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=== Box Size (Important) ===
 * Particle [[EMAN2/BoxSize|box-size]] - Impacts quality and speed of reconstructions!
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 * [[Eman2DataStorage|File Formats, Data storage conventions, and the internal database (what is BDB: ?)]]
 * [[Eman2NFS|Using EMAN2 in environments with NFS or other network-shared directories]]
 * [[Eman2Metadata|Parameters/Metadata appearing in EMData attributes (and stored on disk with the image), accessed with get_attr and set_attr]]
 * [[Eman2AppMetadata|Parameters/Metadata for applications, not associated with a specific image, stored in bdb:project]]
 * Supported [[Eman2DataStorage|image file formats]] and usage
 * How EMAN2 stores data in [[EMAN2/Hdf5Format|HDF5 files]]
 * [[EMAN2/Eman2Metadata|Header information]] (key/value pairs) associated with a specific image
 * Information stored in [[Eman2InfoMetadata|JSON files]] in the ''info/'' folder and elsewhere
 * Setting local and global [[EMAN2/ApplicationPreferences|application preferences]]
 * [[Eman2OtherFiles|Other misc. files]] such as .box and .lst
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 * [[EMAN2/BoxSize|Particle box-size and refinement speed, what size to use]]
 * [[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]]
 * [[EMAN2/Symmetry|Symmetry]] in EMAN2, and generating projections in an asymmetric unit
 * [[EMAN2/AngStep|Angular sampling]], number of projection and resolution
 * 3D and 2D [[Eman2TransformInPython|Transformations]] (rotation, translation, etc.)
 * [[EMAN2/CtfModel|CTF]] model used in EMAN2
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''Note: These pages are often out of date. For up to date details please run'' {{{e2help.py <object type> -v 2}}}

EMAN2 Concepts and Conventions

Box Size (Important)

  • Particle box-size - Impacts quality and speed of reconstructions!

Data Storage

Mathematical Conventions

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Note: These pages are often out of date.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 e2help.py <object type> -v 2

  • 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 2024-02-03 17:16:45 by SteveLudtke)