= EMAN2 Concepts and Conventions = === Box Size (Important) === * Particle [[EMAN2/BoxSize|box-size]] - Impacts quality and speed of reconstructions! === Data Storage === * Supported [[Eman2DataStorage|image file formats]] and usage * How EMAN2 stores data in [[Eman2HDF|HDF5 files]] * [[Eman2Metadata|Header information]] (key/value pairs) associated with a specific image * Information stored in [[Eman2InfoMetadata|JSON files]] in the ''info/'' folder and elsewhere * [[Eman2OtherFiles|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 [[Eman2TransformInPython|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 ''Note: These pages are often out of date.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'' {{{e2help.py -v 2}}} * [[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 {{attachment:single_image_iso_c.png}}