Molecular Devices GenePix 4100A User Manual Download Page 5

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5000499 D

Contents

Foreword . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7

Who This Manual Is For . . . . . . . . . . . . . . . . . . . . . . . . . 7

Conventions . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7

Related Documentation . . . . . . . . . . . . . . . . . . . . . . . . . 7

Chapter 1 Introduction . . . . . . . . . . . . . . . . . . . . . . . . . . 9

Scanner Features. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 9

Scanner Components . . . . . . . . . . . . . . . . . . . . . . . . . . 10

Scanner Specifications . . . . . . . . . . . . . . . . . . . . . . . . . 11

Site Requirements . . . . . . . . . . . . . . . . . . . . . . . . . . . . 12

Chapter 2 Installation and Operation . . . . . . . . . . . . . . 13

Unpacking the scanner and positioning it on the bench. . . 13

Installing the Software . . . . . . . . . . . . . . . . . . . . . . . . . 16

Turning on the Scanner . . . . . . . . . . . . . . . . . . . . . . . . 17

Inserting a Slide . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 17

Shutting Down the Scanner. . . . . . . . . . . . . . . . . . . . . . 19

Chapter 3 Maintenance and Troubleshooting . . . . . . . . 21

Moving the Scanner . . . . . . . . . . . . . . . . . . . . . . . . . . . 22

Interlock Failure Symptoms . . . . . . . . . . . . . . . . . . . . . 23

Fuses . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 23

Appendix A Instrument Components. . . . . . . . . . . . . . . 25

Protective Enclosure . . . . . . . . . . . . . . . . . . . . . . . . . . 25

Optics. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 25

Lasers. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 25

Optical Path. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 25

Emission Filters . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 26

PMT . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 27

Status Lights . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 28

Appendix B Instrument Performance Factors . . . . . . . . 29

Spatial Resolution . . . . . . . . . . . . . . . . . . . . . . . . . . . . 29

Dynamic Range and Detection Limit . . . . . . . . . . . . . . . . 31

GenePix_4100A.book Page 5 Friday, October 22, 2010 3:21 PM

Summary of Contents for GenePix 4100A

Page 1: ...GenePix 4100A Microarray Scanner User Guide 5000449 D October 2010 GenePix_4100A book Page 1 Friday October 22 2010 3 21 PM...

Page 2: ...sage is intended only to designate those manufacturers products as supplied by Molecular Devices for incorporation into its equipment and does not imply any right and or license to use or permit other...

Page 3: ...HAT HAVE INTELLECTUAL PROPERTY RIGHTS IN THE POTENTIAL FIELD OF APPLICATION OF THIS INSTRUMENT INCLUDE WITHOUT LIMITATION AFFYMETRIX INC AFFYMETRIX AGILENT AND OXFORD GENE TECHNOLOGY THIS INSTRUMENT H...

Page 4: ...4 5000499 D GenePix_4100A book Page 4 Friday October 22 2010 3 21 PM...

Page 5: ...stalling the Software 16 Turning on the Scanner 17 Inserting a Slide 17 Shutting Down the Scanner 19 Chapter 3 Maintenance and Troubleshooting 21 Moving the Scanner 22 Interlock Failure Symptoms 23 Fu...

Page 6: ...6 5000499 D Appendix C Warranty and Service 33 Standard Warranty 33 Out of Warranty Repair Service 33 Optional Service Agreement 33 Technical Support 34 GenePix_4100A book Page 6 Friday October 22 201...

Page 7: ...peration that can cause damage to the instrument device or data if precautions are not followed Related Documentation The customer documentation for the 4100A Microarray Scanner includes the GenePix P...

Page 8: ...Foreword 8 5000499 D GenePix_4100A book Page 8 Friday October 22 2010 3 21 PM...

Page 9: ...total time Scanner Features Can be configured with one or two internally installed laser excitation sources Sequential scanning of up to two wavelengths Precisely controlled automatic laser power mon...

Page 10: ...r are Protective enclosure Optics Lasers Optical path Emission filters PMT photo multiplier tube Status lights Figure1 1 GenePix 4100A Microarray Scanner For detailed information about each component...

Page 11: ...PMT Signal digital output 16 bit Image format Single or multi image TIFF Computer interface USB 2 0 Scan time 6 5 minutes per channel for full size scan area at 10 m resolution Dynamic range Four orde...

Page 12: ...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 An additional 6 inches 15 2 cm for clearance Bench support Sufficient to support 4...

Page 13: ...nner 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 WARNING Shock Hazard In an emergency users m...

Page 14: ...can cause misalignment and voids the scanner warranty 2 Lift and then place the scanner on a flat level surface away from direct sunlight dust drafts vibration and moisture Carefully move the scanner...

Page 15: ...er 4 Plug the main power cable into the port on the back of the scanner and the lab s power outlet We recommend you use a surge protector between the main power cable and the power outlet Figure2 1 Co...

Page 16: ...stall the GenePix Pro Software CAUTION Do not to insert the security key into the control computer until after the GenePix Pro Software has been installed 4 Install the security key For more informati...

Page 17: ...ardware performance events into the Hardware Diagnostics Report every two hours during operation Inserting a Slide The slide holder is a precision component designed to ensure proper focusing and fiel...

Page 18: ...g the front of the scanner Figure2 2 Slider holder Ite m Name Description 1 Slide door In raised position 2 Slide holder In load position 3 Slide Place feature side down 4 Barcode Barcode is facing th...

Page 19: ...or 5 Close the slide door The slide holder moves into the scan position Shutting Down the Scanner Proper shutdown of the 4100A Microarray Scanner ensures the scanner or software are not damaged To shu...

Page 20: ...Installation and Operation 20 5000499 D GenePix_4100A book Page 20 Friday October 22 2010 3 21 PM...

Page 21: ...before returning the scanner or any components WARNING Biohazardous Material Never perform any maintenance procedures on the scanner in an environment where potentially damaging gases or liquids are p...

Page 22: ...ties window appears 4 Click Park Scanner for Shipping A message box appears informing you that the scanner has been successfully parked CAUTION Always turn off power to the scanner using the power swi...

Page 23: ...g below the slide after the door is opened The blue Scanning LED on the front of the scanner does not extinguish when the slide door is open The GenePix Pro Software does not recognize the scanner or...

Page 24: ...Maintenance and Troubleshooting 24 5000499 D GenePix_4100A book Page 24 Friday October 22 2010 3 21 PM...

Page 25: ...formance 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...

Page 26: ...ation on custom filters and their applications refer to the filter manufacturer s website Semrock Inc www semrock com Chroma Technology Corp www chroma com Custom Filters The GenePix 4100A Microarray...

Page 27: ...e of incident light intensities However there is a very non linear relationship between the voltage of the PMT and the PMT output Therefore a slide scanned at a PMT voltage of 800 V will not be twice...

Page 28: ...canning Eject FigureA 1 Status lights GenePix 4100A Microarray Scanner Item Name Description 1 Device standby The scanner is powered up and ready to scan a slide 2 Scanning The slide is in the load po...

Page 29: ...sing each Y direction step from 5 m to 10 m Consequently a 10 m scan is twice as fast as a scan at 5 m and outputs the average of each adjacent pair of 5 m spots in the X direction as the value of a s...

Page 30: ...sentation of how the 4100A Microarray Scanner samples 5 m spots and averages them to calculate the values of the image pixels for the various scan modes and pixel sizes On the left side of each image...

Page 31: ...ain is set below this range the probability that each impinging photon will be converted to an electron is diminished and the dynamic range will be limited on the low end Above this range noise begins...

Page 32: ...Instrument Performance Factors 32 5000499 D GenePix_4100A book Page 32 Friday October 22 2010 3 21 PM...

Page 33: ...oducts returned to Molecular Devices for repair should be properly packaged with transportation charges prepaid Molecular Devices will pay for the return shipping of the product to the customer If the...

Page 34: ...ur 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...

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