Difference between revisions of "Developing Fiji"

(Getting started: add a link to Git for Dummies)
(Further reading for developers: another link to a previously-orphan page :))
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*[[Description of ImageJ's plugin architecture]]
*[[Description of ImageJ's plugin architecture]]
*[[Tips for developers]]
*[[Tips for developers]]
*[[Developers HowTo]]
*[http://www.imagingbook.com/index.php?id=102 ImageJ plugin writing tutorial]
*[http://www.imagingbook.com/index.php?id=102 ImageJ plugin writing tutorial]
*[http://albert.rierol.net/imagej_programming_tutorials.html ImageJ programming tutorials]
*[http://albert.rierol.net/imagej_programming_tutorials.html ImageJ programming tutorials]

Revision as of 11:10, 8 April 2010

Fiji is a community effort. So we are happy whenever we see new people developing Fiji!

Getting started

First, you have to download and build Fiji. If you do not know Git yet, we have a concise introduction for you.

The Fiji launcher

After building, you have a program called "fiji" in Fiji's root directory. Its main purpose is to load a Java virtual machine with known-good options, and then launch ImageJA.

However, it is much more powerful than that. Amongst other things, you can

  • Open images: ./fiji example.jpg
  • Call Jython scripts: ./fiji example.py (also works for JRuby scripts when they have an .rb extension)
  • Call the Jython interpreter: ./fiji --jython (the classpath will be the same as when calling ImageJA)
  • Run Fiji with the system Java instead of its own one: ./fiji --system. But beware: this might fail since some plugins need at least Java 1.5, and the 3D viewer needs Java3D.
  • Show the java command line instead of running Fiji: ./fiji --dry-run
  • Run Fiji Build System: ./fiji --build plugins/lens_correction.jar
  • Compile a Java class: ./fiji --javac example.java
  • Run a Java class' main() method: ./fiji --main-class=example
  • Pass some Java options: ./fiji -server -- (everything that comes before a -- is interpreted as Java option)
  • Link Fiji into the PATH: ln -s $(pwd)/fiji $HOME/bin/ && fiji
  • Start Fiji and run a menu entry directly: ./fiji --run Update_Fiji (the underscore was used in place of a space to avoid having to quote the argument)

The Fiji launcher can do more, just call ./fiji --help for a short description.

The Fakefile system

Fiji comes with its own builder, named Fiji Build System. There are already other build systems, such as Ant or Maven, but at least it is simple and small. For details, go to this page.

Adding plugins

After you built Fiji successfully, you can add your own plugins.

  • If you haven't done so, pick a name for your .jar file, say My_Plugin. Make sure that it has at least one underscore in it, otherwise ImageJ will not pick it up. If you cannot think of a name with an underscore, just append one. Then create a subdirectory src-plugins/My_Plugin.
  • Now put your sources into that subdirectory. Please no .class files. Readme or license files are okay, however.
  • Create a staged-plugins/My_Plugin.config file. This will be included in the .jar file as plugins.config.
  • In Fiji's root folder, call ./fiji bin/commit-plugin.py src-plugins/My_Plugin/. Please make sure that it ends with a slash. This command will make the necessary edits to the Fakefile and .gitignore, and staged-plugins/My_Plugin.config, and commit everything needed for your plugin. If you want to do this manually, look in the Git log for an example (e.g. TurboReg) and imitate it.
  • Now build the plugin with ./fiji --build.
  • After testing, you might realize that you need changes. In this case, decide if you want to amend the commit (if there was a silly typo, you might want to hide that fact from the world), or if you want to make a new commit.
  • When everything is done and fine, publish (which is called "push" in Git)!

Writing plugins

Fiji accepts plugins written in Java, Javascript, Jython, JRuby, Beanshell, Clojure and the ImageJ Macro language.

The plugins/Examples folder contains numerous plugins in all supported languages, heavily commented.

There is an introductory tutorial to ImageJ programming in Java. The tutorial contains explanations on ImageJ datastructures (ImagePlus, ImageProcessor, Regions of Interest or ROIs, etc).

See Scripting Help for details on how to develop, test and run ImageJ plugins written in the supported scripting languages.

There are also Scripting comparisons.

See also the PlugIn Design Guidelines.

Adding submodules

Some projects have their own source code repositories. In this case, we do not copy the files into src-plugins/, but use submodules.

If the project uses a different source code management tool than Git, no problem, just mirror it.

Then add the submodule. Example:

# clone the VIB repository
git clone ssh://contrib@pacific.mpi-cbg.de/srv/git/VIB.git
# first time, commit-submodule need to know the target, too ("jars/jgit.jar" in this case)
./fiji bin/commit-submodule.py VIB plugins/VIB_.jar

In the case of VIB, it works as easily as that, because it has its own Fakefile. Submodules do not need to have that, you can provide one in staged-plugins/, and they do not need to be installed in plugins/, either:

# clone the "egit" repository, but name it "jgit"
git clone ssh://contrib@pacific.mpi-cbg.de/srv/git/egit jgit
<create a staged-plugins/jgit.Fakefile>
# first time, commit-submodule need to know the target, too ("jars/jgit.jar" in this case)
./fiji bin/commit-submodule.py jgit jars/jgit.jar

So what does commit-submodule.py do? It

  • verifies that the submodule is pushed,
  • makes sure that the submodule is recorded in .gitmodules,
  • adds the target to the Fakefile,
  • adds the target to .gitignore so it is not committed by accident,
  • adds a precompiled/<target> to ensure that the submodule does not need to be checked out, and
  • finally commits the result


When you're testing Fiji, you may want to measure the code coverage of your tests - one way is described in the page Code Coverage in Fiji.

At some point, you might want to debug whatever you wrote. There's a small Debugging intro page.

Discussing code

When you want to discuss your changes to some Fiji component, the preferred way is to inline a patch and sending it to the fiji-devel mailing list. You can also send a link to your repository, e.g. a fork of Johannes' Fiji repository on github.com, but then commenting is not as easy (and the discussion will involve fewer developers).

When discussing larger chunks of code (or a patch) on IRC, you should not paste them directly, but you should use a pastebin instead.

When you want to point at specific code on IRC or via mail, you can also do so by posting links to our Gitweb. There is even a little shell script in fiji.git that helps you finding the link:

bin/open-in-gitweb.sh fiji.cxx

This script will open the appropriate link with xdg-open. It can deal with files, even in submodules, and commits (for commits, your current directory must be inside the appropriate Git checkout). For files, you can append ":<linenumber>" to the file name to get a link to a specific line.


Please make sure that you are a little familiar with Git. Once you are, you can easily make a local contrib branch and push it.

Forking on GitHub

Alternatively, you can make an account for yourself on GitHub and fork fiji.git:

  1. create an account on GitHub
  2. Fork Fiji:
  1. clone it

If you already worked in an existing checkout of fiji.git, no problem, you can connect that to the new remote:

  1. git remote add github github.com:<user>/fiji (where <user> is your account on GitHub)
  2. git config branch.<branch>.remote github (where "<branch>" is the branch you want to connect to GitHub, typically master)
  3. git config branch.<branch>.merge refs/heads/<branch>
  4. git push github <branch> to push the current state

Letting us know

After you published your contributions, you probably also want to let us know what you did, so just send a mail to the Fiji devel mailing list.

Providing documentation

A plugin wants to be used. Therefore you want to give users some information about it, and most likely also a tutorial how to use it.

If you have an account on this Wiki, you can easily create new tutorials with the Tutorial Maker.

Further reading for developers