Icy: an open bioimage informatics platform for extended reproducible research - PubMed (original) (raw)

. 2012 Jun 28;9(7):690-6.

doi: 10.1038/nmeth.2075.

Stéphane Dallongeville, Nicolas Chenouard, Nicolas Hervé, Sorin Pop, Thomas Provoost, Vannary Meas-Yedid, Praveen Pankajakshan, Timothée Lecomte, Yoann Le Montagner, Thibault Lagache, Alexandre Dufour, Jean-Christophe Olivo-Marin

Affiliations

• PMID: 22743774
• DOI: 10.1038/nmeth.2075

Icy: an open bioimage informatics platform for extended reproducible research

Fabrice de Chaumont et al. Nat Methods. 2012.

Abstract

Current research in biology uses evermore complex computational and imaging tools. Here we describe Icy, a collaborative bioimage informatics platform that combines a community website for contributing and sharing tools and material, and software with a high-end visual programming framework for seamless development of sophisticated imaging workflows. Icy extends the reproducible research principles, by encouraging and facilitating the reusability, modularity, standardization and management of algorithms and protocols. Icy is free, open-source and available at http://icy.bioimageanalysis.org/.

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References

1. 1. Nature. 2010 Dec 9;468(7325):811-4 - PubMed
2. 1. IEEE Trans Image Process. 2005 Sep;14(9):1396-410 - PubMed
3. 1. J Neurosci. 2006 Oct 11;26(41):10508-13 - PubMed
4. 1. Nat Methods. 2012 Jun 28;9(7):676-82 - PubMed
5. 1. IEEE Trans Pattern Anal Mach Intell. 2005 Nov;27(11):1838-42 - PubMed

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