SciJava Common is a shared library for SciJava software. It provides a plugin framework, with an extensible mechanism for service discovery, backed by its own annotation processor, so that plugins can be loaded dynamically. It is used by downstream projects in the SciJava ecosystem, such as ImageJ and SCIFIO.

ImageJ2 is a rewrite of ImageJ for multidimensional image data, with a focus on scientific imaging.

SCIFIO is a library for scientific N-dimensional image I/O.

ImageJ Operations: a framework for reusable algorithms.

Not HDF5

representation of multi-angle, multi-channel (etc.) SPIM images and their registration

Configurable key and mouse event handling

TrackMate plugin for Fiji.

A runtime patcher to introduce extension points into the original ImageJ (1.x). This project offers extension points for use with ImageJ2 and it also offers limited support for headless operations.

flexible scenegraphing and rendering for scientific visualisation

Scenery-backed 3D visualization package for ImageJ.