Computer Processing for 2-D and 3-D Image Reconstruction

In this chapter a brief introduction will be given to the available approaches and software for the digital image processing of electron micrographs containing negatively stained and unstained cryoimages and the subsequent 2-D and 3-D reconstruction of averaged images. It must be emphasized that the electron microscopist now needs to become a competent handler of one or more software packages, if not actually a programmer. In general, the available software is not user friendly, often having been produced by skilled programmers for specific purposes over a period of many years; there are a few exceptions (even PC-based systems running under Windows) and these are likely to increase in number as more people become involved in image processing from electron micrographs and on-line electron images. The simplest approach initially is to define which area of image processing one wishes to pursue (i.e. single particle, crystallographic or helical analysis) and then visit a laboratory where similar work is already in progress. Assistance may be given by direct collaboration or tuition may be given in the use of the available software; the latter could ultimately mean a commitment to many months of work and large expenditure, such as a PC controlled high resolution scanning densitometer or scanning CCD camera system, a high resolution B/W printer or a colour videoprinter. It is apparent that the whole field is currently in the process of slowly moving from the few specialist laboratories with extensive computer facilities, back-up and knowledge, to a situation of more general availability, a trend that will surely continue. Most laboratories have retained their steadily developing software within the public domain, whereas a few others have moved into the commercial area for the further establishment and marketing of their image processing software (see Table 10.1 and Appendix B). Table 10.1 Some software available for image processing and 3-D reconstruction

A. Commercial a crisp (Trimerge, Triview) and eld	Particularly suitable for analysis of 2-D crystals and electron diffraction patterns.
imagic-5	A diverse package, particularly suitable for single particle analysis.
semper	A diverse package, particularly suitable for 2-D crystal analysis.
B. Public domain/academic b MRC image processing programs	Suitable for diverse applications.
spider and web	Particularly suitable for single particle analysis.
The PIC System-III	Suitable for viral structure.
suprim	Suitable for single particle analysis.
Extensible and Object-orientated System (eos)	Particularly suitable for macromolecules.
The Integrated Crystallographic Environment (ice)	Particularly suitable for crystallographic analysis.
The Brandeis Helical Package	Helical analysis.
Image Visualization Environment (ive)	Diverse applications.
phoelix	Helical image processing.
xmipp	Particularly suitable for single particle image processing.
ptool	Useful for spot-scan images.
avs	For 3-D visualization of molecules.
imod	For visualization of 3-D image data.
sigma	Software for imagery and graphics for molecular architecture.

^a

Company addresses given in Appendix B.

^b

Taken from J. Struct. Biol. 116, No. 1. (1996), Special Issue: Advances in Computational Image Processing for Microscopy. For up-to-date information on available software access https://rcr-www.med.nyu.edu/3dem/homepage.html.