Software / Libraries


Icy

dscho's picture

Reproducing an experiment doesn’t stop at the bench when images are concerned. Icy is an open source bioimaging software package that aims to provide a framework for authors to share, and others to reproduce, research once the sample hits the microscope. Icy was released in April 2011 and is being developed at the Quantitative Image Analysis Unit at the Pasteur Institute in France by Jean-Christophe Olivo-Marin and his team. The goal is to provide standardized software architecture, with a visual programming framework and online repository of plugins and protocols, brought together with sophisticated content-management and communication systems for such extended reproducible research.
Icy provides intuitive user interfaces for graphical protocol development for image acquisition, analysis and storage that are easy to use for biologists and developers alike. Developers should find that Icy’s ‘EzPlug’ API library, versioning, and auditing tools make creating a custom plugin from most any source easy. Users will find the automatic error reporting, central repository and on-line community hub great for storing and sharing plugins and protocols. Icy is even developing a cloud-computing framework to address the scalability issues of high-content screening.
As of this writing there are 207 plug-ins 50 scripts and 14 protocols available for download, including those for microscope control, particle tracking, three dimensional segmentation, and even spot detection using wavelets.
Published in Nature Methods (Nat Methods 9(7):690-6 (2012)).
Icy can be downloaded at http://icy.bioimageanalysis.org/
Strength:

  • Open-source.
  • Centralized repository of 205 plugins, 50 scripts and 14 protocols
  • Rate and comment plugins
  • 5D
  • Search and install features directly from Icy
  • Graphical programming with protocols
  • Write scripts in javascript or python
  • Automatic bug reports
  • Native ImageJ integration 100% compatible
  • Native Micro-Manager integration
  • Share your plugins and protocols online
  • Can run headless
  • Intuitive user interface
  • Online management of plugins
  • Connect Icy to Matlab
  • Interactive widgets
  • Build your graphical interface with EzPlug
  • Use the power of your graphic card with OpenCL
  • Loaded with 20 up-to date libs

Weaknesses

License: 
GPLv3
References: 
doi:10.1038/nmeth.2075
Ecosystem: 
Java
Platform(s): 
Win32/64-OSX-Linux
Target Audience(s): 
Analyst / User
Type(s): 
Application
Rating: 
0
No votes yet
Author(s): 
Fabrice de Chaumont and Stephane Dallongeville