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ARRAY PRO
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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Reproducibility:
Array-Pro Analyzer sets a new standard
for automation of spot identification. A patented grid overlay
to define the spots of interest takes advantage of the inherent
periodicity of spot placement. 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.
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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.
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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.
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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.
Extensible:
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.
Partial List of 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)
New in Array Pro version 4.5:
- Pixel-by-pixel cross-correlation method
to segment signal, background and artifact pixels populations.
- Normalization using Loess best-fit,
signal control cells, or all cells, by image or sub-grid.
- Statistical control of pixel segmentation
and signal calculation.
- Re-organization of the toolbar and menus
to be more streamlined, easier to use, and more descriptive
of the functions.
- Complete control via menus in addition
to the toolbar.
- Improved candidate spot finding (for
line determination) via morphological validation of spot
shape.
- Scores of morphological measurements.
This is attractive for quantitative evaluation in production
of microarrays.
- New auto-alignment techniques for grids
that make it easy and faster to make a template and execute
grid finding.
- User can display multiple scatterplots
and histogram displays to look at many variables at once.
- New data graph to show individual measurements
across many image sets. Useful for viewing time series
experiments or other variables across experiments.
- Option for variable cell boundary definition
for each spot.
- Automatic population of cell groups
according to user-defined criteria.
- Equation editor to build practically
any kind of custom measurement.
- Option to store layout and measurements
within an experiment.
- Option to automatically assign image
names to labels and groups.
- Option to automatically tint images.
- Time-based experiments are supported
via rate measurements and input of time via the file or
user.
- Ability to display individual cell histograms
(with statistics indicators) and adjust the threshold
graphically.
- Option to use irregular AOI to select
cells on the scatterplot.
- User assigned axis values for the scatterplot,
histogram and data graphs.
- Option to rename measurements in the
table and hide or rearrange columns.
- Dynamically linked to GeneMaths 2.0
such that updates in Array-Pro can be shown interactively
in GeneMaths.
Contact
us for more information.
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