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 one 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 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
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 GenePix Pro software license 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.
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.
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.
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.
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.
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.
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.
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.
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 one license of GenePix® Pro, the industry-leading microarray image acquisition and first-pass analysis software. You may also purchase additional licenses of GenePix Pro or licenses of Acuity®, a powerful and scalable database, statistical and data visualization software package, at the time of scanner purchase, or at any time afterwards.
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
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 an Intel Pentium “Dual Core” processor 1.6 GHz or faster.
Windows XP or Vista 32-bit edition operating system
Memory requirements:
Full-size scan region at 5 µm resolution:
1 GB RAM for two colors; 2 GB for three or more colors
10 µm scanning or partial-size scan regions at 5 µm resolution:
512 MB RAM for two colors; 768 MB for three or more colors
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)
Integrated Video Card.
Optical drive with CD read and write capabilities (CD-RW).
At least 1 free USB port or network connection (for the USB hardware protection key)*
1080 x 1024 display
Internet Explorer 5.0 or higher
Computer - Recommended
IBM-compatible computer with an Intel “Core 2” processor 2.0 GHz or faster
Windows XP or Vista 32-bit edition operating system.
2 GB RAM or more.
Dedicated Video Card 128MB or greater.
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)
Optical Drive with DVD and CD read and write capabilities (DVD+/-RW)
At least 1 free USB port or network connection (for the USB hardware protection key)*
Internet access (for faster version updates and troubleshooting)
1280 x 1024 display system with 16M colors
Internet Explorer 6.0 SP1
*If your computer does not have a free USB port but has a network connection you can specify a network hardware protection key when ordering GenePix Pro.
Includes one license of industry-leading GenePix Pro image acquisition and analysis software. Additional GenePix Pro and Acuity microarray informatics software licenses may also be purchased with the scanner.
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.
Alexa Fluor® is a registered trademark of Molecular Probes. CyDyes™ is a trademark of Amersham Biosciences.
The 
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.
