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Axon Laboratory Acuity 4.0.0.49

Axon Laboratory Acuity 4.0.0.49
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Acuity. 4.0 Enterprise Microarray Informatics

Acuity is a complete microarray database, data min
and visualization package that has been designed and
optimized for Windows.

Analysis

Normalization
Acuitys Normalization Wizard can normalize an
arbitrary number of microarrays with the click of
button. Choose to normalize on all spots, control
spots, negative controls or any other subset of spots
that you can specify with a fully general database
query. Normalize groups of microarrays to a time point
or a sample. Choose linear ratio based methods or
non linear lowess methods, including print tip groups.
Normalizations are easy to apply and remove so that
you can experiment freely with different methods.
you are finished, unnormalized and normalized data are
displayed side by side in the Normalization Viewer.

Filtering
Establishing data quality is paramount in microarray
experiments, as unbiological outliers can skew
downstream analyses. Acuity has a large number of
analytical and statistical tools that you can use
filter out noise from your data: filter on replicate
statistics, on individual spot characteristics or on
many other quality measures.
Once you have identified outliers, update their flag
values in the database, or define your own custom flag
values.

Replicate Analysis
Tracking replicate substances and microarrays is
intrinsic to Acuity analyses. Replicate substances are
automatically combined, and can be filtered by
standard deviation, coefficient of variation and many
other measures. Replicate microarrays can be easily
combined to construct representative data points from
each time or for each tissue in an experiment.

Find Matching Expression
Use Acuitys Match Expression function to investigate
the behaviour of individual substances in your
experiment. Choose from nine different similarity
metrics to find the substances that are most highly
correlated with a single profile or to an average
profile built from a class of substances.

Many Clustering Methods
There is no single analysis technique that can be used
for all types of data, so Acuity has a suite of
advanced analysis methods, among them Hierarchical
Clustering, Self Organizing Maps, K Means and
K Medians, Gap Statistic, Principal Components
Analysis, Gene Shaving and more. Each algorithm offers
a large choice of similarity metrics, so that you
use the analysis that is appropriate for your data.
Use the output of one algorithm as input to the next.
For example, you can optimally order the branches in a
dendrogram from a hierarchical cluster, with the order
derived from a Self Organizing Map or a Principal
Components Analysis.

Performance Optimization
All Acuity analyses have been optimized for speed and
memory use on very large data sets so that a standard
desktop computer can be used to cluster hundreds of
microarrays. Clustering and other processor intensive
tasks are implemented as background processes, so that
you can queue and execute multiple analysis tasks
while continuing to work on other tasks in Acuity.
Depending on the size of the dataset and the amoun
computer memory available to Acuity, the clustering
algorithms partition the datasets and perform
calculations differently, so that Acuity is always
working most efficiently.

Analysis Audit Trail
All Acuity analysis operations and results are stored
sequentially in the database as they are calculate
so an audit trail is maintained automatically and
displayed in the Acuity project tree for each data
set. You can easily reproduce an analysis, or remove
data transformations from microarrays or datasets.

Substance and Microarray Lists (Quicklists)
Acuity Quicklists are a powerful method of saving
lists of interesting substances, microarrays or
annotations. With the click of the mouse you can save
all selected substances as a quicklist, either
globally or with a dataset. Each list can be assigned
a color. Together with the ability to apply a list to
the current view of the data, so that the substances
and microarrays are colored appropriately, colored
quicklists give you the ability to track multiple sets
of substances through all Acuity visualizations.

Reports and Scripting
Like GenePix Pro, Acuity 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: Acuity scripting i
maximally flexible.

Visualizations

Clear and Interactive
Acuitys clear and interactive display of analyzed
data can reveal subtle structure and relationships in
the data that are not apparent from less elegant
visualizations. Acuity displays clustering results in
many different ways, uses smooth interactive 3 D plots
of principal components data (exportable as AVI
animations), and synchronizes all views so that
substances and their annotations selected in one view
are automatically grouped in all other views.

Color Tables
The Color Table is the central data view in Acuity.
Microarrays are organized into columns, with
substances in rows. The table is colored automatically
based on user specified thresholds, and these colors
are propagated throughout Acuity.

Expression Profiles
Clusters and other color based visualizations do n
always demonstrate the co expression of a set of
substances as effectively as a simple line plot.
Examine the expression profiles of groups of
substances easily with the Acuity Graph tab.

3D Scatter Plots
Some analyses, such as Principal Components Analysis,
are best displayed in three dimensions. Acuitys 3
display is fast, smooth and fully interactive, so that
you can easily rotate, zoom and select points of
interest. You can also export rotating animations as
AVI for display on web sites.

Microarray and Substance Summaries
Display dataset, microarray or substance summaries at
any time.

Single Microarray View
You always have access to your original raw data in
Acuity, including GenePix analysis images. View your
raw data at any time, linked to images, and draw
scatter plots of raw data columns. This is an
essential tool for microarray quality control.

Web Links
With Acuitys web links functionality you are only
ever a click away from looking up a substance in any
web based database. Define as many web links as you
like, and look up substances based on any identifier.

Pathways
Link directly to web based pathway sites such as K
SPA or BioCarta and display and interact with them in
the Acuity interface.

Save As PDF
Easily generate publication quality graphics in
Portable Document Format (PDF) from all your Acuity
analysis visualizations. PDF files are compact enough
to send as email attachments but retain layout and
font information, as well as preserving the resolution
and quality of graphs and images. PDF files are text
searchable and seamlessly import into publishing
software packages such as Adobe Photoshop or
Illustrator as vector graphics, so that they can be
resized without loss of quality.

Data Management

A Scaleable Relational Database
Data management is the essence of bioinformatics: it
is pointless having good data if you cannot store it,
access it and share it with colleagues and
collaborators. Central to Acuity is its powerful and
scaleable relational database that can effortlessly
store and retrieve terabytes of data. Acuity users
connect to a central Acuity server from home, from
another lab or from the other side of the world. All
configurations are as simple as double clicking on the
Acuity icon.

Manage Multiple Users
Acuity now has additional tools for managing multiple
users at the enterprise level: set permissions for
users and groups on a folder by folder basis, show and
hide folders from users and groups. Enterprise
microarray informatics has never been easier or more
affordable.

Full Integration with GenePix Pro
GenePix scanners, GenePix Pro and Acuity form a
single, integrated system. Perform acquisition,
first pass analysis and advanced analysis all within
the one environment. Save your data directly from
GenePix Pro to the Acuity database with the GenePix
Pro "Save To Acuity" command. At the enterprise level,
use the Acuity database as a centralized repository
for GenePix data.
Acuity imports normalized GenePix Pro files in their
normalized state, so that they can be unnormalized
renormalized in Acuity using the same normalization
method that was used in GenePix Pro. Acuity recognizes
GenePix Pro flagged features, so that when you select
features on the image in the Acuity Results tab, the
GenePix flags are displayed (see below).

Familiar Interface
The Acuity Project Tree is a high level view of th
Acuity database. Import thousands of microarrays and
organize them with a Windows Explorer like tree.
The Tree behaves like any other Windows tree. You can
cut, copy, paste, drag and drop, rename and delete
microarrays, folders, datasets and quicklists in the
familiar way, as well as assigning access and
permissions to users.

Full Database Queries
Construct datasets with fully general queries across
the entire database with the Query Wizard. The Query
Wizard allows you to build complex database queries by
combining a series of simple, step by step conditions.

MAGE ML Export
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. Acuity gives you the ability to
export data in this format. Acuity has on the fly
compression during export to minimize file sizes.

Track Microarrays
Manage all the properties of your microarrays, from
slide production through scanning and analysis, and
store them in the database, where they can be searched
or used to filter data. Acuity can be an indispensable
part of your laboratory information management system,
as all your microarray experimental data is recorded,
stored, analyzed and displayed in the one place.

Annotation Management
The Acuity database manages annotations automatically.
Once annotations are imported, they are displayed
whenever a substance is displayed. You can annotate
substances using an unlimited number of properties,
and link directly to an unlimited number of
web accessible databases. Acuity includes a tool to
build standard ontologies (biological process,
cellular component, molecular function) automatically
from your annotations.

Universal Text File Import
Acuity imports tab delimited text files from any
source, including Affymetrix CHP files. Import
microarray data files, experiment descriptions,
substance annotations or any other data in
tab delimited files.

Advanced Database Management Tools
As well as tools to manage users, groups and
permissions, Acuity has advanced tools to manage your
database at a very low level. Add and delete fields,
re build table indexes to optimise database
performance, and create new ODBC connections all f
the Acuity client.

Easy To Use

Acuity makes enterprise microarray informatics
accessible to everyone. From installing and
maintaining the database, to managing users and groups
through to filtering and analyzing your data, Axon
put every effort into giving Acuity an intuitive
interface. Common tasks are all accessible through
small wizards on a toolbar, so that novices can get
started on real work quickly.

Optimized for Windows

Microarray datasets are large, and are only going
get larger. Because Acuity has been designed and
optimized for Windows, it effortlessly manages large
datasets, many simultaneous users, and multiple
concurrent analyses and visualizations. There are no
bottlenecks to accessing, searching, filtering or
analyzing your data. If you work on Windows platforms,
it makes sense to use software that has been designed
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Axon Laboratory GenePix Pro 6.0.0.76

Axon Laboratory GenePix Pro 6.0.0.76
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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,
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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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