J3d Core

3D Viewer for visualizing image stacks three-dimensionally.

The mcib3d library is the core for most of the mcib3d plugins developed.

Trainable Segmentation plugin for Fiji.

Java Utility Lib

Descriptor based registration plugin for Fiji.

GeOxygene SIG 3D GUI

Fijiyama : a versatile registration tool for 3D multimodal time-lapse imaging

MASON is a fast agent-based simulation library core in Java, designed to be the foundation for large custom-purpose Java simulations, and also to provide more than enough functionality for many lightweight simulation needs.

Ebli 3d

TrakEM2 plugin for ImageJ.