Links

Software Based on ImageJ

Bio7
Fiji Project
ICY (includes ImageJ)
ImageJ2
µManager
MBF Collection
ObjectJ
SalsaJ

Documentation

efg's Reference Library
Hypermedia Image Processing
Image File Formats
Image Processing Fundamentals
Java 1.6 API Specification
The Java Tutorial

Imaging Libraries

Acme GIF Encoder
Gnome TWAIN Library
Imagero Java I/O Library
The Java Imaging Utilities
JTwain TWAIN Library
JIMI Software Development Kit
LizardWorks TIFF Library
PixTools for Java
RasterMaster/Java

Image Analysis Software

CellProfiler (cell image analysis)
idoimaging (medical imaging)
ImageSurfer (3D visualization and analysis)
Image SXM (extended version of NIH Image)
Internet Analysis Tools Registry
MIPAV (3D imaging and visualization)
NITRC (Neuroimaging Tools and Resources)

Science and Education

Teaching Image Processing
The Cell: An Image Library

Java Programming

Cafe au Lait
java.net
Java on the Brain
Java Glossary
Java Lobby
java.sun.com
Java Tips Java World
Stack Overflow

Benchmarks

"Plasma"
Sieve of Eratosthenes
SciMark 2.0