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eC-CLEM: flexible multidimensional registration software for correlative microscopies

Nature Methods volume 14, pages 102–103 (2017)Cite this article

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A Corrigendum to this article was published on 28 February 2017

This article has been updated

To the Editor:

Correlative light and electron microscopy (CLEM) is becoming increasingly popular within the life sciences. The diversity of light microscopy (LM) and electron microscopy (EM) modalities has led researchers to develop a multitude of CLEM workflows tailored to different scientific investigations1,2. Finding the corresponding area between LM and EM images can be facilitated with specific sample holders, finder grids, laser marks or pattern recognition1. However, for all these workflows, the accurate association of a fluorescent object with its corresponding ultrastructure from data sets differing in scales by several orders of magnitude remains a universal bottleneck. Although several software solutions to the problem of achieving accurate association have been proposed (Supplementary Note 1), there is currently no available open-access software to achieve high-accuracy localization independent of specific registration fiducials that also offer nonrigid registration both in two and three dimensions (2D and 3D) and semisupervised registration.

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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.

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Acknowledgements

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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Author notes

  1. Perrine Paul-Gilloteaux and Xavier Heiligenstein: These authors contributed equally to this work.

Authors and Affiliations

  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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  1. Perrine Paul-Gilloteaux
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Corresponding authors

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). https://doi.org/10.1038/nmeth.4170

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