“…Our search was over after we tested the Array-Pro software. It is simply the best product out there for automatic spot-calling. We absolutely need Array-Pro in order to handle the steadily increasing volume of microarray image data processed daily by our facility."
--Chris Cheadle Ph.D., DNA Array Facility, National Institute on Aging
"After 6 months of evaluating many array analysis packages our first choice was Array-Pro Analyzer. Array-Pro has very accurate automated spot finding features along with many excellent visual and data analysis tools built in, reducing the need for complicated downstream spreadsheet analysis. We found it to be a comprehensive package which is extremely user friendly."
--Jim Smith, Ph.D., Principal Scientist, Genomic Profiling Systems, Cambridge, MA
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.
Improved candidate spot finding (for line determination) via morphological validation of spot shape
Option for variable cell boundary definition for each spot
Binning of spots for replicate analysis
Time-based experiments are supported via rate measurements and input of time via the file or user
Automatic and reproducible results
Characterize Data
Grouping of spots as negative controls, ignored (bad spots), signal controls (housekeeping genes) and other user-defined criteria.
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)
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)
Automatically assign image names to labels and groups
Automatic population of cell groups according to user-defined criteria.
Numeric and Graphic Feedback
Display interactive graphics and data tables including histograms and scatterplots
Display multiple scatterplots and histograms to view many variables at once
Use data graph to show individual measurements across many image sets. View time series experiments or other variables across experiments
Display individual cell histograms (with statistics indicators) and adjust the threshold graphically
Use irregular AOI to select cells on the scatterplot
Assign axis values for the scatterplot, histogram and data graphs.
Option to rename measurements in the table and hide or rearrange columns
Interactive cell window display with detailed information for each spot in image group (e.g. Cy3, C5, ratio)
Various data display windows
Measurement & Processing Tools
Normalization by mean, median, reference spots
Intensity and spatial calibration
Experiment definition, storage and recall (with associated images and information)
Statistical control of pixel segmentation and signal calculation
Scores of morphological measurements
Equation editor to build practically any kind of custom measurement.
Option to store layout and measurements within an experiment.
Option to automatically tint images
Dynamically linked to GeneMaths 2.0 such that updates in Array-Pro can be shown interactively in GeneMaths
