IJ2 is out
 Sec. 7: Image Types & Formats Up Part II: Working with IJ Sec. 9: Color Images 

8 Stacks, Virtual Stacks and Hyperstacks


ImageJ can display multiple spatially or temporally related images in a single window. These image sets are called stacks. The images that make up a stack are called slices. In stacks, a pixel (which represents 2D image data in a bitmap image) becomes a voxel[?] (volumetric pixel), i.e., an intensity value on a regular grid in a three dimensional space.
All the slices in a stack must be the same size and bit depth. A scrollbar provides the ability to move through the slices and the slider is preceded by a play/pause icon that can be used to start/stop stack animation. Right-clicking on this icon runs the Animation Options… [Alt /]↓ dialog box.
Most ImageJ filters will, as an option, process all the slices in a stack. ImageJ opens multi-image TIFF files as a stack, and saves stacks as multi-image TIFFs. The FileImportRaw…↓ command opens other multi-image, uncompressed files. A folder of images can be opened as a stack either by dragging and dropping the folder onto the ‘ImageJ’ window or or by choosing FileImportImage Sequence… To create a new stack, simply choose FileNewImage… [n]↓ and set the Slices field to a value greater than one. The ImageStacks submenu contains commands for common stack operations.
figure images/StacksHyperStacks.png
Figure 2 Stacks and Hyperstacks in ImageJ: FileOpen SamplesMitosis (26MB, 5D stack). Hyperstacks dimensionality can be reduced using ImageHyperstacksReduce Dimensionality…↓, ImageStacksZ Project… or ImageHyperstacksChannels Tool… [Z]↓. The ‘(V)’ on the window title denotes a virtual image (see Virtual Stacks↓).

Virtual Stacks

Virtual stacks are disk resident (as opposed to RAM[?] resident) and are the only way to load image sequences that do not fit in RAM. There are several things to keep in mind when working with virtual stacks:
ImageJ appends a ‘(V)’ to the window title of virtual stacks and hyperstacks (see Hyperstacks↓). Several built-in ImageJ commands in the FileImport submenu have the ability to open virtual stacks, namely: TIFF Virtual Stack…↓, Image Sequence…, Raw…↓, Stack From List…, AVI… (cf. Virtual Stack Opener). In addition, TIFF stacks can be open as virtual stacks by drag and drop (cf. 4: Opening Virtual Stacks by Drag & Drop↓).
4 Opening Virtual Stacks by Drag & Drop
TIFF stacks with a .tif extension open as virtual stacks when dragged and dropped on the  figure images/tools/Switcher-small.png  toolbar icon.
figure images/DragAndDropVirtualTiff.png


Hyperstacks are multidimensional images, extending image stacks to four (4D) or five (5D) dimensions: x (width), y (height), z (slices), c (channels or wavelengths) and t (time frames). Hyperstacks are displayed in a window with three labelled scrollbars (see Stacks and Hyperstacks↑). Similarly to the scrollbar in Stacks↑, the frame slider (t) has a play/pause icon.
ImageHyperstacks submenu
 Sec. 7: Image Types & Formats Up Part II: Working with IJ Sec. 9: Color Images