Visualization and Rendering

A presentation of the reconstruction as a series of slices (figure 6.7a) is the most comprehensive but least accessible display of the 3D information. By the use of visualization and rendering techniques, 3D models are usually built,

Figure 6.7 Methods for visualization of 3D density maps. (a) 10-A cryo-EM reconstruction of the 50S ribosomal subunit from E. coli, represented as a series of slices. (b) Physical model of a 3D reconstruction of the 50S ribosomal subunit from negatively stained specimens, at 20 A resolution (Radermacher et al., 1987a, b); (c) stereo-view of 50S ribosomal subunit, surface-rendered (Gabashvili et al., 2000).

Figure 6.7 Methods for visualization of 3D density maps. (a) 10-A cryo-EM reconstruction of the 50S ribosomal subunit from E. coli, represented as a series of slices. (b) Physical model of a 3D reconstruction of the 50S ribosomal subunit from negatively stained specimens, at 20 A resolution (Radermacher et al., 1987a, b); (c) stereo-view of 50S ribosomal subunit, surface-rendered (Gabashvili et al., 2000).

enabling us to comprehend the structure as an object with depth and perspective, as objects in our physical world.

Only 20 years ago, the visualization of electron microscopic objects reconstructed by the computer still relied largely on physical model building. Computer output was primarily in the form of crude printouts and contour maps, from which slices could be cut. Meanwhile we have witnessed an explosion of graphics capabilities that have reached the personal computer. A juxtaposition of the hand-built model (figure 6.7b) with a current computer-rendered model, visualized in stereo (figure 6.7c), marks the tremendous progress in visualization. This section cannot possibly cover the many options of representation currently available in both commercial and public-domain software, but can only describe the underlying principles briefly. (For an early overview of the different techniques with potential importance in EM, see Leith, 1992.) Many visualization techniques in biomedical imaging, whose progress is featured in annual conferences (e.g., Visualization in Biomedical Computing; see Robb 1994), can obviously be adopted to EM. Visualization methods important in 3DEM have been the subject of special issues of 3DEM journals (see appendix 5).

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