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This is Fiji

[ Fiji Is Just ImageJ ]

Fiji will provide an easy way to set up Java+ImageJA+TrakEM2+VIB+a lot of other plugins that are useful to biologists, geologists and every other scientist who wants to process images.

At the moment, the following platforms are supported:

  • Windows-x86
  • Windows-x86_64
  • Linux-x86
  • Linux-x86_64
  • MacOSX-PowerPC
  • MacOSX-x86
  • MacOSX-x86_64

The setup should be as easy as unpacking the (portable) application and starting the Java wrapper. The wrapper is a program that starts the Java machine hands-free, i.e. it sets the correct settings to start up ImageJ with the plugins directory and heap size set up for you.

In a way, you could say that the "F" in "Fiji" stands for "painless", "easy", "quick" and "convenient" :-)


Fiji is meant to be distributed without source, to make the download as small as possible. In the basic version, Fiji is a portable application, i.e. it should run wherever you copy it.

The starting point is the ImageJ launcher, which will launch Java, set up the environment, and call ImageJ.

To pass arguments to ImageJ, just specify them on the command line.

To pass arguments to the Java Virtual Machine, specify them on the command line, separating them from the ImageJ arguments (if any) with a --. In other words, if you want to override the memory setting, call Fiji like this:

$ ./ImageJ-linux32 -Xmx128m --

Open Source

We are dedicated to open source. Not only does open source allow other developers to port the application to new platforms that the original authors did not begin to think of, it permits others to use the program in totally new ways, and enhance it in all imaginable ways.

Therefore, Fiji is licensed under the GNU Public License, version 2 (of course, this license only applies to Fiji: the build system and the Java wrapper). Not version 3, because we think that it is not our job to educate everybody to be a decent person; that's every person's own job.

In the same vein, Fiji will contain only Open Source software, unless there are good reasons for a non-open sourced component to be included.

But those would need to be very compelling reasons.




  • Albert Cardona
  • Benjamin Schmid
  • Cornelius Sicker
  • Dan White
  • Erwin Frise
  • Gabriel Landini
  • Greg Jefferis
  • Ignacio Arganda-Carreras
  • Jean-Yves Tinevez
  • Johannes Schindelin
  • Mark Longair
  • Pavel Tomancak
  • Stephan Preibisch
  • Stephan Saalfeld
  • Verena Kaynig
  • and all the good people providing ImageJ and plugins

See also


Our first and foremost thanks go to Wayne Rasband, who is not only a very dedicated developer; he also fosters an active and friendly community around ImageJ.

The rest of our thanks go to everybody who helped this project prosper.

Oh, and Fiji is also an island. We just wanted to let you know.


Fiji Is Just ImageJ






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