3D images
In microscopy (and other disciplines) the concept of standard two-dimensional (2D) digital images, as composed of many pixels with data about colors and intensities, is extended to 3D. A collection of 2D slices acquired along an axis, close to each other build the 3D representation of an object. Thus every pixel in a slice represents the light intensity collected from a small volume: pixels become voxels.This high-quality movie shows dividing cells imaged as a 3D volume, deconvolved, and deconvolved with Huygens. Blue represents DAPI staining, red indicates pericentrin (centrosome) staining, yellow is alpha-tubulin, and green shows actin (phalloidin). The raw image data was acquired on a DeltaVision Elite, with a 60x oil 1.42 NA objective by Dr. Alexia Ferrand, Imaging Core Facility, Biozentrum, University of Basel, Switzerland.
A volume (3D) image represents a physical quantity as a function of three spatial coordinates. In a digital volume image, each sample (voxel) represents this quantity measured at a specific location. The image is made by a spatial sequence of 2D slices that include the object of interest. A slice is represented as an image matrix of pixels (X and Y coordinates). The slice number indicates the Z-coordinate.
But not any collection of 2D stacks is a 3D image: see 3D Microscope.