This is the detailed documentation for STIR: Software for Tomographic Image Reconstruction. Additional documentation (sometimes overlapping) is given in the User's Guide, Overview documents etc are available on the STIR website (http://stir.sourceforge.net). You should probably read those first before looking into the documentation on this page.
The current pages are automatically generated by doxygen from text comments in the files.
As the amount of software is rather large, some guidance is needed. The best place to start is probably the Modules section. This attempts to group files in a sensible way. In particular, a User might only be interested in the Executables module. (Note however that the doxygen documentation for some executables is not very informative. In any case, just executing the utility should give a usage message).
Another way to navigate through this is the Class Hierarchy page, or indeed any of the other alphabetical lists. However, this is not structured at all, and even contains some classes which we'd rather not have in there. So, in the beginning, this might be somewhat confusing.
All documentation depends on the person who writes it. In the end, only the code is what matters...