EMAN2 Concepts and Conventions

Data Storage

• File Formats, Data storage conventions

• Using EMAN2 in environments with NFS or other network-shared directories

• How EMAN2 stores data in HDF5 files

• Parameters/Metadata appearing in EMData attributes (and stored on disk with the image), accessed with get_attr and set_attr

• Parameters/Metadata for applications, not associated with a specific image, stored in bdb:project

• Parameters/Metadata associated with projects stored in the ''info'' folder

Mathematical Conventions

• Particle box-size and refinement speed, what size to use

• Angular sampling, number of projection and resolution

• 3D and 2D Transformations (rotation, translation, etc.)

• Symmetry in EMAN2, and generating projections in an asymmetric unit

• CTF model used in EMAN2

Modular functions in EMAN2

Many aspects of EMAN2 are modular, meaning new functions can be easily added for a variety of tasks. These categories are used in the GUI and from the command-line, and are not just useful for programmers. For example, the '--process' option in e2proc2d.py and e2proc3d.py uses 'processors' as defined below.

• Overview of how to use modular functions

• Processors - Filters, masks and other basic image processing operations

• Comparators (cmp) - Similarity metrics (cmp) for comparing two images/volumes

• Aligners - Algorithms for aligning one image/volume to another

• Averagers - Methods for averaging many images/volumes together

• Projectors - Generate 2-D projections of 3-D volumes (or 1-D projections of 2-D images)

• Reconstructors - Generate 3-D volumetric reconstructions from sets of 2-D images and orientation paramters

• Analyzers - Perform various analyses on sets of images/volumes

• Symmetries - Permissible symmetries to use in EMAN2

• Orientation Generators (orientgen) - Methods for generating sets of orientations filling an asymmetric unit