Array Pro Analyzer - From Images to Answers

The total solution for micro array and high-density array image analysis.

Array-Pro Analyzer is an indispensable tool for the nascent microarray and high-throughput screening research efforts fueling the genomics, proteomics, drug discovery and bioinformatics revolution

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Perfect for micro array gene expression or typing analysis
Automatic grid, subgrid and spot finding overcomes tedious spot template assignment.
Reproducible! Get the same numbers from user to user.
Get low-level expression using extensive background & signal options to optimize results.
Characterize more precisely through grouping by cells, grids, and images.
Statistical feedback to determine experiment quality.
Perform cluster analysis, PCA and self-organizing map analysis across huge datasets of multiple experiments with Gene Maths.

REPRODUCIBILITY

Media Cybernetics has had long experience in extracting image features through pattern recognition. Array-Pro Analyzer sets a new standard for automation of spot identification by taking advantage of the inherent periodicity of spot spacing into grids and subgrids on the substrate. The benefit is the ability to reproduce exactly the same results of analysis from user to user. Through computer algorithm automation, results are absolutely repeatable. This is the key to scientific advancement. One scientist must be able to duplicate the experiments of others within acceptable error.

SPEED

An extremely beneficial side effect is the speed of analysis. Typically a scientist might take days to manually define grid, subgrid, and spot locations for the hundreds of thousands of spots. And the results were never the same since a position change of a single pixel for spot definition can make dramatic differences in quantitation. With Array-Pro Analyzer the execution now takes place in seconds.

INFO EXTRACTION

One of the biggest problems in microarray analysis as applied to gene expression has been the extraction of small signal changes in the presence of the vast sources of background noise (cross-hybridization, optical effects, dust, etc.) Scientists have found that clusters of genes that indicate phenotypes or disease states tend to be expressed at these low levels. Again, with Media Cybernetics’ experience in characterization of signal and noise, users are able to optimize signal/noise by adjustment of several control parameters and numerous choices in background methods.

ANALYSIS WIZARD

An analysis wizard takes the user through grid, subgrid and spot finding parameters in order to establish the methodology for each type of array image. Once these parameters are stored as an experiment type, subsequent analyses can be performed without user
intervention. This is the key to reproducibility.

STATISTICAL FEEDBACK

Array-Pro Analyzer also offers extensive statistical user feedback to establish the quality of the data and the experiment. The old adage of computing, garbage in is garbage out, is certainly appropriate in dealing with the large amounts of data involved with microarrays. The user may accurately calibrate the signal and background based on standards, controls, and replicates.

ADVANCED STATISTICS

Array-Pro Analyzer interfaces seamlessly with GeneMaths from Applied Maths, a Media Cybernetics distribution partner. Information from a series of gene expression experiments in Array-Pro is immediately available in GeneMaths for statistical treatment via cluster analysis, self-organizing maps and principal component analysis.

EXTENSIBILITY

The Image-Pro Plus image analysis platform is a long-established standard that provides a powerful development environment for OEMs, systems integrators, and end users. Array-Pro Analyzer shares this sort of platform development to enable the creation of tailored versions
for analytical high-density array imaging. Unlike most programming tool kits, the Media Cybernetics SDK offers a proven host environment that can be easily and quickly customized to solve specific imaging applications without starting from scratch, thereby reducing development risk and cost.

EXPERIENCE

Make sure you're working with the leader in imaging technology. Since 1985, Media Cybernetics has set the standard for high-performance image analysis software. Leaders in both the imaging and software industries rely on our expertise for image processing applications, tools, and custom solutions.

PARTIAL LIST OF ARRAY-PRO FEATURES

Automatic rotation, grid, subgrid, spot finding in method development
Automatic alignment of grid, subgrid, spots with applied template
Grouping of spots as negative controls, ignored (bad spots), signal controls (housekeeping genes) and other user-defined criteria.
Binning of spots for replicate analysis
Hundreds of techniques to characterize and remove background noise, including global from image or reference spots (zero order, bilinear, biquadratic, bicubic polynomial fit), local perimeter or local corners (with offset, width, erosion, filter control)
Normalization by mean, median, reference spots
Intensity and spatial calibration
Interactive graphics and data tables to elucidate information
User-selectable data for each spot or group of spots: mean, median, min, max, range, sum, standard deviation, ratio (if two images are grouped, as with gene expression)
Experiment definition, storage and recall (with associated images and information)
Histogram display or all spots or any group of spots
Scatterplot of results of results from two images; with interactive graphic selection
Interactive cell window display with detailed information for each spot in image group (e.g. Cy3, C5, ratio)