This is the repository for the source code of the Icy kernel, which was developed and is maintained by the Biological Image Analysis unit at Institut Pasteur. Icy is free and open source (LGPL3 license). It has been funded both by Institut Pasteur and France Bioimaging consortium. You can find more info and download Icy on the Icy website.
Icy is a software to do image analysis,and is mainly oriented toward the analysis of biological images. It was developed as a toolbox containing state-of-the-art methods, like the Gaussian filter, and latest algorithmic developments of the Biological Image Analysis unit at Institut Pasteur. It was also developed as a platform to gather and favor the exchanges between biologists, computer vision scientists, bioimage analysts and developers. It notably has a righ graphical interface to ease the integration of non programming users, as well as possibility for more advanced users to do scripting (in Javascript), graphical programming using the Protocols tool and development of Java plugins. Last but not least, Icy was developed to promote quantitative analysis of biological images and reproducibility of analyses. It includes many possibilities to save and reuse parameters and even save and reuse complete workflows.
In terms of development environment, Icy is coded in Java and uses a Maven project environment. It is a modular software composed of a kernel and plugins. The kernel contains the main functions related to graphical user interface, image visualization (2D and 3D), regions of interest with statistics and basics image data manipulation tools such as image cursors.
Download source code execute mvn copy the content of ./build/icy/ in your dev folder execute icy.jar from Eclipse or IntelliJ
Plugin documentation for users is hosted on the Icy website, in the Resources category. General documentation is available in the Training category. You can also have a look at the article on how to get help on the Icy software.
For developers, there is also an Icy Javadoc.
de Chaumont, F. et al. (2012) Icy: an open bioimage informatics platform for extended reproducible research, Nature Methods, 9, pp. 690-696
https://icy.bioimageanalysis.org
Please mention the version of Icy you used (bottom right corner of the GUI or first lines of the Output tab). Don't forget to also cite the plugins you use.
We acknowledge every person who contributed one way or another to make Icy what is now, in particular:
Kernel architecture and code: Stephane Dallongeville, Fabrice de Chaumont and Thomas Musset
Head of unit hosting the Icy project: Jean-Christophe Olivo-Marin
EzPlug and Protocols (as many others plugins): Alexandre Dufour
Scripting: Thomas Provoost, Timothee Lecomte and Stephane Dallongeville
MicroManager for Icy: Thomas Provoost, Irsath Nguyen and Stephane Dallongeville
Beta testers and main contributors: Nicolas Chenouard, Alexandre Dufour, Nicolas Herve, Vannary Meas-Yedid, Sorin Pop, Thibault Lagache, Jérôme Mutterer and the Biomedical Imaging Group
Icy website graphic design: Marcio de Moraes Marim
Icy website code: Fabrice de Chaumont / Marcio de Moraes Marim
The Icy website hosts a detailed list of all contributors to the Icy software. Contributions include kernel development, plugin development, protocol creation, blog post writing...