Icy
Type
Programming Language
Interaction Level
License/Openness
License
GPLv3
Description
Reproducing an experiment doesnt 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 Icys 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
No tutorial for plugins writing..yet
See here:
http://icy.bioimageanalysis.org/index.php?display=devDoc
http://icy.bioimageanalysis.org/index.php?display=detailTag&tagId=29
and here:
http://icy.bioimageanalysis.org/index.php?display=startDevWithIcy
and also here:
http://icy.bioimageanalysis.org/index.php?display=startDevWithIcy
Image size limited to 2GigaByte per single 2D channel (means that an image of 40.000x40.000 can be handle by Icy. Still big !) Still you can have a stack of 100000x40Kx40kxUnlimited number of channel if you have RAM. Will be improved
Entry Curator
migration
Post date
10/15/2013 - 20:19
Last modified
09/12/2017 - 10:23