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Fiji as a bundle is licensed under the GPL, with exceptions for plugins and other components. This file lists the license under which each component, plugin or plugin bundle (a .jar file) is released.
* GPL: General Public License (latest) as specified at
* GPL 2: General Public License version 2
* LGPL: Lesser General Public License as specified at
* AGPL: Affero General Public License as specified at
* PD: Public Domain
* CPL 1.0: Common Public License 1.0 (
* PSF 2: Python Software Foundation Version 2
* JSF 2.1: Jython Software License 2.0, 2.1
* JPSL: JPython 1.1.x Software License
* SPL: Sun Public License
* MPL: Mozilla Public License as specified at
* BSD: Berkeley Software Distribution
* BSDR: BSD-like license allowing use for research
* EPL: Eclipse Public License (
* AL: Apache License (
Name File Author(s) Contact License
---- ---- --------- -------------- -------
* Anisotropic Diffusion 2D Anisotropic_Diffusion_2D.jar GPL
* Balloon Segmentation BalloonSegmentation_.jar Lionel Dupuy GPL
* Batik batik.jar AL
* Bean Shell language bsh.jar SPL/LGPL
* Bean Shell Interpreter BSH_Interpreter.jar Johannes Schindelin GPL
* Bleach Corrector CorrectBleach_.jar Kota Miura GPL
* Bug Submitter Bug_Submitter.jar Mark Longair, Johannes Schindelin, Curtis Rueden BSD
* bUnwarpJ bUnwarpJ_.jar Ignacio Arganda et al. GPL
* Clojure clojure.jar Rich Hickey EPL
* Clojure Interpreter Clojure_Interpreter.jar Albert Cardona GPL
* Color Histogram Color_Histogram.jar Dimiter Prodanov GPL 2
* Color Inspector 3D Color_Inspector_3D.jar Kai Uwe Barthel PD
* Colour Deconvolution Colour_Deconvolution.jar Gabriel Landini GPL 2 or later
* Dichromacy Dichromacy_.jar Gabriel Landini GPL 2 or later
* Differentials Differentials_.jar Philippe Thevenaz BIG (see below)
* Extended Depth of Focus Extended_Depth_Field.jar Alex Prudencio, Daniel Sage et al BIG (see below)
* Fiji_Plugins.jar Fiji_Plugins.jar Various authors PD,GPL
* Fiji as a framework The Fiji Team GPL
* Graph Cut Graph_Cut.jar Jan Funke GPL 2
* Helmholtz Analysis Helmholtz_Analysis.jar Bob Dougherty BSD
* ij-ImageIO ij-ImageIO_.jar Jarek Sacha LGPL
* ImageJ launcher ImageJ-{win*,linux*,macosx,tiger} Johannes Schindelin et al BSD
* ImageJA ij.jar Johannes Schindelin, Wayne Rasband PD
* imageware.jar imageware.jar Daniel Sage et al BIG (see below)
* Interactive 3D Surface Plot Interactive_3D_Surface_Plot.jar Kai Uwe Barthel PD
* iText itextpdf.jar Bruno Lowagie, Paulo Soares AGPL
* IO package IO_.jar A. Cardona, S. Saalfeld, J. Schindelin, G. Jefferis GPL/public domain
* IPLab Reader IPLab_Reader.jar Wayne Rasband PD
* Jacl jacl.jar BSD
* Java Compiler javac.jar OpenJDK GPL 2
* Java Expression Parser (JEP) jep.jar Nathan Funk, Richard Morris GPL
* Java Matrix package Jama.jar PD
* Javascript Rhino Engine js.jar MPL 1.1/GPL 2 see
* Javascript Interpreter Javascript_Interpreter.jar Albert Cardona GPL
* JFreeChart jfreechart.jar LGPL
* JGraphT jgrapht-jdk1.6.jar LGPL
* JGraphX jgraphx.jar BSD
* JPedal PDF library jpedalSTD.jar GPL/commercial
* JRuby Interpreter JRuby_Interpreter.jar Mark Longair GPL
* JRuby jruby.jar Thomas E. Enebo CPL/GPL/LGPL
* JSch jsch.jar JCraft BSD
* Jython jython.jar PSF 2/JSF 2.1/JPSL
* Jython Interpreter Jython_Interpreter.jar Albert Cardona GPL
* jzlib jzlib.jar ymnk BSD-like
* Kalman Stack Filter contained in Stack_Manipulation.jar Christopher Philip Mauer - BSD-like
* Kuwahara Filter Kuwahara_Filter.jar Wayne Rasband PD
* Multi Kymograph Multi_Kymograph.jar Jens Rietdorf & Arne Seitz BSD
* Linear Kuwahara Linear_Kuwahara.jar Christian Tischer GPL
* Local Thickness LocalThickness_.jar Bob Dougherty BSD
* LOCI loci_tools.jar Melissa Linkert, Curtis Rueden et al. GPL
* Macro Interpreter CLI_.jar Albert Cardona GPL
* Mines Java Toolkit edu_mines_jtk.jar Dave Hale CPL 1.0
* MosaicJ MosaicJ_.jar Philippe Thevenaz BIG (see below)
* MTrack2 MTrack2_.jar Nico Stuurman BSDR
* Multiple Image Processor M_I_P.jar Nathaniel Gonzalez Santiago GPL
* PAL Optimization pal-optimization.jar Alexei Drummond et al LGPL
* Panorama equirectangular view panorama_.jar Stephan Saalfeld GPL
* PDF Viewer PDF_Viewer.jar Albert Cardona GPL
* PointPicker PointPicker_.jar Philippe Thevenaz BIG (see below)
* PostgreSQL JDBC postgresql.jar BSD
* Register virtual stack slices register_virtual_stack_slices.jar Albert Cardona GPL
* Shepp-Logan Phantom SheppLogan_.jar Philippe Thevenaz BIG (see below)
* Sholl Analysis Sholl_Analysis.jar Tiago Ferreira, Tom Maddock GPL 3 or later
* Snakuscule Snakuscule_.jar Philippe Thevenaz BIG (see below)
* Stack Reverser Stack_Reverser.class Anthony Padua, Daniel Barboriak PD
* StackReg StackReg_.jar Philippe Thevenaz BIG (see below)
* Statistical Region Merging SRM_.jar Johannes Schindelin BSD
* Substack Maker Substack_Maker.class Wayne Rasband PD
* Threshold Colour Threshold_Colour.jar Gabriel Landini GPL 2 or later
* TrakEM2 TrakEM2_.jar Albert Cardona, Rodney Douglas GPL
* TurboReg TurboReg_.jar Philippe Thévenaz Citationware (see below)
* UnwarpJ UnwarpJ_.jar Carlos Oscar Sanchez Sorzano BIG (see below)
* VIB as VIB_.jar plugin bundle VIB_.jar, VIB-lib.jar J. Schindelin, Benjamin Schmid, M. Longair GPL
* Vaa3D Reader Vaa3D_Reader.jar Christopher M. Bruns BSD
* Video Editing Video_Editing.jar Benjamin Schmid GPL
* View5D View5D_.jar Rainer Heintzmann GPL 2
* Volume Calculator Volume_Calculator.jar Peter C. Marks BSD
* Volume Viewer / 3D Reslicer Volume_Viewer.jar Kai Uwe Barthel PD
* wavelets.jar wavelets.jar Daniel Sage et al BIG (see below)
TurboReg (Citationware):
On Wed, 18 Feb 2009, Philippe Thévenaz wrote:
> Dear Johannes Schindelin,
> You have my explicit placet to include TurboReg in Fiji.
Note that this blessing is for the (re)distribution within Fiji only.
JEP version included in Fiji is jep-2.4.1-ext-1.1.1-gpl. This version is the last to be distributed
under GPL. Subsequent versions (>3.0) have a commercial license.
BIG (Biomedical Imaging Group at the EPFL):
Date: Mon, 26 Jul 2010 10:58:20 +0200
From: Michael Unser <>
[...] we are happy that Fiji distributes our software: you have
my formal authorization for this (in my quality of lab chief).
"You'll be free to use this software for research purposes, but you
must not transmit and distribute it without our consent": this means
that from now on, you are authorized to distribute any ImageJ pluging
listed at since you have our
Multi Kymograph:
Date: Thu, 31 Mar 2011 09:10:32 +0000
From: Seitz Arne <>
as the plugin is rather simple I think BSD is then the license of
choice. Thanks for your input.
Cheers Arne
Unresolved (TODO):
* Example/ scripts folder
* Java Advanced Imaging jai_codec.jar, jai_core.jar, jai_imageio.jar