ImageMaster 2D Platinum v6.0 - GeneBio

Part of GE Healthcare
Data file 28-4016-97 AA ImageMaster 2D Platinum
ImageMaster 2D Platinum v6.0
ImageMaster 2D Platinum v6.0 offers automated and
accurate analysis of 2-D electrophoresis gels, shortening
the path from data acquisition to protein information. It can
perform analyses on all 2-D gels, both 2-D Fluorescence
Difference Gel Electrophoresis (2D-DIGE) and non-DIGE. Its
flexible and intuitive nature allows you to perform any gel
study according to your specific needs and preferences.
ImageMaster 2D Platinum integrates with other GE Healthcare
2-D electrophoresis products, creating the most comprehensive
analysis package available for 2-D gels.
ImageMaster 2D Platinum was developed by the Swiss
Institute of Bioinformatics in collaboration with GeneBio
and GE Healthcare. It is powered by the innovative and
widely used Melanie gel analysis software.
ImageMaster 2D Platinum v6.0 offers the following benefits:
• Full support of DIGE technology—through the use of
the recognized DeCyder 2-D Differential Analysis
Software (DeCyder 2-D) co-detection algorithm, support
of the internal standard approach, and a set of specific
analysis tools.
• The workspace—where all gel, matching, and analysis
data, as well as results are centralized—enables you to
manage and analyze all your 2-D data (DIGE and non-
DIGE) following exactly the same workflow.
• Extensive display features and a variety of interlinked
images, tables, and graphs—an unlimited number of
gels can be displayed and analyzed.
• Dockable windows—allows an easy redesign of the
application layout according to personal preferences.
• Outstanding spot detection and filtering—minimizing
the influence of gel backgrounds and time spent
manually editing.
• Hierarchical population matching—gel populations can
be directly compared, without the need of a unique
arbitrary reference gel.
• Effortless extraction of protein markers—by using the
most sophisticated and reliable analysis techniques to
quantitate protein expression variations across gels or
between different gel populations.
Fig 1. The new ImageMaster 2D Platinum v6.0 user interface with dockable
windows provides total flexibility for smooth 2-D gel image analysis.
Experiment design and support
Use the unique workspace concept to dynamically design
and manage your experiment:
• All gel, matching, analysis and other experiment-related
data is centralized in the workspace project that guides
you through the typical 2-D image analysis workflow
(Fig 2). At any moment, you can control and verify the
status of your gel analysis.
• A unique analysis pathway is used for all your gel
studies, both for conventional 2-D electrophoresis and
2-D DIGE gels.
• Each user can customize his or her personal work
environment.
• The workspace interface provides direct and unlimited
access to the many data types.

Interface
The software provides a powerful and highly flexible work
environment:
• Analyze a virtually unlimited number of gels. Whether
you work with 10, 50, or 500 images, you can display,
manipulate, and process your gel data with unmatched
flexibility.
• The intelligent multiworksheet display guarantees a
structured and consistent presentation of your gels,
where related images always remain grouped and you
can instantly view the desired gel subsets (Fig 3).
• The application layout and gel images can be freely
reorganized to optimize space and visibility in accordance
with personal preferences.
Image Visualization
Extensive display features allow you to interact with the
results and target the analyses. Comprehensive feedback
through multiple images, tables, and graphs ensures that
the user is fully informed of all analytical procedures, information
that is critical to objective scientific investigation.
Customize the display for your needs with:
• Contrast mapping and pseudo colors that can be
adjusted instantly.
• Color palettes, spot profile, or 3-D view to inspect signal
intensity (Fig 4).
• Various zooming modes and easy moving of gels.
• Gel overview to navigate extensively through gels.
• Full control over how and what information is
displayed (e.g. spot shape and color, visibility of
annotations).
Benefit from the comprehensive and intuitive visual
comparison tools:
• Tile mode instantly shows how the proteins are
expressed through a series of gels.
• Stack mode gives you the possibility to track protein
variations by rapidly flipping between the gels.
• Easily check your matching results by displaying
pair vectors or superimposing spots with the
overlapped mode.
• Automatic warping aligns gel images, eliminating
differences in spot position. Aligned images are then
overlaid to produce dual channel images with clearly
visible differences in protein expression.
• Synchronized and simultaneous 3-D views of multiple
gels can be displayed.
Take advantage of the dynamic display:
• Easily navigate any data, simply by clicking reports
and gels.
• Two-dimensional calibration grids use pI and MW
values of known standards to automatically calculate
values for all other spots and propagate these
through all matched gels.
• Raw image data is automatically loaded and
unloaded when necessary to free memory and speed
up the display-refreshing process.
Workspace
project folders
Detecting
Matching
Analyzing
Data file 28-4016-97 AA 2
Gels
MatchSets
Classes
Reports
Documents
Operation
Exporting
Fig 2. Image analysis from start to finish in the workspace.

Image Processing
The cornerstones of a successful 2-D gel analysis are efficient
spot detection, accurate spot quantitation and robust
gel matching. Our software offers outstanding algorithms
to successfully perform these steps:
• Automatic, sensitive and robust spot detection requiring
minimum user intervention.
• The ImageMaster 2D Platinum algorithm for conventional
2-D gels—provides only a few easily adjustable
spot detection parameters, for distinguishing real spots
from noise.
• The powerful co-detection algorithm from DeCyder 2-D
for DIGE images—simultaneously process one, two, or
three images derived from a single gel.
• Optional spot editing including merging, splitting, and
growing of spots.
• Highly accurate spot quantitation.
• Powerful parameter-free matching algorithm using spot
coordinates, spot abundance, and surrounding.
• Fast landmarking using special annotations for easy
definition of tie points in multiple gel studies.
• No more matching against a unique arbitrary reference
gel. Gel populations, defined as match sets represented
by a master image, can be directly compared. Matches
are automatically propagated at each level of the
unrestrained hierarchical match set structure.
• Merging several gels from the same sample into a
composite gel with fine control over the included proteins.
Calibration and normalization
The reproducibility of the 2-D separation process can be
affected by a number of factors, including differences in
sample preparation and loading, staining and image
acquisition. To accurately compare the abundance of a
spot across gels, it is essential to compensate for these
variations using calibration or normalization methods:
• Removal of image scanning variations, by
intensity calibration.
• Removal of variations due to staining and sample
loading, by relative spot quantitation.
• Compensation for varying staining absorption across
proteins, by normalizing protein expression change.
• Compensation for gel distortions attributable to protein
migration variations, by warping gels.
• Removal of interference and outliers, by using
robust statistics.
Fig 3. Two gel subsets side by side for visual comparison.
Fig 4. 3-D view for several gel regions.
Fig 5. Sophisticated analysis techniques identify and quantitate
protein expression variations.
Data file 28-4016-97 AA 3

Statistical analysis
Extract protein markers effortlessly by using the most
sophisticated and reliable analysis techniques to quantitate
protein expression variations across gels or between different
gel populations (Fig 5):
• Scatter plots, to analyze gel similarities or experimental
variations.
• Descriptive statistics of central tendency and dispersion
calculated and displayed in various reports and histograms.
• Histograms to visualize expression profiles.
• Overlapping measures that summarize each gel class
by an interval and compute the overlap between these
intervals.
• Statistical tests (two-sample Student t-test, Mann-
Whitney/Wilcoxon, Kolmogorov-Smirnov).
• Factor analysis, enabling the identification of similar
gels, and of spots that are characteristic for a particular
population of gels.
• Automatic classification by artificial intelligence
techniques.
• Comparative tables and graphical reports to browse
through, for easy pinpointing of relevant proteins in gels.
Automation
• Use customizable scripts to automate repetitive tasks—
by running and saving a typical analysis on a set of
gels, and subsequently applying it to another set,
possibly after some adjustments.
• Handle large numbers of 2-D gels simultaneously.
Integration
The proteomics scientist works with data from many
sources. Our software covers this need by providing
comprehensive and unlimited annotation capabilities to
link gel objects to external query engines or data sources
of any format:
• Default or user definable annotation categories can
contain any type of information, such as pI/MW, landmark,
comments, and database accession number
(Fig 6).
• Each annotation can be linked with Internet query
engines (databases such as UniProt, SWISS-2DPAGE,
and PDB) or data sources of any format (e.g. mass
spectrometry profiles, text, HTML, spreadsheet, and
multimedia).
• A simple click on a linked annotation displays the
associated data.
Numerous other features enable seamless integration
of our software into your laboratory workflow:
• Direct analysis of image files acquired with GE
Healthcare’s Ettan DIGE Imager, a scanning CCD
camera designed especially for creating high quality
images of 2-D DIGE gels.
• Integration with GE Healthcare's ImageScanner II
imager via the LabScan software (developed by the
ImageMaster software team) .
• Direct image acquisition from Twain-compatible
scanners.
• Support of all 2-D gel image formats, including GEL,
IMG, TIFF, and PNG.
• Open architecture based on the XML standard for
import, export, and reports.
• Fully automated integration with spot-picking robots.
• Clipboard support to copy gel images, graphics, and
data tables to other programs (e.g. tables to spreadsheet
software such as Microsoft Excel, or graphics to
programs like Microsoft Word or Adobe Photoshop).
Fig 6. Annotations contain labels from default or user-definable categories.
Data file 28-4016-97 AA 4

Reporting
The software’s versatile search engine allows you to formulate
complex queries without difficulty. These not only
allow you to select and filter data to compose data subsets
for further analysis or reporting, but will also help you to
answer biological questions based on:
• Sophisticated textual requests.
• Qualitative and quantitative information.
• Distribution of the values for a specific quantitation
measure.
• Protein expression changes, for example by ratio or
similarity.
You can visualize and analyze your data using more than
20 graphical and tabular reports, which together contain
over 50 data types.
• All reports can be saved for further use and easily
retrieved from the workspace.
• Reports are customizable and editable (Fig 7).
• Easy and rapid navigation between gels and associated
reports and graphics, including 3D views.
• Extended support allows you to import data into publications:
WYSIWYP (What You See Is What You Publish).
• Graphics, tables, and gel images can be printed directly
as they appear or can be freely copied to any other
programs.
Quality and data integrity
It is important to protect all your gel data, not only by
ensuring data integrity and consistency, but also by allowing
you to reverse undesired manipulations. Our application
therefore offers:
• Unique identifiers for each gel, report, and spot to
assure data consistency, reliable identification across
networks, and database integration.
• Sophisticated multiple undo/redo function.
• Experiment backup and restore function.
Quality control is an important aspect of the analysis:
• High quality standards are reached using margins
of error and validation tools that help to distinguish
between real protein expression changes and differences
induced by inconsistencies in the detection or
matching processes.
• The history function keeps track of all operations carried
out during a work session, for control and quality
assurance.
Fig 7. Reports are customizable and editable.
Ordering information
ImageMaster 2D Platinum v6.0 11-0034-25
DIGE Enabled, single-seat license
ImageMaster 2D Platinum v6.0 11-0034-29
DIGE Enabled, single-seat
network license
ImageMaster 2D Platinum v6.0 11-0034-30
DIGE Enabled, additional five-seat
network license
ImageMaster 2D Platinum v6.0, 11-0034-27
single-seat license
ImageMaster 2D Platinum v6.0, 11-0034-31
single-seat network license
ImageMaster 2D Platinum v6.0, 11-0034-32
additional five-seat network license
Other packages are available. Note: An e-license is required for access
to ImageMaster 2D Platinum v6.0.
Related products
ImageScanner II, 100–240 V 18-1170-84
Ettan DIGE Imager 63-0056-42
Data file 28-4016-97 AA 5

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General Electric Company reserves the right, subject to any
regulatory approval if required, to make changes in specifications
and features shown herein, or discontinue the product
described at any time without notice or obligation. Contact
your GE Representative for the most current information.
© 2005 General Electric Company—All rights reserved. GE and
GE Monogram are trademarks of General Electric Company.
Amersham Biosciences, DeCyder, Ettan, ImageMaster,
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Application note 28-4016-97 AA 6