= EMAN2 Concepts and Conventions =
=== Data Storage ===
* [[Eman2DataStorage|Supported '''image file formats''' and usage]]
* [[Eman2HDF|How EMAN2 stores data in '''HDF5 files''']]
* [[Eman2Metadata|'''Header information''' stored within image files]]
* [[Eman2InfoMetadata|Information stored in '''JSON files''' in the ''info/'' folder and elsewhere]]
=== Mathematical Conventions ===
* [[EMAN2/BoxSize|Particle '''box-size''' and refinement speed, what size to use]]
* [[EMAN2/AngStep|'''Angular sampling''', number of projection and resolution]]
* [[Eman2TransformInPython|3D and 2D '''Transformations''' (rotation, translation, etc.)]]
* [[EMAN2/Symmetry|'''Symmetry''' in EMAN2, and generating projections in an asymmetric unit]]
* [[EMAN2/CtfModel|'''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.
* [[EMAN2/Modular/Overview|Overview of how to use modular functions]]
* [[EMAN2/Modular/Processors|Processors]] - Filters, masks and other basic image processing operations
* [[EMAN2/Modular/Cmps|Comparators]] (cmp) - Similarity metrics (cmp) for comparing two images/volumes
* [[EMAN2/Modular/Aligners|Aligners]] - Algorithms for aligning one image/volume to another
* [[EMAN2/Modular/Averagers|Averagers]] - Methods for averaging many images/volumes together
* [[EMAN2/Modular/Projectors|Projectors]] - Generate 2-D projections of 3-D volumes (or 1-D projections of 2-D images)
* [[EMAN2/Modular/Reconstructors|Reconstructors]] - Generate 3-D volumetric reconstructions from sets of 2-D images and orientation paramters
* [[EMAN2/Modular/Analyzers|Analyzers]] - Perform various analyses on sets of images/volumes
* [[EMAN2/Modular/Symmetries|Symmetries]] - Permissible symmetries to use in EMAN2
* [[EMAN2/Modular/OrientGens|Orientation Generators]] (orientgen) - Methods for generating sets of orientations filling an asymmetric unit
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