Icy: an open bioimage informatics platform for extended reproducible research


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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Figure 1: Icy graphical user interface.
Figure 2: Protocol development through protocol editor.


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This work was supported in part by the Institut Pasteur and by the Centre National de la Recherche Scientifique. It was also supported in part by a grant from the Agence Nationale de la Recherche (ANR-10-INBS-04-06 FranceBioImaging).

Author information




F.d.C. and J.-C.O.-M. conceived the project. F.d.C. and S.D. conceived and implemented the core application. F.d.C. conceived the online structure. A.D. conceived EzPlug and the protocols. F.d.C., S.D., N.C., N.H., S.P., T.P., V.M.-Y., P.P., T.L., Y.L., T.L. and A.D. wrote Icy plug-ins. J.-C.O.-M. supervised the design of Icy. F.d.C., A.D. and J.-C.O.-M. wrote the manuscript.

Corresponding authors

Correspondence to Fabrice de Chaumont or Jean-Christophe Olivo-Marin.

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The authors declare no competing financial interests.

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Supplementary Figures 1–2, Supplementary Table 1 (PDF 257 kb)

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de Chaumont, F., Dallongeville, S., Chenouard, N. et al. Icy: an open bioimage informatics platform for extended reproducible research. Nat Methods 9, 690–696 (2012). https://doi.org/10.1038/nmeth.2075

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