Imaging Analysis Software For Cells

Cellomics accomplishes this in at least 17 different BioApplications, which are individual image analysis software modules that convert fluorescent images of cells into numeric data that reflect the functional properties of the cells. For example, Cellomics offers BioApplications that can locate and detect the activation of proteins, as well as measure aspects of the cell cycle, changes in cell morphology, and cell differentiation. You can measure properties at the level of individual cells, as well as the whole-well level for multi-well plates. Says Tencza, “each bioapplication reports a unique set of features designed to accommodate different user needs, from therapeutic-area focused applications for screening, to highly flexible algorithms for research, systems biology studies, and specialized assay development.”

According to Tencza, Cellomics’ BioApplications have several advantages—and primary among them is biological validation. “What this means is that they are designed and tested to provide a robust cell biological assay,” explains Tencza. “The software is designed and proven to accommodate the natural variability in cells and still provide excellent screening results.” Like several other companies’ software offerings (see below), BioApplications allow the user to create an automated protocol for routine analysis steps without knowledge of computer programming. Another important feature of the software is the automated transfer of images and BioApplication-derived data from the instrument to a centralized database for secure storage. “The database provides easy access to images and derived data and maintains links between the two to make validation and results viewing easy,” says Tencza.

You can run MCID Elite on a host of equipment by other manufacturers. MCID Elite supports both monochrome (both the North American RS170 and the European CCIR video standards) and digital video cameras, including those made by Dage, Sony, Roper Scientific, Diagnostic Instruments, DVC, Hamamatsu, Cooke, Apogee, and Optronics. For color video-based cameras, the camera must have separate outputs for the red, green, and blue signals. For cameras manufactured by Sony and Dage, the MCID Elite software can also control camera integration. MCID Elite can also be used with any kind of microscope, and can support some types of motorized stages, shutters, and filter wheels.

MetaMorph controls image capture from digital CCD cameras, in addition to image processing and analysis, allowing operations such as time lapse, multi-dimensional acquisition, and 3-dimensional reconstruction, as well as analyzing morphometry, colocalization, and brightness. MetaMorph can control devices such as microscopes, filter wheels, shutters, cooled CCD cameras, video cameras, monochromators, focus motors, Piezo electric focus devices, motorized stages, digital and serial input/outputs, and robotic devices.

MetaFluor is designed to make dual-wavelength intracellular ion measurements, providing simultaneous display of raw data, ratio image, graphs of intensities, ratios and ion concentrations, and a non-ratiometric image such as a bright field or phase-contrast image. Two different ratiometric indicators can be imaged and measured simultaneously. MetaFluor can be used for fluorescent resonance energy transfer (FRET), calcium imaging, and pH measurements. The software allows you to set up and then automate your own customized protocol. Set-up is made easier by the use of toolbars, menus, wizards, and dialog boxes that walk you through the image processing steps without requiring specialized programming knowledge. Indeed, in its design of the MetaSeries line, Molecular Devices strives to offer a user interface that is “intuitive and easy to learn, especially in a multi-use environment,” says Sysko. “We want to balance speed of analysis with accuracy and reproducibility of results.”

Like Molecular Devices, Scanalytics focuses on accessibility and ease of use with its IPLab, a popular choice for image analysis software. Scanalytics also prides itself on allowing scientists to customize their analysis protocols easily, without needing to wrestle with programming languages. The many analysis functions of IPLab “can be ‘scripted’ into a push-button macro using a simple menu-based script editor interface,” says Len Hook, a senior scientist at Scanalytics. Among the primary capabilities of IPLab are multi-dimensional image acquisition, 3-dimensional deconvolution, image segmentation, image enhancement/processing, and 3-dimensional image sequence visualization.

Unlike most companies, Scanalytics offers its software for both Macintosh and Windows operating systems, although the specialized software modules are not available for both platforms—Ratio Plus and Multiprobe are offered only for Windows. Ratio Plus is designed to work with images acquired at different wavelengths over time. Hook explains that this software module “facilitates the measurement of ion concentration using ratiometric dyes such as Fura and Indo. It is also used in Cameleon and FRET experiments that utilize two- and three-filter methods. Ratiometric data are plotted on screen in real time, and the captured image sequences can be exported as movies.” The built-in Ratio Plot Editor lets researchers select individual cells for analysis. The Multiprobe software module is designed to analyze multiple wavelength image data, such as in FISH, GFP, and immunocytochemistry experiments. It allows you to merge fluorescence and brightfield images, adjust color hue, normalize contrast an

CytoShop works in conjunction with Beckman Coulter’s Cell Lab IC 100 image cytometer, so unfortunately another instrument must be bought. However, the payoff is that this combination of tools yields high-quality data. Laris emphasizes that “the cell-by-cell framework is fundamentally important, as is the acquisition of high quality images with instrumentation like the IC 100. Few software products on the market today do either of these tasks well, much less both of them. CytoShop on the IC 100 delivers both of these functions in one system.” The CytoShop software includes a variety of standard protocols for apoptosis, small inhibitory RNA experiments, G-protein-coupled receptor work, function pathway elucidation, transient transfections, z-stacking, and time-delayed experiments.