## 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.