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eC-CLEM: flexible multidimensional registration software for correlative microscopies

Nature Methods volume 14, pages 102103 (2017) | Download Citation

  • A Corrigendum to this article was published on 28 February 2017

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  • 10 February 2017

    In the version of this piece initially published, Xavier Heiligenstein, Graça Raposo, and Jean Salamero were affiliated with Structure Fédérative de Recherche François Bonamy, INSERM, CNRS, Universiteacute; de Nantes, Nantes, France in error. These affiliations have been removed. The grant number ANR-10-INSB-04 was incorrect; it has been replaced with the correct grant number, ANR-10-INBS-04. The errors have been corrected in the HTML and PDF versions of the piece as of 10 February 2017.


  1. 1.

    , & Nat. Methods 12, 503–513 (2015).

  2. 2.

    & in Methods in Cell Biology (Eds. Muller-Reichert, T. & Verkade, P.) xvii–xviii (Elsevier, 2014).

  3. 3.

    et al. Nat. Methods 9, 690–696 (2012).

  4. 4.

    , & eLife 4, e05793 (2015).

  5. 5.

    et al. J. Microsc. 212, 81–90 (2003).

  6. 6.

    , & Ultramicroscopy 24, 7–18 (1988).

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The authors thank the Icy team and, in particular, S. Dallongeville and F. de Chaumont, the Icy CODING party and France-BioImaging infrastructure supported by the French National Research Agency (ANR-10-INBS-04, “Investments for the future”). X.H. was funded by the Labex grant No. ANR-10-LBX-0038 part of the IDEX Idex PSL No. ANR-10-IDEX-0001-02 PSL. We acknowledge the FRM grant No. DEQ20140329491. This work was supported by the Francis Crick Institute, which receives its core funding from Cancer Research UK (grant no. FC001004), the UK Medical Research Council (grant no. FC001004), and the Wellcome Trust (grant no. FC001004). We thank B. Ji and B. Dubertret (Laboratoire de Physique et d'Étude des Matériaux, PSL Research University, Sorbonne Universités, Paris, France) for providing the QDots aggregates; C. Delevoye for his thoughtful reading of the manuscript; M. Schorb and M. Karreman; and Y. Schwab and his team for their support and advice on the software.

Author information

Author notes

    • Perrine Paul-Gilloteaux
    •  & Xavier Heiligenstein

    These authors contributed equally to this work.


  1. Structure Fédérative de Recherche François Bonamy, INSERM, CNRS, Université de Nantes, Nantes, France.

    • Perrine Paul-Gilloteaux
  2. Institut Curie, PSL Research University, CNRS UMR 144 & Cell and Tissue Imaging Facility, Paris, France.

    • Perrine Paul-Gilloteaux
    • , Xavier Heiligenstein
    • , Graça Raposo
    •  & Jean Salamero
  3. CryoCapCell, Paris, France.

    • Martin Belle
  4. The Francis Crick Institute, London, UK.

    • Marie-Charlotte Domart
    •  & Lucy Collinson
  5. Cell Biophysics Laboratory, Ikerbasque Basque Foundation for Science, Research Centre for Experimental Marine Biology and Biotechnology (PiE) & Biofísika Instituto (UPV/EHU, CSIC), University of the Basque Country, Spain.

    • Banafshe Larijani


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Competing interests

The co-first author X.H. and the second author M.B. of this manuscript have interest in the CryoCapCell company. This company develops laboratory tools to simplify sample preparation in CLEM experiment workflows. The quantum dot aggregates presented in this manuscript are a research field of the company. The software presented here is not dependent on the quantum dots aggregates and can be used independently. No patent has been filed for the application of the quantum dots in CLEM experiments with eC-CLEM.

Corresponding authors

Correspondence to Perrine Paul-Gilloteaux or Xavier Heiligenstein.

Supplementary information

PDF files

  1. 1.

    Supplementary Text and Figures

    Supplementary Notes 1–8

Zip files

  1. 1.

    Supplementary Software

    Source code in java of the ICY plugins for eC-CLEM and eC-CLEM Autofinder

  2. 2.

    Supplementary Data 1

    Source data for figures within Supplementary Notes

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