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By Malorye Branca

July 11, 2002 | Genomics is increasingly a story that's told with pictures. These varied images include protein spots that have migrated across a gel, various intensities of gene expression on a chip, the shape of a cell after exposure to a drug, the altered structure of a mutated protein, or samples of tissue from treated and untreated patients. Now, tools to capture, store, search, integrate, and analyze these images are finally available.

One key advance has been the ability to search and compare images directly, particularly 2-D gels for proteomics. Before, researchers would take data from 2-D gels, convert that data into a numerical representation, and compare gels by doing numerical analysis. Recently, advances from companies including Compugen Ltd., Nonlinear Dynamics Ltd., and Scimagix Inc. permit 2-D gel images to be compared directly. This saves a tremendous amount of time and effort. A comparison of two gels that used to require an entire day can now be made in minutes.

Scimagix' ProteinMine software enables researchers to search for a particular set, or signature, of proteins across an entire database of images. If, for example, the signature indicates a known toxic response, that combination of proteins would signal that a prospective drug will cause side effects. "This is based on a new set of algorithms," says Suzanne Mattingly, vice president of marketing at Scimagix. "If you can database the images and actively search them, you will find things that have been there for some time [but that] you did not even know were there."

The company's Scientific Image Management System (SIMS) allows researchers to store a broad range of images with annotation. This Web-accessible, Oracle-based system holds images as diverse as 2-D gels, Western blots, micrographs, and X-rays. Using SIMS, researchers can quickly access a range of related images, do searches based on specific fields, and automate annotation.

Image analysis is also beginning to be applied to new types of images. One young company, Q3DM Inc., provides instruments and software for capturing, storing, and searching images from cellular assays. Such assays are increasingly used to explore gene function for target validation.

Q3DM has developed proprietary high-speed, submicron autofocus and fluorescence light-source stabilization technologies, which automate the photomicroscopy. The company also has software that segments the cellular images. "This allows us to take direct measurements of activity at the subcellular level, including the quantities of proteins moving between compartments within the cell," says Ed Hunter, chief technology officer at Q3DM.

The software allows the user to calibrate the instruments and then define and run screens on all common assay formats. Also included is a set of visualization and data analysis tools to explore the data after the screen is completed. Images can be stored and searched based on a particular feature.

—Malorye Branca

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