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 * [[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]]
 * Supported [[Eman2DataStorage|image file formats]] and usage
 * How EMAN2 stores data in [[Eman2HDF|HDF5 files]]
 * [[Eman2Metadata|Header information]] stored within image files
 * Information stored in [[Eman2InfoMetadata|JSON files]] in the ''info/'' folder and elsewhere
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 * [[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]]
 * Particle [[EMAN2/BoxSize|box-size]] and refinement speed, what size to use
 * [[EMAN2/AngStep|Angular sampling]], number of projection and resolution
 * 3D and 2D [[Eman2TransformInPython|Transformations]] (rotation, translation, etc.)
 * [[EMAN2/Symmetry|Symmetry]] in EMAN2, and generating projections in an asymmetric unit
 * [[EMAN2/CtfModel|CTF]] model used in EMAN2

EMAN2 Concepts and Conventions

Data Storage

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

single_image_iso_c.png

EMAN2/Concepts (last edited 2018-10-08 13:00:17 by SteveLudtke)