Stack Alignment Plugins
Author: J. Anthony Parker, MD PhD (
Dates: 2001/09/20: First version
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.
Description: There are several plugins in the Stack Alignment group including source files.  They are all contained in Align3_TP.jar.

- Alignment (Align3_TP) aligns two stacks.
- Fusion (Fusion_TP) fuses two aligned stacks optionally in color.
- Orthogonal View Stack Display (Display3_TP) displays orthogonal slices (x,y,z) of N aligned stack.
- Reorient Stack (Reorient3_TP) reorients a stack.
- Show Alignment (Show_AlignmentTP) uses B&W fusion or wipers to show alignment of two slices.
- To Axial (To_AxialTP) converts a coronal or sagital stack to an axial stack.
- To Coronal (To_CoronalTP) converts an axial or sagital stack to a coronal stack.
- To Sagital (To_SagiatalTP) converts an axial or coronal stack to an axial stack.
- TwoD Histogram (TwoD_HistorgramTP) shows several the 2-dimensional histogram of two images of interest for mutual information.

See the individual plugin descriptions for more details.
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