The EMAN2 Wiki is the main source for EMAN2 documentation and information
SPARX and SPHIRE are distributed with EMAN2 in a single binary package. If you install one of the packages below, you will get both EMAN2, SPARX and SPHIRE with a single installation. If you need MPI support for either SPHIRE, SPARX or EMAN2, you also need to download that package.
EMAN2 is the successor to EMAN1, and EMAN2.1 eliminated the unpopular BDB system from EMAN2, in favor of flat files. EMAN is a broadly based greyscale scientific image processing suite with a primary focus on processing data from transmission electron microscopes. EMAN's original purpose was performing single particle reconstructions (3-D volumetric models from 2-D cryo-EM images) at the highest possible resolution, but the suite now also offers support for single particle cryo-ET, and tools useful in many other subdisciplines such as helical reconstruction, 2-D crystallography and whole-cell tomography. Image processing in a suite like EMAN differs from consumer image processing packages like Photoshop in that pixels in images are represented as floating-point numbers rather than small (8-16 bit) integers. In addition, image compression is avoided entirely, and there is a focus on quantitative analysis rather than qualitative image display.
SPHIRE is the abbreviation for SParx for High Resolution Electron Microscopy. SPHIRE is a new software suite designed for easy access to cryo electron microscopy with the clear goal of quality assessment and result reproducibility by statistical resampling. While being well suited for cryo-EM novices, experienced users will find comfort in the accessibility of almost every possible variable in advanced option tabs and the transparent, easily customizable Python-based framework for non-standard processing pipelines. In a visually appealing and easy-to-use graphical user interface (GUI) the user will find an array of programs which will guide through the complete process of high-resolution cryo-EM. This begins with movie frame alignments (movie), CTF estimation of raw electron micrographs (cter) and picking/stack creation (window) and continues with reproducible 2-D classification (isac), reproducible initial model generation (viper), automatic gold-standard 3-D refinement (meridien), local resolution estimation and filtering (localres), up to the 3-D sorting of different conformational states based on the statistical 3-D variability of the data (sort3D).
Full installation instructions are at:
http://blake.bcm.edu/emanwiki/EMAN2/Install