GenePix 4100A Microarray Scanner

High quality imaging for two-color microarrays

Afford your own personal scanner with our low priced GenePix® 4100A Microarray Scanner offering simplicity, reliability and flexibility that you require for your microarray-based research, be it in genomics, proteomics, or novel applications. Built on Molecular Devices award-winning (IBO Design Award) optical, electronic and software design, the sequential GenePix 4100A Microarray Scanner has all the quality, but in a price range and bench-top footprint that makes it ideal for individual lab use.


  • Flexibility to Explore Alternative Dyes: A variety of fluorophores can be used with the GenePix® 4100A Microarray Scanner as its optical design incorporates up to six different user-selected emission filters.
  • Reliable Results: Use the included set of calibration slides on a regular basis to calibrate your microarray scanner for repeatable photomultiplier tube (PMT) performance over long periods of time. In addition, Laser power is dynamically monitored during scanning to ensure constant signal output, and the Hardware Diagnostics Report keeps a record of ongoing scanner performance assessments. With these features, you can immediately identify and correct significant changes.
  • Optimize Settings On-The-Fly: GenePix Pro automatically graphs a Histogram of the distribution of pixel intensities. The image and the Histogram are updated dynamically as scanning proceeds; both can be used to optimize scanner settings while you scan.
  • Adjust the Resolution to Your Application: Use the 40-micron Preview Scan to locate the array and optimize hardware settings, and the Data Scan for accurate quantification. The GenePix 4100A Microarray Scanner offers selectable resolution between 5 and 100 microns, just about right for your samples.

Five Micron - GenePix 4100A Microarray Scanner

  • Greater Signal-To-Noise Ratio: The detection system employs a low-noise, high-sensitivity PMT to convert photons into an electrical signal, which is then digitized using world-leading ultra-low-noise digitizer technology. Adjust the PMT gain and average multiple line scans, to achieve even greater signal-to-noise ratio (SNR) on faint samples.
  • Sample Tracking: GenePix® Pro Acquisition and Analysis Software automatically reads barcodes from Preview Scans, Data Scans, and saved images, and are exported with extracted data.

Genomics: Directed at the genome sequence itself, microarrays have been used to identify novel genes, binding sites of transcription factors, changes in DNA copy number, and variations from a baseline sequence, such as in emerging strains of pathogens or complex mutations in disease-causing human genes.

  • SNP genotyping arrays
  • Arrayed comparative genomic hybridization (aCGH) arrays

Transcriptomics: The use of high-density microarrays has impacted the measurement of transcript levels to study complex diseases. With the latest development of microarray technology, it is now possible to quantify transcript levels globally and to integrate such data with information relating to disease. Microarrays based transcriptomics enables mapping a critical genomic region for a disease using affected and unaffected individuals and then pinpointing the responsible gene by identifying differentially expressed genes in the critical region.

  • Gene expression arrays
  • RNA interference (RNAi) arrays
  • MicroRNA (miRNA) arrays

Proteomics: Although the analysis of the full proteome has not yet been achieved, rapid progress is being made with microarrays in the field of proteomics. Proteomes exhibit large and dynamic complexity; the number for distinct proteins in mammals will certainly exceed the number of genes, requiring the right technology to be in place for the analysis. The flexibility of the GenePix Microarray Scanner system, and especially the high-throughput capabilities of the GenePix SL50 Automated Slide Loader provides adequate tools to researchers.

  • Protein arrays
  • Peptide arrays
  • Antibody arrays
  • ELISA arrays
  • Reverse Phase Arrays

Epigenomics: The gene carries the basic unit of information, but this information has an impact only once it is properly programmed by the epigenome. The DNA methylation pattern is cell type specific and correlates with chromatin structure. DNA microarrays are being utilized to identify methylation patterns, and the GenePix Microarray Scanner automation solution allows the researcher to identify these patterns faster.

  • DNA methylation arrays
  • Chromatin immunoprecipitation (ChIP) arrays

Novel Applications: The creativity and broad applicability of microarray-based research has no liSmits and is demonstrated by the vast variety of different microarray applications to conduct large-scale quantitative analysis. With the GenePix® Microarray Scanner ystem you have the most flexible solution and freedom in your research.

  • Tissue arrays
  • Quantum Dots
  • Carbohydrate Arrays
  • Chemical Compound Arrays

The GenePix 4100A Microarray Scanner and GenePix® Pro Microarray Analysis Software have been designed to work  together as a complete integrated platform. The seamless communication between scanner and software ensures unmatched efficiency for data acquisition and analysis, as well as for real-time scanner performance monitoring. Optional Acuity® Microarray Informatics Software completes the package, offering database storage, clustering algorithms, advanced statistics and visualizations.

Performance Specifications

Sample type Standard microscope slides (1" x 3", 25 mm x 75 mm, or 26 mm x 76 mm)
Maximum scan area Standard microscope slides (1" x 3", 25 mm x 75 mm, or 26 mm x 76 mm)
Excitation 532 nm and 635 nm, solid-state lasers
Laser settings Fixed 100% power
Emission filters 8-position filter wheel, 2 standard filters included (optimized for Cy3 and Cy5 or spectrally similar dyes)
Detection 1 photomultiplier (PMT), automatic and manual gain adjustment
Scanning method Sequential
Scan time 6.5 minutes per channel, full scan area, 10 µm resolution
Pixel resolution 5 μm max., adjustable from 5 to 100 μm
Focus Fixed at slide surface
Optics Non-confocal
Digital resolution 16-bit
Dynamic range Four orders of magnitude at SNR > 3
Image type Single- or multi-image TIFF
Barcode reading Image-based barcode reader

General Specifications

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)
Connection USB 2.0 High-Speed (cable included)
Power supply 110 / 220V Universal power supply  

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


GenePix® 4100A Microarray Scanner



Product Number

GenePix 4100A Microarray Scanner GENEPIX 4100A-U STD
GenePix Pro Software v7 license 5004757
Acuity Microarray Informatics Software ACUITY PTO