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LICENSES
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.
Abbreviations:
* GPL: General Public License (latest) as specified at http://www.gnu.org/licenses/gpl.txt
* GPL 2: General Public License version 2
* LGPL: Lesser General Public License as specified at http://www.gnu.org/licenses/lgpl.html
* AGPL: Affero General Public License as specified at http://www.gnu.org/licenses/agpl.html
* PD: Public Domain
* CPL 1.0: Common Public License 1.0 (http://eclipse.org/legal/cpl-v10.html)
* 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 http://www.lowagie.com/iText/MPL-1.1.txt
* BSD: Berkeley Software Distribution
* BSDR: BSD-like license allowing use for research
* EPL: Eclipse Public License (http://opensource.org/licenses/eclipse-1.0.php)
* AL: Apache License (http://xmlgraphics.apache.org/batik/license.html)
* ?: UNKNOWN
Name File Author(s) Contact License
---- ---- --------- -------------- -------
* Anisotropic Diffusion 2D Anisotropic_Diffusion_2D.jar http://rsb.info.nih.gov/ij/plugins/download/Anisotropic_Diffusion_2D.java GPL
* Balloon Segmentation BalloonSegmentation_.jar Lionel Dupuy Lionel.Dupuy@hutton.ac.uk GPL
* Batik batik.jar http://xmlgraphics.apache.org/batik/contributors.html AL
* Bean Shell language bsh.jar http://www.beanshell.org/ SPL/LGPL
* Bean Shell Interpreter BSH_Interpreter.jar Johannes Schindelin Johannes.Schindelin@gmx.de GPL
* Bleach Corrector CorrectBleach_.jar Kota Miura miura@embl.de GPL
* Bug Submitter Bug_Submitter.jar Mark Longair, Johannes Schindelin, Curtis Rueden http://fiji.sc/ BSD
* bUnwarpJ bUnwarpJ_.jar Ignacio Arganda et al. ignacio.arganda@uam.es GPL
* Clojure clojure.jar Rich Hickey http://clojure.sourceforge.net/ EPL
* Clojure Interpreter Clojure_Interpreter.jar Albert Cardona acardona@ini.phys.ethz.ch GPL
* Color Histogram Color_Histogram.jar Dimiter Prodanov dimiterpp@gmail.com GPL 2
* Color Inspector 3D Color_Inspector_3D.jar Kai Uwe Barthel k.barthel@fhtw-berlin.de PD
* Colour Deconvolution Colour_Deconvolution.jar Gabriel Landini G.Landini@bham.ac.uk GPL 2 or later
* Dichromacy Dichromacy_.jar Gabriel Landini G.Landini@bham.ac.uk GPL 2 or later
* Differentials Differentials_.jar Philippe Thevenaz http://bigwww.epfl.ch/thevenaz/differentials/ BIG (see below)
* Extended Depth of Focus Extended_Depth_Field.jar Alex Prudencio, Daniel Sage et al http://bigwww.epfl.ch/demo/edf/ BIG (see below)
* FeatureJ FeatureJ_.jar Erik Meijering http://www.imagescience.org/meijering/software/featurej/ imagescience (see below)
* Fiji_Plugins.jar Fiji_Plugins.jar Various authors http://fiji.sc/Contributors PD,GPL
* Fiji as a framework The Fiji Team fiji-devel@googlegroups.com GPL
* Graph Cut Graph_Cut.jar Jan Funke jan.funke@inf.tu-dresden.de GPL 2
* Helmholtz Analysis Helmholtz_Analysis.jar Bob Dougherty rpd@optinav.com BSD
* ij-ImageIO ij-ImageIO_.jar Jarek Sacha jarek@ieee.org LGPL
* ImageJ launcher ImageJ-{win*,linux*,macosx,tiger} Johannes Schindelin et al fiji@googlegroups.com BSD
* ImageJA ij.jar Johannes Schindelin, Wayne Rasband Johannes.Schindelin@gmx.de PD
* imagescience.jar imagescience.jar Erik Meijering meijering@imagescience.org imagescience (see below)
* imageware.jar imageware.jar Daniel Sage et al http://bigwww.epfl.ch/ BIG (see below)
* Interactive 3D Surface Plot Interactive_3D_Surface_Plot.jar Kai Uwe Barthel k.barthel@fhtw-berlin.de PD
* iText itextpdf.jar Bruno Lowagie, Paulo Soares http://itextpdf.com/terms-of-use/index.php AGPL
* IO package IO_.jar A. Cardona, S. Saalfeld, J. Schindelin, G. Jefferis acardona@ini.phys.ethz.ch GPL/public domain
* IPLab Reader IPLab_Reader.jar Wayne Rasband wsr@nih.gov PD
* Jacl jacl.jar http://sourceforge.net/projects/tcljava BSD
* Java Compiler javac.jar OpenJDK http://hg.openjdk.java.net/jdk6/jdk6/langtools GPL 2
* Java Expression Parser (JEP) jep.jar Nathan Funk, Richard Morris http://www.singularsys.com/jep/ GPL
* Java Matrix package Jama.jar http://math.nist.gov/javanumerics/jama/#Authors http://math.nist.gov/javanumerics/jama/#Authors PD
* Javascript Rhino Engine js.jar http://www.mozilla.org/rhino/ http://www.mozilla.org/rhino/ MPL 1.1/GPL 2 see http://developer.mozilla.org/en/docs/Rhino_License
* Javascript Interpreter Javascript_Interpreter.jar Albert Cardona acardona@ini.phys.ethz.ch GPL
* JFreeChart jfreechart.jar http://www.jfree.org/jfreechart/ http://www.jfree.org/jfreechart/ LGPL
* JGraphT jgrapht-jdk1.6.jar http://jgrapht.org/ http://jgrapht.org/ LGPL
* JGraphX jgraphx.jar http://www.jgraph.com/ http://www.jgraph.com/ BSD
* JPedal PDF library jpedalSTD.jar http://www.jpedal.org/ http://www.jpedal.org/ GPL/commercial
* JRuby Interpreter JRuby_Interpreter.jar Mark Longair Mark.Longair@ed.ac.uk GPL
* JRuby jruby.jar Thomas E. Enebo http://jruby.codehaus.org/ CPL/GPL/LGPL
* JSch jsch.jar JCraft http://www.jcraft.com/jsch/ BSD
* Jython jython.jar http://www.jython.org/Project/contributors.html http://www.jython.org PSF 2/JSF 2.1/JPSL
* Jython Interpreter Jython_Interpreter.jar Albert Cardona acardona@ini.phys.ethz.ch GPL
* jzlib jzlib.jar ymnk jzlib@jcraft.com BSD-like http://www.jcraft.com/jzlib/LICENSE.txt
* Kalman Stack Filter contained in Stack_Manipulation.jar Christopher Philip Mauer - BSD-like
* Kuwahara Filter Kuwahara_Filter.jar Wayne Rasband http://imagej.nih.gov/ij/plugins/kuwahara.html PD
* MTrackJ MTrackJ_.jar Erik Meijering http://www.imagescience.org/meijering/software/mtrackj/ imagescience (see below)
* Multi Kymograph Multi_Kymograph.jar Jens Rietdorf & Arne Seitz http://www.embl.de/eamnet/html/body_kymograph.html BSD
* Linear Kuwahara Linear_Kuwahara.jar Christian Tischer GPL
* Local Thickness LocalThickness_.jar Bob Dougherty rpd@optinav.com BSD
* LOCI loci_tools.jar Melissa Linkert, Curtis Rueden et al. ctrueden@wisc.edu GPL
* Macro Interpreter CLI_.jar Albert Cardona acardona@ini.phys.ethz.ch GPL
* Mines Java Toolkit edu_mines_jtk.jar Dave Hale http://www.mines.edu/~dhale/jtk/ CPL 1.0
* MosaicJ MosaicJ_.jar Philippe Thevenaz http://bigwww.epfl.ch/thevenaz/mosaicj/ BIG (see below)
* MTrack2 MTrack2_.jar Nico Stuurman http://valelab.ucsf.edu/~nico/IJplugins/MTrack2.html BSDR
* Multiple Image Processor M_I_P.jar Nathaniel Gonzalez Santiago http://ciar.rcm.upr.edu/projects/imageprocessor/multiples/ GPL
* PAL Optimization pal-optimization.jar Alexei Drummond et al http://ftp.cse.sc.edu/bioinformatics/PAL/pal-1.4/doc/index.html LGPL
* Panorama equirectangular view panorama_.jar Stephan Saalfeld http://fly.mpi-cbg.de/~saalfeld/Projects/panorama.html GPL
* PDF Viewer PDF_Viewer.jar Albert Cardona acardona@ini.phys.ethz.ch GPL
* PointPicker PointPicker_.jar Philippe Thevenaz http://bigwww.epfl.ch/thevenaz/pointpicker/ BIG (see below)
* PostgreSQL JDBC postgresql.jar http://jdbc.postgresql.org/ http://jdbc.postgresql.org/ BSD
* RandomJ RandomJ_.jar Erik Meijering http://www.imagescience.org/meijering/software/randomj/ imagescience (see below)
* Register virtual stack slices register_virtual_stack_slices.jar Albert Cardona acardona@ini.phys.ethz.ch GPL
* Shepp-Logan Phantom SheppLogan_.jar Philippe Thevenaz http://bigwww.epfl.ch/thevenaz/shepplogan/ BIG (see below)
* Sholl Analysis Sholl_Analysis.jar Tiago Ferreira, Tom Maddock http://fiji.sc/Sholl_Analysis GPL 3 or later
* Snakuscule Snakuscule_.jar Philippe Thevenaz http://bigwww.epfl.ch/thevenaz/snakuscule/ BIG (see below)
* Stack Reverser Stack_Reverser.class Anthony Padua, Daniel Barboriak http://rsb.info.nih.gov/ij/plugins/substack-maker.html PD
* StackReg StackReg_.jar Philippe Thevenaz http://bigwww.epfl.ch/thevenaz/stackreg/ BIG (see below)
* Statistical Region Merging SRM_.jar Johannes Schindelin http://fiji.sc/Statistical_Region_Merging BSD
* Substack Maker Substack_Maker.class Wayne Rasband http://rsb.info.nih.gov/ij/plugins/reverser.html PD
* Threshold Colour Threshold_Colour.jar Gabriel Landini G.Landini@bham.ac.uk GPL 2 or later
* TransformJ TransformJ_.jar Erik Meijering http://www.imagescience.org/meijering/software/transformj/ imagescience (see below)
* TrakEM2 TrakEM2_.jar Albert Cardona, Rodney Douglas acardona@ini.phys.ethz.ch GPL
* TurboReg TurboReg_.jar Philippe Thévenaz philippe.thevenaz@epfl.ch Citationware (see below)
* UnwarpJ UnwarpJ_.jar Carlos Oscar Sanchez Sorzano http://bigwww.epfl.ch/thevenaz/UnwarpJ/ BIG (see below)
* VIB as VIB_.jar plugin bundle VIB_.jar, VIB-lib.jar J. Schindelin, Benjamin Schmid, M. Longair bene.schmid@gmail.com GPL
* Vaa3D Reader Vaa3D_Reader.jar Christopher M. Bruns christopher.bruns@gmail.com BSD
* Video Editing Video_Editing.jar Benjamin Schmid bene.schmid@gmail.com GPL
* View5D View5D_.jar Rainer Heintzmann heintzmannd@gmail.com GPL 2
* Volume Calculator Volume_Calculator.jar Peter C. Marks peter.c.marks@gmail.com BSD
* Volume Viewer / 3D Reslicer Volume_Viewer.jar Kai Uwe Barthel k.barthel@fhtw-berlin.de PD
* wavelets.jar wavelets.jar Daniel Sage et al http://bigwww.epfl.ch/ 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 <michael.unser@epfl.ch>
[...] 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 http://bigwww.epfl.ch/algorithms.html since you have our
consent.
imagescience (Erik Meijering; http://www.imagescience.org/meijering/software/):
Date: Fri, 17 Sep 2010 13:47:28 +0200
From: Erik Meijering <meijering@imagescience.org>
[...] Nice to hear from you. Yes, you have my permission to redistribute
TransformJ (and also FeatureJ and RandomJ if you're interested) as part of
Fiji. That would be great!
Best wishes,
Erik
Multi Kymograph:
Date: Thu, 31 Mar 2011 09:10:32 +0000
From: Seitz Arne <arne.seitz@epfl.ch>
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
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