Links

Software Based on ImageJ

AstroImageJ
Bio7
Fiji
ICY (includes ImageJ)
ImageJ2
µManager
MBF Collection
NIH Image
ObjectJ
QuPath (includes ImageJ)

Documentation

Hypermedia Image Proc.
Image File Formats
ImageJ API
Java 8 API
The Java Tutorial

Imaging Libraries

Acme GIF Encoder
Gnome TWAIN Library
JTwain TWAIN Library

Image Analysis Software

CellProfiler (cell image analysis)
ImageSurfer (3D visualization)
Image SXM (based on NIH Image)
MIPAV (3D imaging and visualization)
NITRC (Neuroimaging Resources)
OsiriX DICOM Viewer

Science and Education

Teaching Image Processing
The Cell: An Image Library

Java Programming

Cafe au Lait
Java on the Brain
Java Glossary
Java World
Stack Overflow

Benchmarks

"Plasma"
Sieve of Eratosthenes
SciMark 2.0