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GenePix 4000B

Microarray scanner for microarrays, tissue and cell arrays, and fluorescence studies

 
The Axon GenePix® 4000B microarray scanner sets a new standard in the acquisition and analysis of expression data from DNA microarrays, protein microarrays, tissue arrays and cell arrays. This fully-integrated scanner and software system is a product of our extensive experience in the design and manufacture of precision scientific instruments and software. Each scanner comes with one Axon GenePix Pro software license.

Features include:

  • 5 µm pixel size
  • dynamic monitoring of laser power
  • user-selectable laser power
  • user-selectable focus position
  • one-touch calibration and scanner matching

The Axon GenePix 4000B scanner and Axon GenePix Pro software is powerful, flexible, and easy to learn and use.

  • Simultaneously scans microarray slides at two wavelengths using a dual laser scanning system, which dramatically reduces scan time
  • User-selectable laser power
  • User-selectable focus position
  • Displays images from up to four channels and three ratios as they are acquired in real time
  • Automatically reads barcodes
  • Precisely controls the scan area, further reducing scan time and image storage requirements
  • Automatically logs all scanning and analysis procedures in a Lab Book
  • Includes one Axon GenePix Pro software license for maximum efficiency and full microarray spot finding and analysis capability
  • Backed by unlimited technical support.

Choosing Your Axon GenePix Scanner

The performance and many features of the different GenePix models are similar, so check the GenePix Scanner Comparison Table to see the key differences.

Product Overview

The Axon GenePix 4000B is the fastest, smallest, and most user-friendly microarray scanner on the market today. Our commitment to engineering excellence guarantees that the Axon GenePix 4000B is the benchmark in microarray scanning technology.

Simultaneous Dual Laser Scanning

Unlike most commercially available microarray scanners, the Axon GenePix 4000B scanner acquires data at two wavelengths simultaneously. Using 532 nm (17 mW) and 635 nm (10 mW) lasers, simultaneous acquisition of data means drastically reduced scan times—about 6.5 minutes for a full scan at 10 microns (13 minutes for a full scan at 5 microns), and much less for user-defined sub-scans—and hence greater laboratory efficiency. Apart from superior speed, simultaneous scanning eliminates potential errors associated with aligning two separately scanned images, and provides real-time access to data as they are acquired.

High Resolution Acquisition

Accepting standard microscope slides (1" x 3", or 25 mm x 75 mm), the Axon GenePix 4000B acquires data at resolutions between 5 microns and 100 microns. A 40-micron preview scan is used to preview the microarray and set the scan area for a high-resolution scan (5 to 100 micron resolution). The software-controlled scan area setting, which requires the user to resize a box on the microarray image (occasionally in a series of scans), further reduces scan time. However, where increased scan time is needed to image faint or damaged slides, the Axon GenePix 4000B has user-selectable longer acquisition times.

Pre-set Hardware Controls

The Axon GenePix 4000B has pre-set hardware controls with very wide dynamic ranges, so it is unlikely that you will ever need to make hardware adjustments. In contrast with other microarray scanners, Axon GenePix does not require a week of training to use, nor are there complicated and frustrating settings of lasers and photomultiplier tubes each time a new slide is scanned. Our engineers have ensured that Axon GenePix is ready to begin routine laboratory work straight out of the box.

Calibration and Matching

All Axon GenePix scanners come with performance validation standards so that you can verify performance when you receive your scanner and at any time in the future. Axon GenePix Pro includes one-touch calibration to restore any Axon GenePix scanner to benchmark performance. Calibration can also be used to match the signal output from multiple Axon GenePix scanners, even different models.

Integrated Hardware and Software

The Axon GenePix 4000B is the only microarray scanner on the market for which hardware and software have been designed and constructed together to produce a single integrated scientific instrument. The intimate connection between hardware and software ensures efficiency and data quality that pieced-together scanner and software packages cannot match. Included in the package is all cabling needed by the system, so that installation is truly plug and play. See Axon GenePix Pro for details on the acquisition and analysis software.

Fluorescent Dye Compatibility

The dyes included in this chart have excitation and emission spectra that are compatible with the lasers and filters in the Axon GenePix 4000B scanner. Axon GenePix lasers excite at 532 nm (green) and 635 nm (red). The emission filters are 575DF35 (green; ~557-592 nm) and 670DF40 (red; ~650-690 nm). These lasers and filters are optimized for Cy3 and Cy5. Performance with other dyes will vary. Dyes with spectra most similar to Cy3 and Cy5 will offer the most successful results. This chart should be used as a rough guideline only. Actual performance of any dyes in the Axon GenePix scanners will depend on dye properties (including extinction coefficient, quantum yield, excitation spectra, emission spectra, and sensitivity to environmental conditions) and biological parameters (including age of dye, moles of dye incorporated into the probe, hybridization efficiency, and environmental conditions.) Inclusion in this list does not guarantee or imply any level of performance on Axon GenePix scanners. The user should carefully evaluate the specific excitation and emission spectra from the manufacturer of any dyes before making any purchases.

Axon GenePix 4000B Feature List

See the Axon GenePix Pro page for more information about the software that accompanies the Axon GenePix 4000B scanner.

Features and Specifications

  • Accepts standard microscope slides (1" x 3" or 25 mm x 75 mm)
  • 22 x 71.5 mm scan area with user-defined sub-scans
  • Standard dual laser excitation at 532 nm (17 mW) and 635 nm (10 mW)
  • Laser is controlled for constant power output
  • User-selectable laser power
  • User-selectable focus position
  • 5 micron resolution, high resolution mode
  • 40 micron resolution, pre-scan mode
  • Other user-selectable resolutions between 5 microns and 100 microns
  • 16-bit digitization
  • Dynamic range of detection:  4 orders of magnitude, linear over 3 orders
  • Extra-high signal-to-noise scan mode (accomplished by averaging)

 

  • Simultaneous scan of both wavelengths in about 6.5 minutes at 10 microns, or in 13 minutes at 5 microns (full 22 x 71.5 mm scan area)
  • Image acquisition of registered images—no post-hoc registration required
  • Detection limit of 0.1 fluor/micron² for Cy 3 and Cy 5
  • Simple USB connection to PC computer
  • Long-life mechanical design
  • Universal power supply (110/220 V)
  • Small footprint: 13.5" wide x 8" high x 17.5" deep (342 mm x 203 mm x 444 mm)
  • Approximately 30 lbs. (13.6 kg)
  • Design protected by intellectual property

Accessories

Test Slide Kit #1
Contains GenePix Geometric Test Slide (GP-10).

Test Slide Kit #2
Contains GenePix Intensity Calibration Slides (GP-7 and GP-8).

 

Test Slide Kits #1 and #2 are included with the Axon GenePix 4000B and are used to validate scanner performance. You can also order additional kits.

Software

The Axon GenePix 4000B includes one license of Axon GenePix® Pro, the industry-leading microarray image acquisition and first-pass analysis software.  You may also purchase additional licenses of Axon GenePix Pro or licenses of Axon Acuity®, a powerful and scalable database, statistical and data visualization software package, at the time of scanner purchase, or at any time afterwards.

Axon GenePix Pro:

  • Integrated package for one-step image acquisition and analysis
  • Industry-standard file formats GenePix Array List (GAL) and GenePix Results (GPR) files
  • Find and analyze features of any shape—elliptical, square, and arbitrary irregular
  • Additional metrics and visualization tools for quality control analysis
  • Export results as MAGE-ML files
  • Seamlessly export results to Axon Acuity database
  • Widely acclaimed for its ease-of-use and as the most popular microarray analysis software available
See the Axon GenePix Pro page for complete information.

Axon Acuity:

  • Fast, scalable SQL database for individual or enterprise-level users
  • Comprehensive statistical analysis, normalization, clustering and visualization features
  • Analysis audit trail
  • No license fees

See the Axon Acuity page for complete information.

Computer Requirements

Axon GenePix is fully functional with the Minimum computer requirements. However, satisfactory performance depends on the size of the files you will generate. The RAM and hard disk configuration is the most critical. If you plan to scan areas smaller than a full slide, or to scan regularly at 10 µm resolution, the Minimum requirements will provide satisfactory performance of all Axon GenePix Pro features. However, if you plan to scan full slides at 5 µm, or if you plan to run other applications simultaneously, we strongly suggest the Recommended configuration. Computer workstations purchased from Molecular Devices will meet or exceed the Recommended configuration.

Computer  -  Minimum

  • IBM-compatible computer with an Intel Pentium "Dual Core" processor 1.6 GHz or faster
  • Operating system: Windows XP or Vista 32-bit edition operating system
  • Memory requirements: 4GB RAM
  • 160 GB hard drive (for image storage)
  • Integrated Video Card
  • Optical drive with CD read and write capabilities (CD-RW)
  • At least 2 free USB port or network connections (one for the USB software protection key*, and one for the scanner)
  • 1280 x 1024 display
  • Internet Explorer 6.0 or higher

Computer  -  Recommended

  • IBM-compatible computer with an Intel "Quad Core" processor 1.8 GHz or faster
  • Windows XP or Vista 64-bit edition operating system
  • 8 GB RAM or more
  • Dedicated Video Card 256MB or greater
  • 250 GB hard drive (for image storage)
  • Optical Drive with DVD and CD read and write capabilities (DVD+/-RW)
  • At least 2 free USB port or network connections (one for the USB software protection key*, and one for the scanner)
  • Internet access (for faster version updates and troubleshooting)
  • 1280 x 1024 display system with 16M colors
  • Internet Explorer 7

Ordering Information

Axon GenePix 4000B

  • Includes one license of industry-leading Axon GenePix Pro image acquisition and analysis software. Additional Axon GenePix Pro and Axon Acuity microarray informatics software licenses may also be purchased with the scanner.

  • Package includes the Axon GenePix 4000B scanner, USB and power cables, and unlimited technical support.

  • Available with a fully configured Dell computer with Axon GenePix 4000B hardware and Axon GenePix Pro / Axon Acuity software installed. This option is highly recommended.

 


Part #: GENEPIX 4000B
GenePix 4000B Scanner
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