Virtual Stack Opener

Author: Wayne Rasband (wsr at nih.gov)
Source: Virtual_Stack_Opener.java
Installation: The Virtual Stack Opener is built into ImageJ 1.38q and later. To use it, check "Use Virtual Stack" in the File>Import>Image Sequence dialog box.
Description: This plugin opens images as a virtual (disk resident) stack. It allows image sequences too big to fit in RAM to be opened but image access time is slower and changes are lost when you switch to another image.

Five built in ImageJ commands now have the ability to open virtual stacks. The File>Import>TIFF Virtual Stack command opens a TIFF file as a virtual stack and the following commands have "Use Virtual Stack" options in their dialog boxes:

  • File>Import>Image Sequence
  • File>Import>Raw
  • File>Import>Stack From List
  • File>Import>AVI
In addition, the Bio-Formats plugin can open virtual stacks.

There are several things to keep in mind when working with virtual stacks:

  • Virtual stacks are read-only, so changes made to the pixel data are not saved when you switch to different slice. You can work around this by using a macro (e.g., Process Virtual Stack).
  • You can easily run out of memory using commands like Image/Crop because any stack not directly generated by this plugin will be RAM resident.
  • TIFF virtual stacks can usually be accessed faster than JPEG virtual stacks. A JPEG sequence can be converted to TIFF by opening the JPEG images as a virtual stack and using File/Save As>Image Sequence to save in TIFF format.
History: 2003/12/05: First version
2004/08/11: Uses IJ.getDirectory() to select directory
2006/10/13: Sorts file names in numeric order
2007/04/25: Built into ImageJ 1.38
See Also: Process Virtual Stack macro
Virtual Stack From List macro

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