by Catherine Shaffer
Image analysis software has become a cornerstone of life sciences research, since nearly every experiment has an imaging component. In addition, graphics files are some of the largest data files, and manipulation of them in real time requires massive computational resources. Advances in computer hardware have allowed image analysis software to keep up with the demand for better, clearer, faster image data in the life sciences.
Carestream Molecular Imaging (formerly Kodak Molecular Imaging Systems) is a pioneer in image analysis, with products on the market for more than twenty years—basically, the dawn of time in the world of molecular biology. Carestream Molecular Imaging offers imaging systems and agents for a wide range of modalities including fluorescence, chemiluminescence, radioisotopic, and x-ray for in vitro and in vivo applications. A major strength of Carestream Molecular Imaging products is the consistency of the software interface across its different platforms and instrument systems. Says Doug Wood, PhD, software development manager for Carestream Molecular Imaging: "You don't have to learn a different software package every time you decide to buy a different instrument from us."
The latest release of Carestream Molecular Imaging Software, version 5.0, scheduled for release in April 2008, will include protocols for mechanical hardware automation—essentially, "automation of the automation." It allows the user to program a set of image capture operations, and chain them together in one long process to streamline the workflow and ensure consistent results. "Once a scientist has figured out what they want to image, they generally want to image it over and over again, day after day, for different gels or blots, or for different animal models," says Wood.
MDS Analytical Technologies is another longtime player in the image analysis market, with its Metamorph® software package dating back, again, to the earliest epoch of molecular biology. Metamorph® is a Windows-based application with a full set of acquisition options so that it can interface with a wide array of third party hardware. Prebuilt application modules guide the user through the image analysis process, to extract data or information from the images. Says Chris Kier, PhD, director of marketing for Metamorph®, "It's compatible with pretty much every single system, and if it isn't, we work very hard and very quickly to get drivers available." MDS also has a development program geared toward improving usability for the novice user, and to improve data handling for increasingly large loads of image data.
BD Biosciences AttoVision™ software is the imaging software used on the BD Pathway™ Bioimager, which enables image acquisition, image analysis, data analysis, and visualization for high content cellular analysis. The software is specifically designed for both end-point cellular assays and kinetic assays, depending on which BD Pathway Bioimager system is chosen. The BD Pathway systems have been selected as the main imaging platform for the multi-site European RNAi consortium INTACT. As a result of this group, a number of very interesting applications around RNAi are underway. One recent publication uses the BD Pathway to explore the dependence of the AKT pathway on bacterial growth within cells.1 Says Jeff Knipe, software product manager of bioimaging systems for BD Biosciences, "With the BD Pathway's confocal imaging capabilities, we also have a number of customers who are using the instrument for imaging model organisms, such as arabidopsis and zebrafish and also in the stem cell area."
"The greatest challenge is the diversity of questions that researchers are investigating, and therefore, the diversity of image analysis methods that are required to fulfill their needs," says Jeff Knipe. "We meet this challenge using two approaches: the first is the flexibility of the software, which enables the appropriate measurements to be made to answer the researcher's questions; and the second is through our worldwide field application scientists who work with our customers at the customer's site to ensure optimal results."
Lumenera Corporation is a developer and manufacturer of megapixel digital cameras and software packages. All Infinity cameras include Infinity Analyze image analysis software as well as Infinity Capture—an intuitive user interface. Infinity Analyze supports applications customized for the clinical market, the industrial market, and the life sciences market. Within life sciences, specialties include low-light fluorescent imaging, where users take consecutive monochrome images and apply pseudo colors—images are taken with different filters, at various spectral wavelengths, and then the images are reassembled with added color and overlaid for viewing and analysis. Alternatively, Infinity Capture is capable of live cell imaging, creating a movie file of your live cell application.
One particularly useful feature of Infinity Analyze is its three-dimensional rendering capability. Brian Graydon, B.Sc., director of business development for Lumenera, explains: "One of the challenges often found, especially with stereomicroscopes, is getting a 3D view. If you're looking at a large object like a bumble bee, the top of the bumble bee will be in focus whereas other portions will be out of focus. The software allows you to do a depth of focus operation—taking images at different focal lengths and combining them into one fully focused image."
Andor Technology's iQ 2.0 is a Windows-based package customized for live cell light microscopy imaging. It was recently overhauled to change its organization, GUI, and functionality, and to include a broad range of control modules for instrumentation, including cameras, microscopes, lasers, spinning disks, filter wheels, and stages. The device controllers are included with the core package.
Live cell imaging has some special challenges, including acquiring and managing the enormous amounts of data produced. Andor iQ uses multi-dimensional data sets with a powerful virtual memory system. "Gigabytes of data stream to disk, and are seamlessly swapped in and out of memory as needed, and transferred to graphics processors for real-time rendering," says Mark Browne, PhD, director of bioimaging for Andor Technology.
In live cell and intravital imaging, with applications from embryology to physiology to virology, control and synchronization of complex equipment are important. A publication by Dr. Thomas Diacovo of Columbia University illustrates the use of Andor iQ with a spinning disk laser confocal microscope system. He was able to visualize and characterize thrombus formation in mouse blood vessels.2
Andor iQ also handles single molecule detection, when paired with a highly sensitive camera such as the Andor iXon 897BV. It allows scientists to study a single fluorescent molecule and use temporal bleaching characteristics to count molecule number and localize a single molecule to nanometer resolution.3
Imaging is one of the more computationally intense tasks that can be done on a computer, and as a result there is rapid growth and innovation in the field of image analysis software. It is human nature to attempt to visualize molecular interactions and data, but without a powerful software solution for image analysis, these pictures can be nearly meaningless. Improvements in software engineering have delivered improved speed, function, and usability, and promise more for the future.
References:
1Kuijl C et al., “Intracellular bacterial growth is controlled by a kinase network around PKB/AKT1,” Nature 450, 725-732, 2007.
2Chen J et al., “Modifying murine von Willebrand factor A1 domain for in vivo assessment of human platelet therapies,” Nature Biotechnology 26: 114-119, 2008.
3Shu D et al., “Counting of six pRNAs of phi29 DNA packaging motor with customized single-molecule dual-view system,” The EMBO Journal 26: 527-537, 2007.
