GenePix Pro is the complete standalone image analysis software for microarrays, tissue arrays and cell arrays
Why Upgrade To GenePix Pro 6?
In developing GenePix® Pro 6 we have concentrated on adding and improving automation functionality:
New spot-finding algorithms mean better reliability and full spot finding automation.
Automatic balancing of PMT gain for all GenePix scanners.
Batch Analysis tab for browsing and analyzing batches of images.
Morphological background subtraction.
Enhanced support for opening and analyzing third-party images.
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 inside 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 review 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 drawn 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'), highlighted 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 with 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 URLs to choose from, or store a preferred URL 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 be 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 their 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 of 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.
Click on thumbnails below
GenePix Pro 6 finds and analyzes square and irregular features, displaying feature-indicators directly on the image. A circularity metric calculated and reported in the GenePix Results (GPR) file is then a powerful quality control measure.
Select features for flagging with lasso selection.
Display local background pixels on the image.
Generate customized color maps with GenePix Pro's Color Map Editor.
Measure intensities of subregions of the image using a number of different measuring tools: lines, polylines and arbitrary regions. In this example, we measure the intensity along a straight line through a dilution series of features.
Plot the pixel intensity and background values for each feature to assess the quality of a particular feature find. In this example, the feature and background pixels are very well separated, which provides confidence that the segmentation is accurate.
The Feature Viewer gives instant access to a large amount of individual feature data, without requiring complete analysis of the entire image.
The Navigation window on the Image tab allows you to orient yourself on large images and zoom in to regions of interest.
Pixel intensity histogram at four scanning wavelengths. Use it during scanning to balance the signal in each channel.
The Flag Features dialog box in which you can construct fully general Boolean quality control queries.
Use the Scatter Plot to plot any two Results columns against each other. In this case, Log ratio is plotted against Sum of Medians (on a log scale) to assess the intensity-dependence of ratio data (much like an M vs A plot).
Draw analysis histograms of any Results column. This example shows the log ratio column is symmetrical about zero, which means that the data does not need normalizing.
Export as MAGE-ML
Export microarrays in MAGE-ML format for upload to web-based databases such as
ArrayExpress. A growing number of journals,
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 files 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 scanning.
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 tab 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 data. GenePix Pro supports standard scripting languages such as VBScript and JavaScript as well as any other scripting languages supported by Internet 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.
GenePix Pro 6 Feature List
Imaging
Image sets saved in single-image or multi-image TIFF format.
Export color images in 24-bit JPEG format.
Four-channel image analysis with user-configurable color palettes.
Third-party image registration, manual or automatic.
Image rotation.
Automated block and feature alignment for circular, square or irregular features.
Automated software barcode reading directly from any scanned image.
Linear and area measurement tools.
Lasso selection of feature-indicators on the image.
Analysis
Batch Analysis automates spot finding and data extraction.
Multiple methods of background subtraction: local, global, negative controls, morphological opening and closing.
Feature Viewer and Feature Pixel Plot for detailed feature assessment.
Multiple methods of ratio calculation.
Manual and automatic feature flagging for quality control and normalization with user-defined criteria.
Normalization of images and numerical data.
Visualizations
Display background pixels on the image.
Automatically generate Histogram or Scatter Plot of any analysis measurements, including regression and standard deviation lines.
Images, graphs, and results can be printed and/or copied to the Windows clipboard for easy transfer to other applications.
Generate reports of any visualization in PDF format.
Automation
Control all GenePix scanner models.
Automatically set the PMT gain when scanning.
Integrated Array List Generator easily maps feature information (e.g., name) onto array image and into Results file.
One-touch calibration for the GenePix 4000B and 4100A scanners.
Saved template files for hardware, acquisition, analysis and display settings.
Full integration with web-based genomics databases.
Scripting of all acquisition and analysis functions.
Link directly to Acuity microarray informatics software.
Lab Book records all hardware and software operations.
File Formats
Full support for 16-bit grayscale TIFF images.
Results (GPR) file containing substance names, feature locations and all extracted data saved in ASCII file format for easy import into advanced analysis packages.
Export Results in MAGE-ML format.
Array List (GAL) files allow user-defined columns.
Computer Requirements
GenePix is fully functional with the Minimum computer requirements. However, satisfactory performance
depends on the size of the files you will generate. The RAM and hard disk configuration is the most
critical. If you plan to scan areas smaller than a full slide, or to scan regularly at 10 µm
resolution, the Minimum requirements will provide satisfactory performance of all GenePix Pro features.
However, if you plan to scan full slides at 5 µm, or if you plan to run other applications
simultaneously, we strongly suggest the Recommended configuration. Computer workstations purchased
from Molecular Devices will meet or exceed the Recommended configuration.
*NOTE: GenePix Pro 6 will not operate on 64-bit processors.
Minimum Computer
IBM-compatible computer with an Intel Pentium “Dual Core” processor 1.6 GHz or faster.
Windows XP or Vista 32-bit edition operating system.
1 GB RAM or more.
Hard disk with 10 GB free
Integrated Video Card.
Optical drive with CD read and write capabilities (CD-RW).
1280 x 1024 display system with 65K colors
Internet Explorer 5.0 or higher
At least 1 free USB port or network connection (for the USB hardware protection key)*
*If your computer has a network connection, but: (1) does not have a USB port, or (2) is running
Windows NT, you must specify a network hardware protection key when ordering GenePix Pro.
Recommended Computer
IBM-compatible computer with an Intel “Core 2” processor 2.0 GHz or faster.
Windows XP or Vista 32-bit edition operating system.
2 GB RAM or more.
Dedicated Video Card 128MB or greater.
Hard disk with 30 GB free
Optical drive with DVD and CD read and write capabilities (DVD+/-RW).
1280 x 1024 display
Internet Explorer 5.0 or higher
At least 1 free USB port or network connection (for the USB hardware protection key)*
Internet access (for faster version updates and troubleshooting)
GenePix Pro on a Mac
GenePix Pro is fully compatible with Virtual PC 6 running on Macintosh OS X 10.2.
We have tested the following minimum configuration:
Mac OS 10.2
1 GHz G4 iMac
256 MB RAM
Virtual PC 6.0 running Windows 2000 with 160 MB dedicated to it
A GenePix Pro network security key installed on a networked Windows computer
Note that we have not tested GenePix Pro on a Macintosh being used to control a GenePix scanner, and we do not recommend this. Use GenePix Pro on a Macintosh only for microarray image analysis.
GenePix Pro Demo Software
Use the Literature link in the right menu to download a demonstration copy of GenePix Pro software.
Price includes unlimited Ph.D.-level technical support
If your computer has a network connection, but: (1) does not have a USB port, or (2) is running
Windows NT, you must specify a network hardware protection key when ordering GenePix Pro.
