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.

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

BigDataViewer core classes with minimal dependencies.

This library contains ImageJ's core image data model, based on ImgLib2. It is the primary mechanism by which image data is managed internally by ImageJ2.

ImageJ Operations: a framework for reusable algorithms.

Not HDF5

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

SciJava user interface components for Java Swing.

TrackMate plugin for Fiji.

Fiji plugins for starting BigDataViewer and exporting data.

3D mesh structures for ImageJ.