensity for normal variations on a pixel-by-pixel basis. With the GenePix 4000B Microarray Scanner, laser power can be set to 100%, 33%, or 10% of the total laser output. This feature can be used when the fluorescence of the sample is too bright, or when photobleaching is a problem.

  • Page 26: Optical Path

    +200 μm relative to the zero position. Positive positions refer to focal planes above the microarray surface while negative positions are within the slide. Emission Filters The GenePix 4000B Microarray Scanner is equipped with two lasers. Each laser (red and green) includes a matching pre-installed emission filter. •...

  • Page 27: Pmt

    GenePix 4000B Microarray Scanner User Guide The GenePix 4000B Microarray Scanner uses two high-sensitivity, low- noise PMTs 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

    Instrument Components Status Lights Three lights on the front of the GenePix 4000B Microarray Scanner indicate status. • Device standby • Scanning • Eject Figure A-1 Status lights – GenePix 4000B Microarray Scanner ® Item Color Name Description Green Device standby...

  • Page 29: Appendix B Instrument Performance Factors

    4000B Microarray Scanner operation. ® Spatial Resolution In the GenePix 4000B 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. The spatial resolution of the system refers to the size of the pixel.
  • Page 30 X-direction. This speeds image acquisition for balancing the PMT gains while minimizing photobleaching. Figure B-1 Data scans.is a representation of how the GenePix 4000B Microarray Scanner samples 5 μm spots and averages them to calculate the values of the image pixels for the various scan modes and pixel sizes.

  • Page 31: Dynamic Range And Detection Limit

    GenePix 4000B 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 GenePix 4000B Microarray Scanner has a dynamic range of 10 .
  • Page 32 Instrument Performance Factors 5000450 D...

  • Page 33: Standard Warranty

    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 4000B Microarray ® Scanner, contact our Technical Support group. In the US, contact us at 1-800-635-5577.

  • Page 34: Technical Support

    Once you register your name, you can then register your instrument. If you require advice on the use of your GenePix 4000B Microarray Scanner, do not hesitate to contact Molecular Devices Technical Support. Visit the website http://support.moleculardevices.com...

Table of Contents