====== EMAN2 Concepts and Conventions ======

==== Box Size (Important) ====
  * Particle [[EMAN2:BoxSize|box-size]] - Impacts quality and speed of reconstructions!

==== Data Storage ====
  * Supported [[EMAN2:DataStorage|image file formats]] and usage
  * How EMAN2 stores data in [[EMAN2:Hdf5Format|HDF5 files]]
  * [[EMAN2:EMAN2:Metadata|Header information]] (key/value pairs) associated with a specific image
  * Information stored in [[EMAN2:InfoMetadata|JSON files]] in the //info/// folder and elsewhere
  * Setting local and global [[EMAN2:ApplicationPreferences|application preferences]]
  * [[EMAN2:OtherFiles|Other misc. files]] such as .box and .lst

==== Mathematical Conventions ====
  * [[EMAN2:Symmetry|Symmetry]] in EMAN2, and generating projections in an asymmetric unit
  * [[EMAN2:AngStep|Angular sampling]], number of projection and resolution
  * 3D and 2D [[EMAN2:TransformInPython|Transformations]] (rotation, translation, etc.)
  * [[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.

//Note: These pages are often out of date. For up to date details please run// <code>e2help.py <object type> -v 2</code>

  * [[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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