Table of Contents
Images are ubiquitous objects used on all electronic media, implemented in a large number of ways with different file formats, different access strategies and different notions of information. The most general notion of an image is a 2D raster of values representing gray scale or colour values at particular sampled points within the image. An extension of the basic image model is the time-evolving model (i.e., movie or animation), with time representing a third dimension. In structural biology, we deal with 3D structures, often viewed as static, but in reality subject to time-dependent variation. In electron microscopy, the images taken are approximations of 2D projections of 3D structures. The problem with most available software is that none supports the concept of an image in its most general form.
The structures studied in structural biology is inherently 3D, thus the basis of the image model is also 3D. In addition, we would like to pack multiple 2D images into a single file. However, packing 2D images as the sections of a 3D map confuses the distinction between 2D and 3D and should be avoided. Furthermore, we also want to be able to store multiple 3D maps, requiring an additional dimension.
Most of the data sets we work with have single values at each pixel or voxel (gray scale values), but situations may arise where each voxel may have multiple values. The most common usage of multiple pixel values is to represent colour, such as RGB (Red-Green-Blue) and CMYK (Cyan-Magenta-Yellow -blacK). More extensive use may be to associate a list of values or spectrum at each pixel. This requires yet another dimension in the image model. The meaning of the channels is captured in the notion of a color model, including gray scale, RGB, and CMYK.
The five dimensions are therefore (in storage order):
Channels - one or more values associated with each voxel
X-dimension
Y-dimension
Z-dimension
Images - a series of images, typically with some relationship (such as 2D projections of the same particle, a tilt series, or a time series)