Downloading and Building Fiji From Source

Revision as of 04:24, 30 August 2008 by Mark (talk | contribs)

Downloading the Source Code with Git

After creating this page, I subsequently realized that there already was a more detailed page on this wiki (called Git mini howto) describing how to do this - it has more detailed information, including information about how to contribute back to the project. This page only has minimal instructions for downloading and building Fiji; for more information see Git mini howto. --Mark 12:19, 30 August 2008 (CEST)

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. (There will be very little in the way of tutorial information about git on this page, but there are many such resources available on the web and you may wish to see the pages on this wiki in the Category Git.) You 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 depends on 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

... but if you are short of disk space you may with to only initialize the java submodules that are necessary for your platform by doing:

git submodule init ImageJA TrakEM2 VIB micromanager1.1 mpicbg

... and then one of the following, 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

Building Fiji from Source

You should now be able to build Fiji with:


... 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