XMIPP introductory demo

1 General introduction1.1 Welcome to XMIPP!XMIPP was introduced to the scientific society more than a decade ago (Marabini et al., 1996).Originally it was written in C, but in 2004 it was completely re-implemented in a hierarchicalstructure of C++ libraries (Sorzano et al., 2004). In its current state, XMIPP contains more than100 stand-alone programs.Let’s have a first look at the XMIPP package. Open a Unix-like shell, and type:xmipp_ [+TAB]to see a list of all available XMIPP commands. You will see there are more than a hundreddifferent programs. Any XMIPP program may be called from the command line, and if you donot give any options, a limited description of its parameters is shown. Just try typing the nameof any of them, for example:xmipp_reconstruct_wbpgives the following output to the screen:2104:Argument -i not found or invalid argumentFile: libraries/data/args.cpp line: 508Usage: WBP -i : selection file with input images[ -o : filename for output volume[ -radius ] : Reconstruction radius[ -sym ] : Enforce symmetryetc etc.This is the program to perform a 3D reconstruction using an algorithm called weighted backprojection.A complete list of the available programs may be found on the ListOfPrograms.at theXMIPP (Wiki) website. The links on that page points to more detailed manual pages for each ofthe programs.Some programs are numerical-only and will run in the shell (i.e. xmipp_reconstruct_wbpprogram mentioned above). Other programs have a graphical interface (like xmipp_show, theprogram to visualize images, volumes, self-organizing maps etc.), i.e. they will launch an additionalwindow. There are several programs that have an implementation for parallel execution(using message-passing interface, or MPI). The names of parallel programs always start withxmipp_mpi_.1.2 File formats1.2.1 2D imagesXMIPP uses the (single-file) SPIDER file format for 2D images. This is a relatively well-knownformat in the field and guarantees that users may interchange their data with other packages.3