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Microarray Data Analysis

Image Analysis Software

Institutions or companies which produce scanning or image analysis software for spotted DNA microarray slides.

• Alpha Innotech Corporation. Produce the AlphaArray microarray reader and associated software.
• Amersham Biosciences. Produce ArrayVision and ArrayStat software.
• Analytic Biostatistics Section, National Institutes of Health. Produce the P-Scan and F-Scan software written in MATLAB for capturing microarray images. Follow the link for "gene expression". Data on spot intensities is passed out to JMP for further statistical analysis.
• Applied Precision. Produce the ArrayWoRX microarray scanner and associated software.
• BioDiscovery. Produce Imagene and GeneSight software.
• BlueGnome. Produce BlueFuse software. A Bayesian model is used to generate a confidence measure for each spot.
• Eisen Lab, Lawrence Berkeley National Lab. Produce ScanAlyze image analysis software. Also Cluster and TreeView software for cluster analysis and GMEP software for expression profile analysis.
• Genomic Solutions. Produce the GeneTac scanner and associated software.
• GridGrinder. Corning Incorporated released GridGrinder as open source under the BSD license in 2002.
• GSI Lumonics. Formerly produced QuantArray software now sold to Packard Bioscience.
• Image Analysis Group, CSIRO. Produce Spot software. Spot builds upon more than a decade of image analysis work by Australian CSIRO scientists. At this time we believe it to do the best job of image analysis for microarray slides.
  • SPOT Image Analysis Software. 30 day license available for download.
  • Imview. Free software for image viewing. Hugues Talbot.
  • Spot Manual.
  • Spot: Description of Output.
• Imaxia. Produce ArrayFox software. 30-day trial available.
• INRA (French National Institute for Agricultural Research) Toulouse. Produce AGScan software. GNU General Public License.
• Institut Curie. Produce MAIA software for automatic processing of one and two colour images produced in spotted DNA microarray experiments.
• Jain Lab, Cancer Center, University of California, San Fransisco. Produce UCSF Spot for Windows. Free for academic use.
• Jeremy Buhler, Washington University of St Louis. Author of Dapple software. Free software.
• Koada Technology. Produce Koadarray software for automated analysis and quantification of microarray images.
• MediaCybernetics. Produce Image-Pro Plus software.
• Molecular Devices. Produce the GenePix image scanner and associated software.
  • GenePix Pro. Guides to ATF (Axon Text File), GAL (GenePix Array List), GPR (GenePix Results) and other files formats.
• Molecular Neuroscience Core, Center for Behavioral Neuroscience, Atlanta. Producers of GLEAM software.
• MolecularWare. Produced Digital Genome microarray scanning software, but now appears to be defunct. Website is not operational.
• NHGRI Microarray Project. Produce the ArraySuite Software Package, a collection of IPLab extensions for the Macintosh computer.
• Nutec Sciences. Produce GLEAMS software, but there is no mention of this on their www page.
• PerkinElmer Life Sciences. Produce ScanArray scanners and QuantArray software.
• Raytest. Produce AIDA software.
• ScanAlytics. Produce Scanalytics MicroArray Suite software including the DeArray module.
• TIGR: The Institute for Genomic Research. Produce SpotFinder software.
• Virtek Vision International Inc. Produce Virtek ChipReader software.