Skip to main content

Thank you for visiting nature.com. You are using a browser version with limited support for CSS. To obtain the best experience, we recommend you use a more up to date browser (or turn off compatibility mode in Internet Explorer). In the meantime, to ensure continued support, we are displaying the site without styles and JavaScript.

Icy: an open bioimage informatics platform for extended reproducible research

Nature Methods volume 9, pages 690–696 (2012)Cite this article

Subjects

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/.

This is a preview of subscription content, access via your institution

Relevant articles

Open Access articles citing this article.

Access options

Rent or buy this article

Prices vary by article type

from$1.95

to$39.95

Learn more

Prices may be subject to local taxes which are calculated during checkout

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

References

  1. Swedlow, J.R., Goldberg, I., Brauner, E. & Sorger, P.K. Informatics and quantitative analysis in biological imaging. Science 300, 100–102 (2003).

    Article  CAS  Google Scholar 

  2. Peng, H., Ruan, Z., Atasoy, D. & Sternson, S. Automatic reconstruction of 3D neuron structures using a graph-augmented deformable model. Bioinformatics 26, i38–i46 (2010).

    Article  CAS  Google Scholar 

  3. Kalinka, A.T. et al. Gene expression divergence recapitulates the developmental hourglass model. Nature 468, 811–814 (2010).

    Article  CAS  Google Scholar 

  4. Meijering, E. et al. Design and validation of a tool for neurite tracing and analysis in fluorescence microscopy images. Cytometry A 58, 167–176 (2004).

    Article  CAS  Google Scholar 

  5. Zimmer, C. et al. On the digital trail of mobile cells. IEEE Signal Process. Mag. 23, 54–62 (2006).

    Article  Google Scholar 

  6. Chenouard, N., Dufour, A. & Olivo-Marin, J.-C. Tracking algorithms chase down pathogens. Biotechnol. J. 4, 838–845 (2009).

    Article  CAS  Google Scholar 

  7. Fomel, S. & Claerbout, J. Introduction: reproducible research. Comput. Sci. Eng. 11, 5–7 (2009).

    Article  Google Scholar 

  8. Ince, D.C., Hatton, L. & Graham-Cumming, J. The case for open computer programs. Nature 482, 485–488 (2012).

    Article  CAS  Google Scholar 

  9. Vandewalle, P., Kovacevic, J. & Vetterli, M. Reproducible research in signal processing—what, why, and how. IEEE Signal Process. Mag. 26, 37–47 (2009).

    Article  Google Scholar 

  10. Allan, C. et al. OMERO: flexible, model-driven data management for experimental biology. Nat. Methods 9, 245–253 (2012).

    Article  CAS  Google Scholar 

  11. Abramoff, M.D., Magalhaes, P.J. & Ram, S.J. Image Processing with ImageJ. Biophotonics Int. 11, 36–42 (2004).

    Google Scholar 

  12. Schindelin, J. et al. Fiji: an open-source platform for biological-image analysis. Nat. Methods 9, 676–682 (2012).

    Article  CAS  Google Scholar 

  13. Carpenter, A.E. et al. CellProfiler: image analysis software for identifying and quantifying cell phenotypes. Genome Biol. 7, R100 (2006).

    Article  Google Scholar 

  14. Kankaanpää, P. et al. BioImageXD: an open, general-purpose and high-throughput image-processing platform. Nat. Methods 9, 683–689 (2012).

    Article  Google Scholar 

  15. Olivo-Marin, J.-C. Extraction of spots in biological images using multiscale products. Pattern Recognit. 35, 1989–1996 (2002).

    Article  Google Scholar 

  16. Cabal, G. et al. SAGA interacting factors confine sub-diffusion of transcribed genes to the nuclear envelope. Nature 441, 770–773 (2006).

    Article  CAS  Google Scholar 

  17. Alonso, M. et al. Olfactory discrimination learning increases the survival of adult-born neurons in the olfactory bulb. J. Neurosci. 26, 10508–10513 (2006).

    Article  CAS  Google Scholar 

  18. Grassart, A. et al. Pak1 phosphorylation enhances cortactin–N-WASP interaction in clathrin-caveolin-independent endocytosis. Traffic 11, 1079–1091 (2010).

    Article  CAS  Google Scholar 

  19. Genovesio, A. et al. Multiple particle tracking in 3D+t microscopy: method and application to the tracking of endocytozed quantum dots. IEEE Trans. Image Process. 15, 1062–1070 (2006).

    Article  Google Scholar 

  20. Arhel, N. et al. Quantitative four-dimensional tracking of cytoplasmic and nuclear HIV-1 complexes. Nat. Methods 3, 817–824 (2006).

    Article  CAS  Google Scholar 

  21. Gousset, K. et al. Prions hijack tunneling nanotubes for intercellular spread. Nat. Cell Biol. 11, 328–336 (2009).

    Article  CAS  Google Scholar 

  22. Nicolas, E., Chenouard, N., Olivo-Marin, J.-C. & Guichet, A. A dual role for actin and microtubule cytoskeleton in the transport of golgi units from the nurse cells to the oocyte across ring canals. Mol. Biol. Cell 20, 556–568 (2009).

    Article  CAS  Google Scholar 

  23. Zimmer, C. & Olivo-Marin, J.-C. Coupled parametric active contours. IEEE Trans. Pattern Anal. Mach. Intell. 27, 1838–1842 (2005).

    Article  Google Scholar 

  24. Dufour, A. et al. Segmenting and tracking fluorescent cells in dynamic 3-D microscopy with coupled active surfaces. IEEE Trans. Image Process. 14, 1396–1410 (2005).

    Article  Google Scholar 

  25. Dufour, A., Thibeaux, R., Labruyère, E., Guillén, N. & Olivo-Marin, J.-C. 3-D active meshes: fast discrete deformable models for cell tracking in 3-D time-lapse microscopy. IEEE Trans. Image Process. 20, 1925–1937 (2011).

    Article  Google Scholar 

  26. Melki, M.-T., Saïdi, H., Dufour, A., Olivo-Marin, J.-C. & Gougeon, M.-L. Escape of HIV-1-infected dendritic cells from TRAIL-Mediated NK cell cytotoxicity. A pivotal role of HMGB1. PLoS Pathog. 6, e1000862 (2010).

    Article  Google Scholar 

  27. Blazquez, S. et al. Human tumor necrosis factor is a chemoattractant for the parasite Entamoeba histolytica. Infect. Immun. 74, 1407–1411 (2006).

    Article  CAS  Google Scholar 

  28. Thibeaux, R. et al. Newly visualized fibrillar collagen scaffolds dictate Entamoeba histolytica invasion route in the human colon. Cell. Microbiol. 14, 609–621 (2012).

    Article  CAS  Google Scholar 

  29. de Chaumont, F. et al. Computerized video analysis of social interactions in mice. Nat. Methods 9, 410–417 (2012).

    Article  CAS  Google Scholar 

Download references

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).

Author information

Authors and 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
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Stéphane Dallongeville
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Nicolas Chenouard
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. Nicolas Hervé
    View author publications

    You can also search for this author in PubMed Google Scholar

  5. Sorin Pop
    View author publications

    You can also search for this author in PubMed Google Scholar

  6. Thomas Provoost
    View author publications

    You can also search for this author in PubMed Google Scholar

  7. Vannary Meas-Yedid
    View author publications

    You can also search for this author in PubMed Google Scholar

  8. Praveen Pankajakshan
    View author publications

    You can also search for this author in PubMed Google Scholar

  9. Timothée Lecomte
    View author publications

    You can also search for this author in PubMed Google Scholar

  10. Yoann Le Montagner
    View author publications

    You can also search for this author in PubMed Google Scholar

  11. Thibault Lagache
    View author publications

    You can also search for this author in PubMed Google Scholar

  12. Alexandre Dufour
    View author publications

    You can also search for this author in PubMed Google Scholar

  13. Jean-Christophe Olivo-Marin
    View author publications

    You can also search for this author in PubMed Google Scholar

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.

Ethics declarations

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)

Rights and permissions

Reprints and Permissions

About this article

Cite this article

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

Download citation

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1038/nmeth.2075

This article is cited by

Search

Advanced search

Quick links

Nature Briefing

Sign up for the Nature Briefing newsletter — what matters in science, free to your inbox daily.

Get the most important science stories of the day, free in your inbox. Sign up for Nature Briefing