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.

  • Correspondence
  • Published:

FISH-quant: automatic counting of transcripts in 3D FISH images

Nature Methods volume 10, pages 277–278 (2013)Cite this article

Subjects

To the Editor:

FISH-quant first detects and then localizes mature mRNA in three dimensions by fitting Gaussians to fluorescent spots5; each mRNA then undergoes a quality test based on the measured point-spread function (PSF) (Fig. 1a and Supplementary Note 2). This provides the three-dimensional (3D) position of mRNAs inside cells and the distribution of mRNA counts across the cell population (Fig. 1a). We validated this method in simulations and experimentally by dual-color FISH against mRNA of RPB1, which encodes the largest subunit of RNA polymerase II, and we obtained excellent agreement in the number of estimated spots and a high degree of colocalization (Fig. 1b–d, Supplementary Note 3 and Supplementary Methods).

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

Relevant articles

Open Access articles citing this article.

Access options

Buy this article

  • Purchase on Springer Link
  • Instant access to full article PDF
Buy now

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

Figure 1: Counting mature and nascent mRNA in FISH-quant.

References

  1. Li, G.-W. & Xie, X.S. Nature 475, 308–315 (2011).

    Article  CAS  Google Scholar 

  2. Zenklusen, D., Larson, D.R. & Singer, R.H. Nat. Struct. Mol. Biol. 15, 1263–1271 (2008).

    Article  CAS  Google Scholar 

  3. Itzkovitz, S. & Van Oudenaarden, A. Nat. Methods 8, S12–S19 (2011).

    Article  CAS  Google Scholar 

  4. Raj, A., Van den Bogaard, P., Rifkin, S.A., Van Oudenaarden, A. & Tyagi, S. Nat. Methods 5, 877–879 (2008).

    Article  CAS  Google Scholar 

  5. Thomann, D., Rines, D.R., Sorger, P.K. & Danuser, G. J. Microsc. 208, 49–64 (2002).

    Article  CAS  Google Scholar 

  6. Boireau, S. et al. J. Cell Biol. 179, 291–304 (2007).

    Article  CAS  Google Scholar 

Download references

Acknowledgements

This research was supported by the Agence Nationale de la Recherche (ANR-10-BLAN-1222, ANR-09-PIRI-0024, ANR-10-INTB-1401), Sidaction, the Région Ile-de-France under C'Nano IdF (the Center of Competences in NanoSciences for the Paris region), the Fondation pour la Recherche Médicale en France (FRM) and the Institut Pasteur. We thank J. McNally for editing the manuscript.

Author information

Authors and Affiliations

  1. Institut Pasteur, Unité Imagerie et Modélisation, Centre National de la Recherche Scientifique (CNRS) Unité de Recherche Associée 2582, Paris, France

    Florian Mueller, Hervé Marie-Nelly & Christophe Zimmer

  2. Imagerie de la machinerie transcriptionnelle, Institut de Biologie de l'Ecole Normale Supérieure, CNRS Unité Mixte de Recherche 8197, Paris, France

    Florian Mueller, Adrien Senecal, Nathalie Ly, Olivier Collin & Xavier Darzacq

  3. Institut de Génétique Moléculaire de Montpellier, CNRS, Unité Mixte de Recherche 5535, Montpellier, France

    Katjana Tantale, Eugenia Basyuk & Edouard Bertrand

Authors
  1. Florian Mueller
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Adrien Senecal
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Katjana Tantale
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. Hervé Marie-Nelly
    View author publications

    You can also search for this author in PubMed Google Scholar

  5. Nathalie Ly
    View author publications

    You can also search for this author in PubMed Google Scholar

  6. Olivier Collin
    View author publications

    You can also search for this author in PubMed Google Scholar

  7. Eugenia Basyuk
    View author publications

    You can also search for this author in PubMed Google Scholar

  8. Edouard Bertrand
    View author publications

    You can also search for this author in PubMed Google Scholar

  9. Xavier Darzacq
    View author publications

    You can also search for this author in PubMed Google Scholar

  10. Christophe Zimmer
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding authors

Correspondence to Edouard Bertrand, Xavier Darzacq or Christophe Zimmer.

Ethics declarations

Competing interests

The authors declare no competing financial interests.

Supplementary information

Supplementary Text and Figures

Supplementary Notes 1–6 and Supplementary Methods (PDF 8880 kb)

Rights and permissions

Reprints and permissions

About this article

Cite this article

Mueller, F., Senecal, A., Tantale, K. et al. FISH-quant: automatic counting of transcripts in 3D FISH images. Nat Methods 10, 277–278 (2013). https://doi.org/10.1038/nmeth.2406

Download citation

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1038/nmeth.2406

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