Fiji is Just ImageJ -- batteries included
For users, Fiji is easy to install and update, bundles a set of plugins in a coherent menu structure (and updatable), along with comprehensive documentation.
For developers, Fiji as an open source project is hosted on a git source version control
... [More] repository, with access to the source code of all internals, libraries and plugins, and eases the development and scripting of plugins. [Less]
Jato is an implementation of the Java virtual machine. It includes a VM and a JIT compiler for the x86 machine architecture and supports the JNI API. Jato uses Boehm GC as its garbage collector and relies on GNU Classpath to provide essential Java APIs.