Stack Alignment (Align3_TP)
Author: J. Anthony Parker, MD PhD (
Dates: 2001/09/20: First version
2001/10/01: Undo option added
2001/11/05: Mouse translation, rotation, and resizing added
2002/01/10: Restructured using an align3tp package
2002/02/22: Restructured to avoid name conflicts
2002/04/26: Save data for external registration options added
2004/07/10: Support for 32-bit floating data added
2004/11/25: Automatic slice and volume registration added
2007/07/16: Output calibration changed
2007/12/29: Relative origins of input stacks used for initial registration
2008/07/18: Automatic mode added
2010/12/12: Updated to fix crashing
Source: Several source files are included in Align3_TP.jar
Installation: Download Align3_TP.jar, into ImageJ's plugins folder and restart ImageJ.  The "Align3 TP" plugin will be in a folder called, "Align Stacks".
Description: Operating manual [pdf ].
Align3_TP is one of the ImageJ plugins in the "Align Stacks" directory.  It allows the user to align two source stacks.  The default source stacks are the first and second open stacks in the ImageJ "Window" menu.  The alignment may optionally be applied to a third stack, the current stack.  For example, a PET transmission scan could be aligned with a CT, and the alignment applied to a PET emission scan.  Suggestions welcome.

Align3_TP defaults to a stack orientation which goes from inferior to superior (right handed).  Install with an Argument which contains "Left", for stacks which goes from superior to inferior (more typical in Radiology).  Install with an Argument which contains "About", to show the about message.  Install with an Argument which contains "External", to include options for saving and retrieving data.  Align3_TP is intended to be used interactively; however, if installed with an Argument which contains "Automatic" some commands can be used in an automatic mode (see "plugins\Align Stacks\Align3_TP_Template.script".

To recompile, make sure the "Align Stacks" folder is in the ImageJ classpath, then just use ImageJ's "Compile and Run ..." option.  (Utility classes are in the package, align3tp, in the "Align Stacks" directory.)

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