My Microarray Software Comparison - Image Analysis Software


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Definition of image analysis Software
Suggested readings
Image analysis software (in alphabetical order)

[ Able Image Analyser | AIDA Array Metrix | ArrayFox | ArrayPro Analyzer | ArrayVision | Dapple | F-scan | GenePix Pro | GeneSpotter | GridGrinder | ImaGene | Iconoclust | Iplab Microarray Suite | Koadarray | Lucidea Automated Spotfinder | Matarray | MicroVigene | Phoretix Array | P-scan | QuantArray | ScanAlyze | Spot | SpotReader | TIGR Spotfinder | UCSF Spot ]

Definition of image analysis software

Image analysis software performs three fundamental processes of image analysis: gridding, segmentation and information extraction. Gridding is a process to locate each spot on the slide. Segmentation is a process to differentiate the pixels within a spot-containing region into foreground (true signal) and background. Information extraction includes two parts, the spot intensity extraction and background intensity extraction. Spot intensity extraction refers to the calculation of fluorescence signal from the foreground from segmentation process, while background intensity extraction utilizes different algorithms to estimate the background signal due to the non-specific hybridization on the glass.

Suggested image analysis readings

  1. Yang YH, Buckley MJ, Speed TP. Analysis of cDNA microarray images. Brief Bioinform. 2001 Dec;2(4):341-9. [PubMed]; a similar online full-text technical report called "Comparison of methods for image analysis on cDNA microarray data." by the same group of authors is available here.

Image analysis software (in alphabetical order)



Product
Authors/ Company/ Institute
Interface/ Operating System
Features
Price
Remarks
Able Image Analyser mulabs.com
 Windows
 Able Image Analyser supports image analysis functions that include dimensional, gray scale and 24 bits color measurements with statistics that calculate basic statistics and frequencies. US$100 Demo available
AIDA Array Metrix Raytest GmbH Windows Automated spot identification, background subtraction and normalization, automated elimination of bad spots, scatter plot, simple data filtering, schematic result display Euro 5900 Demo available
ArrayFox Imaxia Corp.
 Windows
 Automatic spot recognition and grid alignment; Automatic flagging of “bad” spots; Seven adjustable parameters for evaluating spot quality; Automatic detection of background noise and contaminations;
$1980
additional 30% discount for academic users
 Demo available; product-key: ArrayFox-demo
ArrayPro Analyzer Media Cybernetic Windows Image processing; automated spot identification; simple statistical analysis; simple database function; can analyze image for Affymetrix system ~US$6000 demo availabe upon request; The automated spot identification algorithms is very good! combined seamlessly with GeneMaths for downstream data mining; brochure;self demo manual;
ArrayVision 8.0 Imaging Research Inc. Windows Spot identification, data visualization, scatter plot, various spot quality measures and statistical tools US$6900 Demo available upon registration; Application note available upon registration
Dapple 0.86 Jeremy Buhler lab; Department of Computer Science; Washington University in St. Louis. UNIX-like operating systems Quantitating spots on a two-color DNA microarray image GNU General Public License Source code; Dapple technical report [pdf][ps]
F-scan 1.3 P. J. Munson, V. V. Prabhu, L. Young; Analytical Biostatistics Section; Mathematical and Statistical Computing Laboratory; Center for Information Technology; National Institutes of Health Windows, Mac, Linux/ Unix running MATLAB environment Quantification and analysis of fluorescently probed microarrays; scatterplots; multiple image comparison; data merging and web links.  Free for academic Download available upon registration; Manual; sample images for testing [pc][mac][unix]; reference [PubMed]
GenePix Pro 4.0 Axon Instruments Windows Spot identification, scatter plot, histogram, normalization US$3000 (USA & Canada only) Demo available upon registration; Although designed for Axon scanner, it can also act as an independent feature analysis software for image acquired with third-party scanners
GeneSpotter
 MicroDiscovery
 Windows
 Import files from various platforms, Automatic grid finding, Quality Control,  Batch Mode
 no pricing information is available Demo availabe upon registration;
GridGrinder
 Open Source at SourceForge ; Tanner C., Tepesch P., and Shulyakov M.; Corning Inc. Engine: cross-platform;
GUI: Windows 95/98/NT 
automated origin location, skew detection, and grid placement;  can handle an arbitrarily large number of color channels;  files can be processed in batch mode, and output data can be tailored to meet the
user's needs
 BSD license (open-source)
 Download;Manual; Source code (GUI) (Engine);
ImaGene 5.0 BioDiscovery Windows 95/98/NT4/2000/XP, Linux, Mac
 Array platform independent, Scanner independent, Multiple channel capability,  Flexible grid design and alignment, Various segmentation, quantification and visualization tools, Customizable automated quality flagging, Optional Batch Automation Module ~ US $7995 Demo available upon registration; video tour
Iconoclust
 Clondiag  Windows 98/Me/NT/2000/XP Image analysis; various visualization tools, automated/pure spot identification; scripting (Python) ~420 Euro  Demo available upon registration; brochure; interface with PARTISAN arrayLIMS
Iplab Microarray Suite Scanalytics, Inc Mac Image analysis, various visualization tools, array platform independent, scripting (IPLab script), gene databasing capabilities ~ US$6500 Demo available upon registration;  brochure;
Koadarray Koada Technology Windows NT4, 2000, XP, 98, Me automatic spot finding and image analysis, spot quantification, flexible data output, accept major array platforms. from US$3700 to US$4900, depending on the number ordered. Demo available;
Lucidea
Automated Spotfinder		 Amersham Bioscience Windows 2000/ NT Spot identification; batch processing; quality metrics no pricing information is available brochure;
Matarray X. Wang et al., Max McGee National Research Center for Juvenile Diabetes, Windows? An integrated image analysis package that performs spot detection, signal/background segmentation, signal intensity determination and quality determination. It employs a simple algorithm that utilizes both spatial and intensity information for spot detection and signal segmentation and the procedure can be iterated to improve performance. available free of charge; contact authors for further information reference [PubMed][pdf]
MicroVigene
 VigeneTech Inc
 Windows
 Spot identification, quantitation, support plug-ins and batch process, flexible grids, 3D on screen visualization to check spot accuracy.
$9800 (Academic discount available)
 brochure [pdf]; Demo, Try version,
Phoretix Array 3 Nonlinear Dynamics Windows Spot identification, quantitation and normalization, analyze any format of macro-, micro- array and distorted images, label replicated spots. no pricing information is available user friendly GUI; evaluation available; brochure available upon request;
P-scan 1.2 (Peak quantification using Statistical Comparative ANalysis) P. J. Munson, V. V. Prabhu, L. Young; Analytical Biostatistics Section; Mathematical and Statistical Computing Laboratory; Center for Information Technology; National Institutes of Health Windows, Mac, Linux/ Unix running MATLAB environment Quantification and analysis membrane cDNA array; scatterplots; multiple image comparison; data merging and web links. Free for academic registration before download; manual; samples images available; reference [PubMed]
QuantArray Packard Bioscience Windows NT Quantitation, spot quality measures and normalization; can analyze up to five color microarray images no pricing information is available brochure;
ScanAlyze 2 Michael Eisen's lab;Lawrence Berkeley  National Lab (LBNL) Windows 95/98/NT  Process fluorescent images of  microarrays. Semi-automatic definition of grids and complex pixel and spot analyses. Outputs to tab-delimited text files for transfer to any database. Free for academic Download;Manual; source code;
Spot CSIRO Mathematical and Information Sciences Windows NT/2000/XP, Linux,  Solaris , Digital Unix running R environment Automatic grid location; Flexible spot segmentation; Morphological background estimation.  Depends on number of users User guide; installation instruction; Demo version available upon registration
SpotReader
 Niles Scientific
 Windows
Automated Grid Creation, Automated Flagging, Batch processing
 Depends on number of users
 Demo available;
TIGR Spotfinder The Institute of Genomic Research (TIGR) Windows Spot identification; Microarray image processing Free (Open source)
 Registration before any download; User guide; Reference [PubMed]
UCSF Spot Jain Lab;
UCSF		 Windows Spot identification; can use a counterstained, DAPI image for segmentation based on the DNA distribution in the spots Free for academic download;examples;
last updated: 10 Sep 2004
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