Icy: an open bioimage informatics platform for extended reproducible research

Nature Methods volume 9, pages690–696(2012)Cite this article

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

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Acknowledgements

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).

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Affiliations

  1. Institut Pasteur, Unité d'Analyse d'Images Quantitative, Centre National de la Recherche Scientifique, Unité de Recherche Associée 2582, Paris, France

    Fabrice de Chaumont, 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

Authors
  1. Fabrice de Chaumont
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  2. Stéphane Dallongeville
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  3. Nicolas Chenouard
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  4. Nicolas Hervé
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  5. Sorin Pop
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  6. Thomas Provoost
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  7. Vannary Meas-Yedid
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  8. Praveen Pankajakshan
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  9. Timothée Lecomte
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  10. Yoann Le Montagner
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  11. Thibault Lagache
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  12. Alexandre Dufour
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  13. Jean-Christophe Olivo-Marin
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Contributions

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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Competing interests

The authors declare no competing financial interests.

Supplementary information

Supplementary Text and Figures

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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