GenePix 4000B
Microarray scanner for microarrays, tissue and cell arrays, and fluorescence studies
The 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 two GenePix Pro software licenses.
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 GenePix 4000B scanner and 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
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  • 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 two GenePix Pro software licenses for maximum efficiency and full microarray spot finding and analysis capability
  • Backed by unlimited technical support.

Choosing Your 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 GenePix 4000B is the fastest, smallest, and most user-friendly microarray scanner on the market today. Our commitment to engineering excellence guarantees that the GenePix 4000B is the benchmark in microarray scanning technology.
Simultaneous Dual Laser Scanning
Unlike most commercially available microarray scanners, the 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 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 GenePix 4000B has user-selectable longer acquisition times. / / Pre-set Hardware Controls
The 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, 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 GenePix is ready to begin routine laboratory work straight out of the box.
Calibration and Matching
All 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. GenePix Pro includes one-touch calibration to restore any GenePix scanner to benchmark performance. Calibration can also be used to match the signal output from multiple GenePix scanners, even different models.
Integrated Hardware and Software
The 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 a SCSI adapter and all cabling needed by the system, so that installation is truly plug and play. See 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 GenePix 4000B scanner. 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 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 GenePix scanners. The user should carefully evaluate the specific excitation and emission spectra from the manufacturer of any dyes before making any purchases.
GenePix 4000B Feature List
See the GenePix Pro page for more information about the software that accompanies the 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)
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  • 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 SCSI connection to PC computer (SCSI adapter included)
  • 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-2).
Test Slide Kit #2
Contains GenePix Intensity Calibration Slides (GP-7 and GP-8). / / Test Slide Kits #1 and #2 are included with the GenePix 4000B and are used to validate scanner performance. You can also order additional kits.
Software

The GenePix 4000B includes two software licenses, one for GenePix® Pro, the industry-leading microarray image acquisition and first-pass analysis software, and one license for Acuity®, a powerful and scalable database, statistical and data visualization software package. Alternatively, choose two licenses for GenePix Pro.
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 Acuity database
  • Widely acclaimed for its ease-of-use and as the most popular microarray analysis software available
See the GenePix Pro page for complete information.
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 Acuity page for complete information.
Computer Requirements

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 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 a 1 GHz Pentium (32-bit) or faster
  • Windows 2000 or XP operating system
  • Memory requirements:
  • Full-size scan region at 5 µm resolution: 1 GB RAM
  • Full-size 10 µm scan or partial-size scan regions at 5 µm: 512 MB RAM
  • 40 GB hard drive (for image storage)
  • Available full-size PCI slot for SCSI adapter (Note: the provided PCI SCSI adapter will not fit in a low-profile or slimline case)
  • CD-ROM drive
  • 1024 x 768 display system with 65K colors
  • Internet Explorer 5.0 or higher
Computer - Recommended
  • IBM-compatible computer with a 2 GHz Pentium (32-bit) or faster
  • Windows 2000 or XP operating system
  • 1 GB RAM or more
  • 80 GB hard drive (for image storage)
  • Available full-size PCI slot for SCSI adapter (Note: the provided PCI SCSI adapter will not fit in a low-profile or slimline case)
  • DVD-RW drive
  • 1280 x 1024 display system with 16M colors
  • Internet Explorer 6.0 SP1
Ordering Information

GenePix 4000B
  • Includes two software licenses, one for GenePix Pro and one for Acuity. Alternatively, specify two licenses for GenePix Pro.
  • Package includes the GenePix 4000B scanner, SCSI adapter, cables, and unlimited technical support.
  • Available with a fully configured Dell computer with GenePix 4000B hardware and GenePix Pro / Acuity software installed. This option is highly recommended.