GenePix 4000B Microarray Scanner

Fast, high-quality imaging for two-color microarrays

The GenePix® 4000B Microarray Scanner is a benchmark for quality, reliability and ease-of-use in microarray scanning technology. Coupled with GenePix® ProMicroarray Image Analysis Software and Acuity® Microarray Informatics Software, the GenePix System sets the highest standards in the acquisition and analysis of data from all types of arrays, including nucleic acids, proteins, tissues, and cells.


  • Simultaneous Dual-laser Scanning. Unlike most commercially available microarray scanners, the GenePix 4000B Microarray Scanner acquires data at two wavelengths simultaneously. This means drastically reduced scan times and hence greater workflow 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.
  • Reliable Results. The performance calibration standards that come with your GenePix 4000B Microarray Scanner allow you to check the performance when you receive your scanner and at any time in the future. GenePix® Pro Acquisition and Analysis Software includes one-touch calibration to restore any GenePix scanner to benchmark performance. You can rest assured knowing the signals you generate today are the same as a couple of years ago and in the future.
  • Automated Workflow. With automated photomultiplier (PMT) balancing, the fully integrated GenePix Pro Acquisition and Analysis Software controls the GenePix 4000B Microarray Scanner and can automatically evaluate the required PMT gain values for fast and easy optimization of signal intensity and channel balance. The GenePix 4000B Microarray Scanner then acquires data at your selected resolution between 5-100 microns, allowing the adjustment of image resolution and file size for each experiment.
  • More Publications. For over 10 years and close to 6000 literature references, the GenePix 4000B Microarray Scanner has expanded the overall sample compatibility, with user-adjustable focus offset and laser power settings. This allows proper imaging of slides with either a raised surface, as with membrane-coated glass, or a recessed surface, as in embedded arrays.

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 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 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 limits and is demonstrated by the vast variety of different microarray applications to conduct large-scale quantitative analysis. With the GenePix® Microarray System you have the most flexible solution and freedom in your research.

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

The GenePix® 4000B 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 slide (1" x 3", 25 x 75 mm or 26 x 76 mm)
Scan area Adjustable, 22 x 71.5 mm max.
Excitation 532 nm and 635 nm solid-state lasers
Laser power settings User-selectable 100%, 33% or 10% laser power
Emission filters Two, optimized for Cy3 and Cy5 or spectrally similar dyes
Detection Dual photomultipliers (PMTs), automatic and manual gain adjustment
Focus offset Adjustable between -50 and +200 μm (5 μm increments)
Optics Non-confocal
Scanning method Simultaneous, 2-channel
Scan time 6.5 minutes for both channels, 10 μm resolution, full scan area
Pixel resolution Adjustable from 5-100 μm
Digital resolution 16-bit
Dynamic range Four orders of magnitude at SNR > 3
Image type Single- or multi-image TIFF
Barcode reading Image-based software barcode reader

General Specifications

Dimensions (in.) 13.5 (W) x 8.0 (H) x 17.5 (D)
Dimensions (cm) 34 (W) x 20 (H) x 44 (D)
Weight 45 lbs. (20 kg)
Power supply 110/220V universal


GenePix® 4000B Microarray Scanner



Part Number

GenePix 4000B Microarray Scanner GENEPIX 4000B-U
GenePix Pro Software v7 license 5004757
Acuity Microarray Informatics Software ACUITY PTO