Jeffrey Perkel has been a scientific writer and editor since 2000. He holds a PhD in Cell and Molecular Biology from the University of Pennsylvania, and did postdoctoral work at the University of Pennsylvania and at Harvard Medical School.
In the world of molecular biology, weeks of benchwork can come to a head in a single gel. Did you get your clones? Do your mice exhibit the expected mutations? Is your protein expressing well?
The answers usually lie within the bands and lanes of DNA or protein gels. In the “old days,” those gels were examined on light boxes and captured on film. The researcher would then scrutinize the images—manually, say with a ruler—to determine whether or not a given band was of the expected size.
Today, users need no longer hunch over their UV light boxes. Just pop the gel into a gel-documentation system and go. These devices use computer software to largely automate the process of gel photography, whether those be ethidium bromide-stained DNA gels, Coomassie-stained protein gels or even chemiluminescent or fluorescent Western blots. And once the image is captured, additional tools help users decipher the data.
Here we review some of the key features to look for in your next gel-analysis software product.
Functionality
Gel-documentation software tools perform a relatively narrow set of functions. The most popular, though, according to Paul Ellwood, managing director at Syngene, are automated lane and band identification. “People want automatic lane and band finding,” Ellwood says. “What you don’t want to have to do is highlight and find each band manually; it takes too much time.”
Image-analysis tools can also generally determine band molecular weight and intensity, and, in the case of Western blots, perform quantification and normalization tasks, too. (LI-COR Biosciences’ Image Studio Lite is a free version of its software specifically for analysis of Western blotting data captured on its own or other vendors’ imaging platforms, as well as film.) Some tools also perform image acquisition itself, whereas others separate capture and analysis in separate applications.
2D protein gel analysis is typically a more specialized application in which users often compare two gels (or two samples on one gel labeled with two fluorescent dyes), looking for differences in spot population or abundance Bio-Rad Laboratories allows users to automate spot detection and matching in its PDQuest 2-D Analysis Software. Syngene’s 2D analysis tool is called Dymension. (Syngene’s image-acquisition and 1D gel-analysis tools are included with the company’s gel-documentation systems gratis, but each Dymension license costs £1000, or about $1,640, Ellwood says.)
Syngene offers another package, called GeneDirectory, for storing and searching gel patterns for genetics and forensics applications. GeneDirectory, Ellwood explains, “is simply a database which remembers or stores all the various tracks the system has seen before. It is a band-matching database that tells you if you’ve seen the track before, and where.”
Bundling
Although free and third-party applications do exist, just about every major vendor of gel-documentation systems also supplies proprietary software for image capture and analysis, typically tailored to the hardware. As a result, says Maggie Pochyla, global product manager for electrophoresis at Bio-Rad Laboratories, users seldom need to look elsewhere for solutions.
Users of Bio-Rad’s gel- and chemi-doc systems, for instance, receive the company’s Image Lab™ software, for use on an unlimited number of computers. “All the essential functions plus more can be done in Image Lab, so there’s no need to use additional software,” she says.
Syngene supplies two applications with its imagers: GeneSys controls the image-acquisition process, and GeneTools facilitates data analysis. Similarly, Thermo Fisher Scientific bundles its myImageAnalysis software with its myECL Imager, as does LI-COR with its Image Studio and UVP with VisionWorks®LS Image Acquisition and Analysis Software.
Just the same, some users still opt for third-party options, says Suk Hong, a senior scientist at Thermo Fisher Scientific, for instance, if the lab is already using another company’s image-analysis software. ImageJ—a free, open-source application—and TotalLab’s commercial TotalLab Quant are two such options.
Cost
Another reason to use third-party or free software is price. Data acquisition occurs at the gel-documentation station, but analysis is often performed elsewhere, if for no other reason than to free up the imager for the next user.
Some companies, such as Syngene and Bio-Rad, provide unlimited licenses or software copies so users can install their image-analysis applications on as many workstations as they need. Others, though, have more restrictive policies, and costs can mount in large labs.
Thermo Fisher Scientific, for instance, provides five licenses to myImageAnalysis with the purchase of a myECL Imager, says Hong. Additional licenses cost $1,599 for two seats. LI-COR imagers include a single license to the company’s Image Studio software, says senior product marketing manager Jeff Harford; a five-user license will run around $3,500, and a 25-user license about $6,500, he says.
Still, there often are advantages to sticking with your imaging vendor’s software, says Pochyla. These include free software updates, technical support, training and strong integration with the hardware.
File format
Some image-acquisition and data-analysis tools use industry-standard file formats, such as TIFF, BMP, PNG, GIF and JPEG, meaning users can open images in the compatible program of their choice; others use closed or proprietary formats, which can limit your ability to manipulate images in another software tool if, for instance, your original analysis tool becomes outmoded.
UVP’s VisionWorksLS software supports several standard standard formats, including TIFF and JPEG, according to marketing product manager Mike Capps. So does Thermo’s myImageAnalysis. But Bio-Rad’s Image Lab natively saves images in a proprietary format called .SCN. And LI-COR uses a proprietary version of the TIFF format to handle the company’s large dynamic range, Harford says. In both cases, though, images can be exported in standard formats for publication, presentations, and the like.
Regulatory concerns
Gel-analysis software can generally print images, store them electronically in various formats and prepare reports for inclusion in electronic lab notebooks. But that doesn’t mean they actually support the U.S. Food and Drug Administration’s requirements for electronic record keeping and signatures, called 21 CFR Part 11.
UVP’s VisionWorksLS software supports laboratory compliance, says Capps, performing such tasks as logging users and recording all changes to an image in the file metadata in accordance with regulatory requirements. Bio-Rad offers a 21 CFR 11-compliant version of Image Lab. Thermo’s myImageAnalysis and LI-COR’s Image Studio, however, do not currently adhere to Part-11 specifications.
Ease of use
Image-acquisition and analysis software used to be relatively painful to use, says Pochyla, with considerable manual manipulation required simply to capture a good image and do analysis. Users often needed to tweak filter choice, time of exposure, light source and aperture, and during analysis, to manually manipulate lane and band placement, adjust background, and more. “We’ve removed a lot of that,” she says.
Today, users insist on ease of use, and image-analysis-tool developers are paying attention, often implementing one-click operations and more intuitive workflows. “With one click, you can take a picture and do the analysis, and that resonates with a lot of our customers,” Pochyla says.
LI-COR’s Image Studio bundles functions in a series of application “ribbons” (akin to the function grouping seen in the Microsoft Office suite) “to take the functionality to the next level,” Harford says. And UVP recently added user templates, enabling users to store and reuse parameters in later experiments.
Given the maturity and depth of the field, it’s likely you can’t make a bad decision; most users will be satisfied with just about any of these tools. But try to take a test drive, just in case. It can’t hurt to know what you’re getting before you commit.