ImageJ Plugins

Ellipse ROI
Live Histogram
Measure Stack
Multi Measure
NTSC DV2Float
QuickTime Capture Movie   Needs updating for Java 1.4 and on.
QuickTime Grab Movie Frames   Needs updating for Java 1.4 and on.
Layers
Stack Sorter
Measure Roi
Polynomial Fit
PLOT3D I/O   (.unf file reader and writer)
Polar Gradient
3D Fast Hartley Transform
Swap Quadrants 3D   Use with FHT3D for an alternate Hartley coefficeint order.
Iterative Deconvolution   2D code.   Called DAMAS2 in aeroacoustics.
Convolve 3D
Iterative Deconvolve 3D   Called DAMAS3 in aeroacoustics.
Diffraction PSF 3D
3D Local Thickness and Distance Map
MicroArray Profile
Cubic Float Resize and Rotate  An experiment with constrained interpolation.
Other plugins, mostly obsolete

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Links
ImageJ site
Documentation Wiki
Photos from the 2006 ImageJ Conference at the Henry Tudor Institue