Icy: an open bioimage informatics platform for extended reproducible research

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.

References

  1. 1

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

    CAS  Article  Google Scholar 

  2. 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).

    CAS  Article  Google Scholar 

  3. 3

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

    CAS  Article  Google Scholar 

  4. 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).

    CAS  Article  Google Scholar 

  5. 5

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

    Article  Google Scholar 

  6. 6

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

    CAS  Article  Google Scholar 

  7. 7

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

    Article  Google Scholar 

  8. 8

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

    CAS  Article  Google Scholar 

  9. 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. 10

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

    CAS  Article  Google Scholar 

  11. 11

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

    Google Scholar 

  12. 12

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

    CAS  Article  Google Scholar 

  13. 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. 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. 15

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

    Article  Google Scholar 

  16. 16

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

    CAS  Article  Google Scholar 

  17. 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).

    CAS  Article  Google Scholar 

  18. 18

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

    CAS  Article  Google Scholar 

  19. 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. 20

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

    CAS  Article  Google Scholar 

  21. 21

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

    CAS  Article  Google Scholar 

  22. 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).

    CAS  Article  Google Scholar 

  23. 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. 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. 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. 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. 27

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

    CAS  Article  Google Scholar 

  28. 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).

    CAS  Article  Google Scholar 

  29. 29

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

    CAS  Article  Google Scholar 

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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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Authors

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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The authors declare no competing financial interests.

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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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