Downloading and Building Fiji From Source

Revision as of 12:06, 9 November 2008 by Mark (talk | contribs)

Downloading the Source Code with Git

Warning: the source code for Fiji is rather large; make sure that you have two gigabytes of disk space free before beginning this.

To fetch the Fiji source code you should use git. If you are not familiar with Git, you might want to read this page or these pages instead.

Your first step should be to "clone" the fiji repository with the following command:

git clone git://

This should start downloading the base fiji repository and unpack it into a directory called "fiji" in your current directory. Once this has successfully completed, change into the newly created "fiji" directory.


This will not yet be complete tree that you can build, since the fiji repository has a number of submodules. (For more on submodules, see the Git submodule tutorial.) If you have lots of disk space available, these submodules can be initialized with:

git submodule init ImageJA TrakEM2 VIB micromanager1.1 mpicbg

... but if you are short of disk space you may skip that step. However, if you do not have Java 1.5 or newer installed, you need to initialize at least the java submodule for your platform by doing, depending on your system:

git submodule init java/linux          # For 32-bit Linux systems
git submodule init java/linux-amd64    # For 64-bit Linux systems
git submodule init java/macosx-java3d  # For MacOS X systems
git submodule init java/win32          # For 32-bit Windows systems
git submodule init java/win64          # For 64-bit Windows systems

You can then update the submodules with:

git submodule update

Getting a snapshot without Git

If you insist on not using Git, you can download a snapshot of Fiji here, but you need to make sure that you have a new enough Java version installed.

Building Fiji from Source

You should now be able to build Fiji with:

sh run

... which will invoke Fiji's multi-platform build system. If all goes well, after some time you should see the main Fiji window:

Fiji's main window