Xmipp: Introduction to Visualization

The visualization system in Xmipp is mainly done through external programs. As the basic image type is Spider (not a standard) normal visualization programs cannot open our images. However, you can always convert the Spider format to any other format either using Xv, either using the BioImage tools. Xv is a general purpose shareware image viewer, we have modified slightly its code in such a way that now it recognizes the Spider format. Spider itself has got its own image viewer named Web. There are interesting points about the coordinate systems these two programs use.

Coordinate system in Xv and Web
Euler coordinate system in Web

Coordinate system in Xv and Web

The coordinate system (x,y,z) in both visualization programs are the same as in Xmipp.

If the file being visualized is a volume then first slices (slices with smaller indexes, the most negative) are at the beginning of the compound image (top left corner, see the following scheme for a 9x9x9 volume). In Xv all the slices might not be represented but only a subset of them if the volume is too large (for example 1 out of every 2, and then the slices represented would be z=0,2,4,6,8, ...).

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Euler coordinate system in Web

You must be careful with the Surface representation in Web because it is not coherent with the convention taken in Spider, after which a (rot=0,tilt=0,psi=0) is a top view, while in WEB surface representation is a side one. I don't feel like to find out which one it is exactly.

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