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README.txt
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README.txt
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Icy - copyright 2019 - Institut Pasteur
An open community platform for bio image analysis - http://icy.bioimageanalysis.org
Icy has been created by the Bio Image Analysis team at Institut Pasteur - https://research.pasteur.fr/fr/team/bioimage-analysis
Icy is free and open source, it has been funded both by Institut Pasteur and the FBI consortium - https://france-bioimaging.org
Source code is provided in the main application package (in the icy.jar archive file) but can also be found on the GitHub repository - https://github.com/Icy-imaging/Icy-Kernel
Note for OSX users
------------------
First, you need to have java installed on your system. Sometime java is installed but just for web applications (JRE) in which case you need to install the JDK 8 for Mac OSX.
We strongly recommend to keep JDK 8 which is more stable than newer version of Java (9 or above) so if possible try to keep Java 8 as the default version.
Then be sure to have Icy installed in Applications folder. The first time you try to launch the application it may not work because of the default Security preferences.
You can force it by doing right click on the application icon (or Ctrl+click) and use 'Open' command, then validate the operation. You should now be able to use Icy normally :)
Contributors
------------
Kernel architecture and code
Stephane Dallongeville and Fabrice de Chaumont
Website graphic design
Marcio de Moraes Marim
Website code
Fabrice de Chaumont
EzPlug and Protocols (as many others plugins)
Alexandre Dufour
Scripting
Thomas Provoost, Timothée Lecomte and Stephane Dallongeville
MicroManager for Icy
Thomas Provoost, Irsath Nguyen and Stephane Dallongeville
Head of unit
Jean-Christophe Olivo-Marin
Many thanks to beta testers and contributors
Nicolas Chenouard
Alexandre Dufour
Nicolas Hervé
Vannary Meas-Yedid
Sorin Pop
Thibault Lagache
Biomedical Imaging Group - http://bigwww.epfl.ch/
M. Geissbuehler and T. Lasser - http://www.opticsinfobase.org/oe/abstract.cfm?URI=oe-21-8-9862
"How to display data by color schemes compatible with red-green color perception deficiencies" Opt. Express 21, 9862-9874 (2013)
Libraries used in Icy
Bio-Formats - http://www.openmicroscopy.org/site/products/bio-formats
VTK - http://www.vtk.org/
Substance / Insubstancial - https://github.com/Insubstantial/insubstantial
Flanagan - http://www.ee.ucl.ac.uk/~mflanaga/java/
Jama - http://math.nist.gov/javanumerics/jama/
JFreeChart - http://www.jfree.org/jfreechart/
JTransforms - https://sites.google.com/site/piotrwendykier/software/jtransforms
Xuggler - http://www.xuggle.com/xuggler/
Libraries/tools integrated within the Icy website
phpBB - TinyMCE
Development tool for profiling/debugging
YourKit is kindly supporting open source projects with its full-featured Java Profiler.
YourKit, LLC is the creator of innovative and intelligent tools for profiling Java and .NET applications.
Take a look at YourKit's leading software products: YourKit Java Profiler and YourKit .NET Profiler.