Microarray scanner for microarrays, tissue and cell arrays, and fluorescence studies
Eliminate the inconvenience of waiting to use a scanner in a core facility or your neighbor's lab. High-performance microarray scanning is now more affordable than ever. Built on our award-winning optical, electronic and software design, the Axon GenePix® 4100A microarray scanner (winner of an IBO Design Award) has all the quality and ease-of-use of more expensive scanners, but in a price range and bench top footprint that makes it ideal for individual lab use. Achieve your personal best with the Axon GenePix microarray scanner.
How We Do It
Although lower priced, the Axon GenePix microarray scanner has the sensitivity, throughput, reliability and flexibility that you absolutely require for your microarray-based research, be it in genomics, proteomics or drug discovery.
The sequential scanning mode incorporated in the Axon GenePix made it possible to reduce the development and manufacturing cost without sacrificing the superb quality that you've come to expect from us. But don't just take our word for it - ask your colleagues about the outstanding quality of the industry-leading Axon GenePix microarray scanner.
Choosing Your Axon GenePix Scanner
The performance and many features of the different Axon GenePix models are similar, so
check the Axon GenePix Scanner Comparison Table
to see the key differences.
Eight-Position Filter Wheel for Flexible Fluorophore Selection
A variety of fluorophores can be used with the Axon GenePix microarray scanner.
Its new optical design incorporates an eight-position emission filter wheel (Figure 1) with
two standard filters for red and green fluorophores. Up to six additional filters can be
installed, providing flexibility to explore alternative dyes (Table 1). The emission filter
is easily selected in Axon GenePix Pro (Figure 2; click for larger image).
Figure 1. Emission filter wheel in Axon GenePix microarray scanner.
Figure 2. Selecting emission filters in Axon GenePix Pro.
Emission filter wheel with two standard filters for green and red fluorophores and up to six additional filters for greater customization.
Superior Optics and Digitization
Highly efficient optical path ensures greater light-gathering capacity coupled with Molecular Devices unparalleled low-noise digitization electronics for maximum signal-to-noise ratio.
Quality You Expect
Many of the same powerful features as the popular Axon GenePix 4000 series microarray scanner:
Up to two lasers: green (532 nm) and red (635 nm).
Single-laser version is upgradeable to two-laser version.
Automatic calibration instantly tunes scanners to factory performance, and matches output from multiple scanners.
Ready-to-use scripts for scan control, scanner monitoring, and batch processing.
Multiple pixel resolutions between 5 and 100 microns.
Barcodes read automatically through software.
All scan events are logged automatically.
Scanner control is accessible through scripting for customized automation, analysis, and reports.
Control multiple scanners from a single computer.
Powerful Software
Includes Axon GenePix Pro, the highly popular and powerful acquisition and analysis software-widely recognized as the industry standard.
Smaller Size
Similar in size to a micro-centrifuge or a PCR machine—save valuable bench top space.
Greater Value
Affordable microarray scanning can be brought right into your lab.
Single-laser versions available for even lower prices.
Gateway to Informatics
Seamlessly pass your Axon GenePix results directly to Axon Acuity®, our powerful database analysis and visualization software (Axon Acuity sold separately).
Unparalleled and Industry-Leading Ph.D-level Technical Support
Molecular Devices has long been recognized for its outstanding technical and application support, which is included with every Axon product. Our application scientists come from an academic research background with Ph.D. and post-doctoral experience in a field of molecular biology, cell biology or neuroscience and extensive experience with laboratory instrumentation and software. When you call technical support, you're also getting a trained scientist who understands the biological basis of your experiment in addition to the details of Molecular Devices microarray products.
New Scanning Design
Sequential scan design permits flexible optical configuration at reduced cost. Scans standard microscope slides.
Ultra-low-noise Signal Digitization
Molecular Devices has built its reputation designing ultra-low noise amplifiers and digitizers
for electrophysiology measurements. The Axon GenePix detection system employs a low-noise,
high-sensitivity photomultiplier tube (PMT) to convert photons into an electrical signal,
which is then digitized using world-leading ultra-low-noise digitizer technology.
High Resolution Imaging for Precise Detail
The Axon GenePix microarray scanner allows the same flexibility for scan resolution as
the Axon GenePix 4000B. Use the 40-micron Preview Scan to locate the array and optimize hardware
settings, and the Data Scan for accurate quantitation. The Axon GenePix has selectable
scanning resolution between 5 and 100 microns for flexibility in a variety of samples.
Resolution of 10 microns is suitable for most nucleic acid microarrays with larger feature
sizes (>100 microns), whereas 5-micron resolution provides more precise quantitation for
smaller features (<100 microns) or for scanning cell or tissue samples. A 5-micron
resolution target illustrating the resolving power of the Axon GenePix is shown in Figure 3.
Real 5-micron imaging resolution Figure 3. Each bar is 5-microns wide separated by 5-micron spacing.
Uniformity
The Axon GenePix microarray scanner was specified and tested for field uniformity using
a proprietary low-bleaching test standard array. The slide was scanned twice; first with
the slide in one orientation ('forward') and then rotated 180° and scanned again
('reverse'). Mean variability of the intensity ratio (forward/reverse) for all features
was 7% and 3.7% (total range) for the red and green channels, respectively.
Repeatability and Calibration
Repeatability, both day-to-day and scanner-to-scanner (for facilities with multiple scanners)
is possible with Axon GenePix scanner calibration slides, which are included with every Axon GenePix
microarray scanner. These calibration slides are optimized for fluorescence with
635 nm and 532 nm excitation, respectively, and exhibit negligible photobleaching. As such,
they can be used on a regular basis to calibrate your microarray scanner for repeatable PMT
performance over long periods of time.
Automatic Laser Power Correction
Laser power is dynamically monitored during scanning to ensure constant signal output. High-quality lasers coupled with exclusive intensity correction circuitry guarantee that all pixels in the image have equal effective exposure.
Dynamic Scan Monitoring
During scanning, Axon GenePix Pro automatically graphs a histogram of the distribution of pixel intensities for whichever part of the image is displayed. The image and the histogram are updated dynamically as scanning proceeds. Both can be used to optimize scanner settings on the fly. Axon GenePix Pro automatically logs all scanning, file saving, and file loading events.
Performance Diagnostics
The status of each major scanner subsystem, such as laser power and scanning motor force and position is monitored and available at all times. The Hardware Diagnostics Report keeps a record of ongoing scanner performance assessments so that you can immediately identify and correct significant changes. Axon GenePix Pro allows you the option to compensate for gradual changes inherent to all lasers and PMTs through an automated Calibrate System function in Axon GenePix Pro. Each Axon GenePix scanner comes with a set of performance calibration standards—simply insert the standard into the slide holder and click "Calibrate" to restore your scanner to factory-set signal output benchmarks.
Automation and Customization
Once you have determined the appropriate settings for a batch of slides, you can use a simple list of checkboxes to direct Axon GenePix Pro to automatically run any steps in the scanning and analysis process. Automation steps include Preview and/or Data scanning, saving images, analyzing data using a saved array template, and saving Results files. The built-in scripting interface gives you even greater control and flexibility for totally customized automation of any Axon GenePix commands from scanning through analysis and reporting. Example scripts provide building blocks for you to create and customize your own reports including scanner control, images, tables, and graphs.
Flexible Scan Parameters
PMT gain is adjustable to maximize signal-to-noise ratio. The Axon GenePix microarray scanner allows user-selectable averaging of multiple scans lines for even greater signal-to-noise ratio on faint samples.
Barcode Reading
Axon GenePix Pro automatically reads barcodes from Preview Scans, Data Scans, and saved images. Barcodes can be included automatically in file names, and are exported with extracted data.
The Axon GenePix microarray scanner is ideally suited for a variety of fluorescence
applications including tissue and biopsy imaging, protein microarrays and biomarker and
diagnostic panels. The following images show the versatility of the Axon GenePix
microarray scanner.
Specimens were scanned with the Axon GenePix 4100A microarray scanner.
Protein Arrays
BD Biosciences Clontech Ab Microarray 380 (catalog # K1847-1) double-labeled with Cy3 and Cy5. Specimen courtesy of O. Andersson, BD Biosciences Clontech, Palo Alto, CA.
Diagnostic Arrays
Diagnostic microarray for drug susceptibility testing (RIF) in M. tuberculosis. Specimen courtesy of Drs. V. Mikhailovich and A. Mirzabekov, Center for Biological Microchips, Englehardt Institute of Molecular Biology, Moscow, Russia.
Biomarker and Diagnostic Panel Arrays
Two-color genotyping panel. Specimen courtesy of Dr. J. DeRisi, University of California, San Francisco, Department of Biochemistry, San Francisco, CA.
Whole-Mount Tissue Imaging
Skin biopsy with normal follicles and skin carcinoma. Specimen courtesy of Drs. S. Iwamoto and R. Burrows, University of Washington Department of Medicine, Seattle, WA.
Spot Quality Determination
Irregular spot morphology and missing spots on an unlabeled DNA microarray can be easily identified by imaging 635 nm reflectance signal. Specimen courtesy of Dr. J. DeRisi, UCSF, Department of Biochemistry, San Francisco, CA.
Standard microscope slides (1" x 3", 25 mm x 75 mm, or 26 mm x 76 mm)
Maximum scan area
22 mm x 71.5 mm
Excitation
532 nm and 635 nm
Scan time
6.5 minutes per channel, full scan area, 10 µm resolution
Pixel resolution
Adjustable from 5 to 100 µm
Digital resolution
16-bit
Dynamic range
Four orders of magnitude
Images
Single- or multi-image TIFF
Connection
USB 2.0 High-Speed (cable included)
Power supply
110 / 220V Universal power supply
Weight
Approximately 40 lbs. (18 kg)
Dimensions
14.2" wide x 11.7" high x 14.2" deep (362 mm x 298 mm x 360 mm)
Safety Regulatory Standards
Electromagnetic Emissions: EN 55011 61326 04:1997
Electromagnetic Immunity: EN 50082-2 61326 04:1997
Low Voltage Directive: EN 61010
Laser Safety: EN 60825-1
Electrical Safety: UL 3101-1
CSA 1010
CE Marked
SA Marked
All Axon GenePix Personal scanners come with Axon GenePix Pro, USB and power cables. A Dell computer optimized and configured for Axon GenePix scanner is available for an extra charge.
Configuration
Laser 1
Laser 2
Filter 1
Filter 2
Standard
635 nm
532 nm
655-695 nm
550-600 nm
Red only*
635 nm
-
655-695 nm
-
Green only*
-
532 nm
-
550-600 nm
* Factory upgradeable to Standard configuration
Optional Emission Filters Available
Please read our application note "GenePix 4100A Choosing Emission Filters," available from the Literature link
in the right menu, or contact your sales representative for assistance.
The Axon GenePix 4100A 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
Create multiple scan areas, pre-define your settings, and have them all scanned automatically
Industry-standard Axon file formats GenePix Array List (GAL), GenePix Results (GPR), and GenePix Image Sets (GIS) 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
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)
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.
Two lasers (635/532 nm) is standard. Optionally order one laser (specify 635 nm or 532 nm).
Package includes the Axon GenePix 4100A scanner, USB and power cables, and unlimited technical support.
Available with a fully configured Dell computer with Axon GenePix 4100A hardware
and Axon GenePix Pro / Axon Acuity software installed. This option is highly recommended.
Eliminate the inconvenience of waiting to use a scanner in a core facility or your neighbor's lab. High-performance microarray scanning is now more affordable than ever. Built on our award-winning optical, electronic and software design, the 
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