eC-CLEM: flexible multidimensional registration software for correlative microscopies

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Figure 1: eC-CLEM covers a broad range of 2D and 3D image registration applications for correlative LM and EM.

Change history

  • 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

    de Boer, P., Hoogenboom, J.P. & Giepmans, B.N. Nat. Methods 12, 503–513 (2015).

    CAS  Article  Google Scholar 

  2. 2

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

    Google Scholar 

  3. 3

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

    CAS  Article  Google Scholar 

  4. 4

    Korogod, N., Petersen, C.C. & Knott, G.W. eLife 4, e05793 (2015).

    Article  Google Scholar 

  5. 5

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

    CAS  Article  Google Scholar 

  6. 6

    Luther, P.K., Lawrence, M.C. & Crowther, R.A. Ultramicroscopy 24, 7–18 (1988).

    CAS  Article  Google Scholar 

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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.

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Correspondence to Perrine Paul-Gilloteaux or Xavier Heiligenstein.

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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.

Supplementary information

Supplementary Text and Figures

Supplementary Notes 1–8 (PDF 3765 kb)

Supplementary Software

Source code in java of the ICY plugins for eC-CLEM and eC-CLEM Autofinder (ZIP 153 kb)

Supplementary Data 1

Source data for figures within Supplementary Notes (ZIP 2965 kb)

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Paul-Gilloteaux, P., Heiligenstein, X., Belle, M. et al. eC-CLEM: flexible multidimensional registration software for correlative microscopies. Nat Methods 14, 102–103 (2017).

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