Axon Laboratory GenePix Pro 6.0.1.09

Axon Laboratory GenePix Pro 6.0.1.09
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GenePix Pro is the complete standalone image analysis
software for microarrays, tissue arrays and cell arrays

Why Choose GenePix Pro?

GenePix Pro is the industry standard microarray image
analysis software because of its unique combination of
imaging and analysis tools, visualizations, automation
capabilities, performance and ease of use.

IMAGING TOOLS

Display
GenePix Pro displays each of up to four single
wavelength images in a different user configurable
color, then constructs color ratio images from any
three pairs of channels as specified by the user.
Four channel imaging can be used to analyze multiple
channels from the same scan, or multiple one or
two color images from different scans. Select colors
from a fully customizable color palette.

Zooming buttons, hot keys, a Navigation Map and an
efficient Windows implementation make it fast and easy
to move around large images.

Feature Finding
GenePix Pro uses a set of proprietary feature finding
algorithms to find circular, square or irregular
features. Every pixel in a region around the feature
is examined by a local alignment algorithm and
assigned to feature or background. Global alignment
algorithms determine the translation, rotation and
skew of blocks of features.

Measuring Tools
Use the Measuring Tools to make detailed calculations
from specific regions on your arrays. GenePix Pro
automatically calculates statistics and graphs the
pixel data in the drawn region. Draw lines, polylines,
and wide lines to generate an intensity profile graph
of the line. Draw rectangles, polygons, and ellipses
to generate a histogram of pixel intensities insid
the region. Use these tools to obtain quick
measurements and channel comparisons without gridding
or analysis.

Image Alignment
If your non Axon images have to be aligned before they
can be analyzed, you have a number of methods of
aligning them in GenePix Pro. Drag one image over
another, or let GenePix Pro find the optimal alignment
for you.

Barcode Reading
GenePix Pro automatically reads barcodes from images.
Barcodes can be included automatically in file names,
and are exported with extracted data.

ANALYSIS TOOLS

Background Subtraction
Choose your background subtraction method from a
number of local and global methods, or correct your
data based on negative controls. Local background
correction is recommended for most microarrays because
even small variations in the background signal can
affect ratio values. For arrays on which the spots are
too close together to calculate an accurate local
background, you can specify a single value to subtract
from all features, for each channel. If you have
negative controls on your microarray, use the nearest
negative control, the mean of the nearest n negative
controls, or the mean of all negative controls as the
background value. At any time you can visually rev
the local background region assigned to a feature.

The Feature Viewer
Use the Feature Viewer to get on the fly access to
individual feature data, without analyzing the entire
image. The Feature Viewer displays images and data for
all acquisition wavelengths, and the three
user specified ratios. Feature Indicators are draw
directly in the Feature Viewer to instantly evaluate
individual features on a large array without having to
zoom in on each one.

The Feature Pixel Plot
The Feature Pixel Plot provides additional detailed
information about individual features, including a
scatter plot comparing individual pixels in the
selected wavelength channels.

Advanced Quality Control Flagging
General Boolean queries allow you to flag or highlight
data based on user defined criteria. Complex criteria
can be defined based on any measurements from the
Results table. Features identified by the query can be
marked with quality flags (good, bad), highlig
for further evaluation, or used to calculate a
normalization factor. Queries can be saved for use on
other arrays. Speed through analysis by defining in
advance the criteria you need to identify and isolate
both good and poor data, or control features.

Find
Use the Find function to search for all features w
a given Name or ID from anywhere in the GenePix Pro
interface.

Extracting Data from Images
A single click of the Analyze button automatically
calculates up to 108 different measurements for each
feature and displays the data on the in a spreadsheet.

Normalization
Normalize data with linear, ratio based methods, on
normalization features, selected features or all
features. For advanced users, GenePix Pro provides
fully general Boolean searches to define normalization
features.

Web Integration
GenePix Pro is fully integrated with web accessible
databases. No longer is your data isolated, waiting to
be imported into a larger database or analysis
program. Create a list of your favorite s to choose
from, or store a preferred in each GenePix Array
List file. Point at a feature, select Go To Web, and
your default web browser opens the database and
automatically queries the database for information
about the selected substance name or ID.

As with all other GenePix Pro features, Go To Web is
fully scriptable, so you can construct a custom view
of the data in a Report and embed hyperlinks to your
favorite databases.

Automation
Using a simple series of checkboxes, you can specify
automation for any or all steps in the GenePix system
from scanning through analysis and file saving.
Scripting allows even greater flexibility for
customized automation.

Standard Data Formats
Axon Instruments GAL and GPR file formats are
standards in the microarray industry.

GenePix Array List (GAL) Files
Easily construct lists describing the position and
content of each spot on an array from plain text
files. Substance name and ID lists can be pasted
directly into the array settings file to create a
GenePix Array List (GAL) file. GAL files can also
created from a collection of microwell plate files
using the GenePix Array List Generator. Add as many
columns as you like to the GAL file to track any
sample information along with GenePix results. See the
GenePix File Formats page for instructions.

GenePix Results (GPR) Files
GenePix Pro analysis Results are displayed in thei
own spreadsheet. Quality and normalization flags
appear graphically in their own column for easy
identification. Sort, flag, review images, save or
export all from the Results tab. Save data directly to
Acuity microarray informatics software.

GenePix Pro calculates up to 108 different
measurements for each spot, including:

Number of feature and background pixels for each
feature at each scan wavelength

Mean, median, and sum of pixel intensities at each
scan wavelength, for both feature and background
pixels

Ratio of mean pixel intensities, and ratio of median
pixel intensities

Signal to noise ratio

Medians and means of pixel by pixel ratios

Regression ratios

Sum of mean feature pixel intensities, and sum of
median feature pixel intensities

Standard deviations of feature and background pixel
intensities

Several spot quality measurements such as percent
saturated pixels, feature and background coefficients
of variation, and feature circularity

For a complete list and description of GenePix Pro
measurements, see the GenePix Results format on the
GenePix File Formats page.

Export as MAGE ML
Export microarrays in MAGE ML format for upload to
web based databases such as ArrayExpress. A growing
number of jouals, such as Nature, are requiring that
microarray data is made available in MAGE ML format as
part of publication. GenePix Pro gives you the ability
to export data in this format, and includes on the fly
compression during export to minimize file sizes.

Export as PDF
Easily generate high quality documents in Portable
Document Format (PDF). As one of the most widely used
electronic document formats in the world today, PDF
files are compact enough to send as e mail
attachments, but they still retain the original
formatting and preserve the high resolution and
quality of images and graphs. Unlike HTML, PDF fil
are self contained within a single file and make
cataloging and archiving GenePix Reports remarkably
easy. PDF files are searchable and import easily into
publishing software packages such as Adobe Photoshop
or Illustrator. For more information, read our
Knowledge Base Article on exporting graphics in
GenePix Pro.

Operation with Non Axon Scanners
While GenePix Pro cannot acquire images from
third party scanners, it can analyze these images.
GenePix Pro reads standard unsigned 16 bit grayscale
TIFF images acquired from any scanner, aligns the
scanned channels, and analyzes data from them as if
they were acquired on a GenePix scanner.

VISUALIZATIONS

Histograms
The Histogram tab automatically graphs a histogram of
the distribution of pixel intensities at each scanned
wavelength. The Histogram tab is updated instantly as
the image view changes so you can balance the signal
output for each channel dynamically during scannin

Also generate histograms of any analysis column, so
that you can review ratio or intensity distributions.

Scatter Plots
View scatter plots of pixels in individual features,
Whereas the Feature Pixel Plot plots the pixel
intensities from a single spot, the Scatter Plot t
automatically plots any analysis measurements from
every spot on the array. Clicking on a point on the
Scatter Plot displays the associated feature in the
Feature Viewer. Instantly assess the precision of your
data using regression and standard deviation lines on
the Scatter Plot. Data points selected on the Scatter
Plot are automatically highlighted on the Image and
Results tabs (and vice versa.)

LAB BOOK

The GenePix Pro Lab Book logs all file events that
occur while GenePix Pro is running. It automatically
records all saving of images, results, settings, and
Array List files. It also functions as an archive of
images and Results files: clicking on an image or
results file name opens that file directly into
GenePix Pro.

REPORTS AND SCRIPTING

GenePix Reports give the user unprecedented access to
scanner control and microarray data, as well as an
extensive set of tools to manipulate and display d
GenePix Pro supports standard scripting languages such
as VBScript and JavaScript as well as any other
scripting languages supported by Inteet Explorer,
such as PerlScript and PythonScript. Extract data via
script, write custom analyses through ActiveX objects,
generate HTML reports: GenePix Pro scripting is
maximally flexible.

Ready to use Analysis Reports generate quality control
reports of individual features and whole arrays,
identify interesting features according to
user defined criteria, evaluate replicates, and more.
Hardware Diagnostic Reports streamline and log ongoing
scanner performance validation. Example Reports give
you the building blocks to create and customize your
own scripts including scanner automation, images,
tables, and graphs without a degree in programming!
All scripts are editable for even greater flexibility.

GenePix Pro online help includes an extensive
Scripting Tutorial, which takes users through a full
course in HTML, VBScript and GenePix Pro scripting.

PRINTING

Print images, histograms and scatter plots directly
from GenePix Pro. The user can specify printed header
information, page formatting, and the full range of
fonts.

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