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Overview of Fiji's source code

    This page will give you an idea how Fiji’s source code is organized. Every directory referred to is relative to the Fiji root, i.e. the directory into which you cloned fiji.git.

    The Fiji launcher

    The Fiji Launcher is now called ImageJ launcher and lives in its own repository . It is built by Travis CI.

    The plugins

    The plugins served from Fiji’s update site are all Open Source. The source code lives on GitHub , in repositories reflecting the name of the .jar file generated from the source code. Example: the source code for Fiji_Plugins.jar lives in https://github.com/fiji/Fiji_Plugins.

    The only special rule applies for plugins whose file names end in an underscore: that underscore will be stripped. Example: the sources of Arrow_.jar are stored in https://github.com/fiji/Arrow.

    All of our plugins are maintained as Maven projects; this allows developers to build the code with their integrated development environment of choice.

    Plugins maintained in Maven projects consist of

    1. a pom.xml file in the top-level directory
    2. the Java sources in the src/main/java/ directory, and
    3. the plugins.config file in src/main/resources/

    If the plugin sources contain unit tests, their sources are in src/test/java/ so that the generated test classes will not be included in the final .jar file.


    Most libraries are available as regular Maven dependencies (you can search for them on Maven Central).


    Fiji used to maintain relationships with projects developed outside the fiji.git repository via Git submodules. This proved too cumbersome and too unintuitive for the affected parties.

    All submodule couplings are now replaced by proper Maven dependency management.

    The Fiji Build system

    Fiji used to have its home-brewn build system. We switched to using Maven in 2012, though.

    For convenience, there is a "”Mini Maven”” project that allows building Fiji without a full-blown Maven; however, for serious development, real Maven, or even better, Eclipse or Netbeans is recommended.

    For backwards-compatibility, Mini Maven can be called via ./Build.sh in the top-level directory of a fiji.git checkout. Despite the name, it does not really build anything, but only draws in all Fiji components as Maven dependencies.

    The bin/ directory

    Quite a few tasks – such as committing a new submodule or sources for a plugin, or releasing a new version of Fiji – are performed by scripts. These scripts live in the */bin/* subdirectory.

    Some of these scripts are shell scripts, others are Jython scripts with special shebang lines which trigger them to be called with the current Fiji launcher.