## Glossary

1D

  one-dimensional.

2D

  two-dimensional.

3D

  three-dimensional.

bitmap

  an image consisting of a binary data type, i.e., each voxel has one of only two possible values.

CMYK

  Cyan-Magenta-Yellow-blacK four-colour scale for printers.

color model

  the way in which colors are represented within a data structure. Typical color models are gray scale, bitmap, RGB and CMYK.

complex data type

  a data type composed of a real number and an imaginary number.

contrast transfer function

  in the context of an electron microscope, the transfer function introduced by objective projection lenses manifested as phase shifts in images and limiting resolution.

data type

  the size and type of each element of an image data block. Typical data types are byte, short, integer, float, and complex_float.

image

  a 1D, 2D, or 3D data set of elements, each element composed of one or more values. An image may also refer to a series of 1D, 2D, or 3D data sets arranged in some logical order (such as particle images from a micrograph, a tilt series of micrographs, or a time series).

map

  synonym for image, most often used for a 3D reconstruction made from 2D images.

montage

  a way to package 2D images or 2D slices from a 3D image into a large 2D matrix mainly for display purposes.

origin

  the origin of an image is defined by the intersection of the symmetry axes of a symmetric object it contains, or by the rotation origin for operations to transform it.

periodogram

  the intensity map of a Fourier transform used as an estimator of the power spectrum. A better power spectrum estimator is obtained from averaging multiple periodograms from different samples of the same signal.

pixel

  a single raster element in a 2D image (see voxel).

pixel size

  the sampling interval or pixel/voxel size on a regular grid in each dimension. (see sampling)

polar data type

  a data type composed of an amplitude and a phase. Typically used for Fourier transforms. power spectrum -

power spectrum

  the power in a signal (intensity or squared amplitude) as a function of spectral frequency (also called the spectral density), typically estimated by calculating periodograms.

projection

  average of density along the line of sight and represented by a view vector and rotation angle around that vector (see view).

quaternion

  also called a hypercomplex number, it is composed of one real value and three imaginary values. Quaternions are compact descriptions of rotations in 3D space, requiring fewer elements and constraints than rotation matrices.

reslicing

  the storage order of a map is reorganized, so that axes are switched and/or mirrored. This is equivalent to single or multiple 90 degree rotations, with or without mirroring.

RGB

  Red-Green-Blue three-colour scale for monitor displays.

sampling

  the sampling interval or pixel/voxel size on a regular grid in each dimension. (see pixel size)

Single particle analysis/processing

  Acquiring images of different single particles presumed to be identical copies of each other, and finding the relative orientations of these 2D images to allow merging into a 3D reconstruction.

SPA

  See Single particle analysis/processing.

SPP

  See Single particle analysis/processing.

STAR

  Self-defining Text Archiving and Retrieval.

tomography

  acquiring images of a single object from a series of different views, aligning these images with respect to each other, and generating a 3D reconstruction.

view

  orientation of a viewer described by a vector along the line of sight and a rotation angle around that vector (an alternative to using Euler angles).

voxel

  a single raster element in a 3D image (see pixel).

wrapping

  view the image or map as having periodic boundaries, so that enlargement of the image (without scaling!) would produce repeated copies of the image or map.