Tools for 3-D visualization

Researchers from the University of North Carolina at Chapel Hill have reviewed hardware and software for 3-D biological imaging.

The authors contend that hardware limitations for 3-D biological imaging are disappearing, thanks to economic demand driven by computer gamers. High-performance yet inexpensive consumer-grade computer hardware can handle 3-D images, which can place intense demands on computer memory. To represent 3-D images on 2-D computer displays, computer scientists can borrow tricks from artists including shading, perspective and occlusion. A true 3-D experience requires binocular disparity, which can be conveyed using stereoscopic glasses or displays with built-in stereoscopic features. Whereas 2-D controllers such as keyboards and mice remain inadequate for navigating through 3-D images, multidimensional controllers are emerging.

The authors wrote that biologists can use consumer-grade hardware but need discipline-specific software, which does not enjoy economic demand. As a result, commercial software remains relatively costly and “unimaginative.” The authors add that the popular public domain program ImageJ works well in 2-D but can perform only basic 3-D functions conferred by plug-ins. Although ImageJ and other programs like it are open source and therefore can be edited to provide new imaging tools, this requires biologists to know computer code or to collaborate with computer scientists.

To address the need for quality yet inexpensive 3-D visualization software, the authors have designed the free program ImageSurfer. Originally created for neuroscience studies using multichannel confocal light microscopy, the program has since proved useful for diverse biological disciplines and various imaging modalities. It allows each channel to be rendered independently using various methods, and it includes a slice extractor feature that enables users to examine a cross section of the volume at any orientation, in 2-D as well as 3-D. Users can share data through a Web browser, and data can be imported into other popular 3-D imaging programs. (The Journal of Neuroscience, Nov. 21, 2007, pp. 12757-12760.)