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Icy - copyright 2021 - Institut Pasteur
An open community platform for bio image analysis - http://icy.bioimageanalysis.org
# Icy, a bioimage analysis software
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
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Source code is available on the GitLab repository: https://gitlab.pasteur.fr/bia/icy
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](https://research.pasteur.fr/en/team/bioimage-analysis/). Icy is free and open source (**GPL3 license**). It has been funded both by Institut Pasteur and [France Bioimaging consortium](https://france-bioimaging.org). You can find more info and download Icy on the [Icy website](http://icy.bioimageanalysis.org/).
## Description
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 :)
**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](https://research.pasteur.fr/en/team/bioimage-analysis/)**. 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](http://icy.bioimageanalysis.org/developer/using-image-cursors-when-developing-plugins/).
Contributors
------------
## Installation
Kernel architecture and code
Stephane Dallongeville and Fabrice de Chaumont
As user of the application: [download Icy from the Icy website](http://icy.bioimageanalysis.org/download/) and follow the [installation instructions](http://icy.bioimageanalysis.org/tutorial/installation-instructions-for-icy-software/). You can reach the Icy development team to report a bug or ask for a new feature via the [image.sc forum](https://forum.image.sc/). For bug or feature request related questions, choose the "Usage and Issue" category. For more general questions, use the "Image Analysis" category. In any cases, don't forget the tag "icy".
Website graphic design
Marcio de Moraes Marim
As developer willing to contribute to the kernel or to write a plugin for Icy, please get started by reading our blog posts on [how to set your development environment for Icy](http://icy.bioimageanalysis.org/developer/setting-icy-development-environment/), [how to create a new Icy plugin](http://icy.bioimageanalysis.org/developer/create-a-new-icy-plugin/) and [how to migrate your old Icy plugin to Maven](http://icy.bioimageanalysis.org/developer/migrate-your-old-icy-plugin-to-maven/). You can reach the Icy development team via the [image.sc forum](https://forum.image.sc/). For development related questions, choose the "Development" category and don't forget the tag "icy".
Website code
Fabrice de Chaumont / Marcio de Moraes Marim
Last but not least, we invite you to read our [Contributing guidelines](https://gitlab.pasteur.fr/bia/icy/-/blob/master/CONTRIBUTING.md) and our [Code of Conduct](https://gitlab.pasteur.fr/bia/icy/-/blob/master/CODE-OF-CONDUCT.md).
EzPlug and Protocols (as many others plugins)
Alexandre Dufour
## Documentation
Scripting
Thomas Provoost, Timothee Lecomte and Stephane Dallongeville
Plugin documentation for users is hosted on the Icy website, in the [Resources category](http://icy.bioimageanalysis.org/plugins/). General documentation is available in the [Training category](http://icy.bioimageanalysis.org/trainings/). You can also have a look at the article on [how to get help on the Icy software](http://icy.bioimageanalysis.org/tutorial/how-to-get-help-on-icy/).
For developers, there is also an [Icy Javadoc](http://icy.bioimageanalysis.org/javadoc/).
MicroManager for Icy
Thomas Provoost, Irsath Nguyen and Stephane Dallongeville
Head of unit
Jean-Christophe Olivo-Marin
## Citation information
Many thanks to beta testers and contributors
Nicolas Chenouard
Alexandre Dufour
Nicolas Herve
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)
de Chaumont, F. et al. (2012) Icy: an open bioimage informatics platform for extended reproducible research, [Nature Methods](https://www.nature.com/articles/nmeth.2075), 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.
## Acknowledgements to main kernel and main plugins contributors
We acknowledge every person who contributed one way or another to make Icy what is now, in particular:
*Kernel architecture and code*: Stephane Dallongeville and Fabrice de Chaumont
*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](http://bigwww.epfl.ch/)
*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**](http://icy.bioimageanalysis.org/contributors/) to the Icy software. Contributions include kernel development, plugin development, protocol creation, blog post writing...
<!-- 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) -->
## Main 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)
- [EHCache](https://www.ehcache.org/)
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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
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.
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