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CIDRE: an illumination-correction method for optical microscopy

Nature Methods volume 12, pages 404–406 (2015)Cite this article

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Abstract

Uneven illumination affects every image acquired by a microscope. It is often overlooked, but it can introduce considerable bias to image measurements. The most reliable correction methods require special reference images, and retrospective alternatives do not fully model the correction process. Our approach overcomes these issues for most optical microscopy applications without the need for reference images.

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Figure 1: Summary of illumination correction using CIDRE.
Figure 2: Comparison of 13 illumination correction methods, averaged over 12 image collections.

References

  1. Goldman, D.B. IEEE Trans. Pattern Anal. Mach. Intell. 32, 2276–2288 (2010).

    Article  Google Scholar 

  2. Carpenter, A.E. et al. Genome Biol. 7, R100 (2006).

    Article  Google Scholar 

  3. Young, I.T. Curr. Protoc. Cytom. 14, 2.11 (2001).

    Google Scholar 

  4. Model, M. Curr. Protoc. Cytom. 68, 10.14 (2014).

    Google Scholar 

  5. Ljosa, V. & Carpenter, A.E. PLoS Comput. Biol. 5, e1000603 (2009).

    Article  Google Scholar 

  6. Shariff, A., Kangas, J., Coelho, L.P., Quinn, S. & Murphy, R.F. J. Biomol. Screen. 15, 726–734 (2010).

    Article  Google Scholar 

  7. Ray, S.F. Applied Photographic Optics 3rd edn. (Focal, 2002).

  8. Varga, V.S. et al. Cytometry A 60, 53–62 (2004).

    Article  Google Scholar 

  9. Sigal, A. et al. Nat. Methods 3, 525–531 (2006).

    Article  CAS  Google Scholar 

  10. Can, A. et al. in Proc. IEEE Int. Symp. Biomed. Imaging 288–291 (IEEE, 2008).

  11. Schwarzfischer, M. et al. in Micro. Image Anal. Appl. Biol. (MIAAB, Heidelberg, Germany, 2011).

  12. Sternberg, S.R. Computer 16, 22–34 (1983).

    Article  Google Scholar 

  13. Leong, F.J., Brady, M. & McGee, J.O. J. Clin. Pathol. 56, 619–621 (2003).

    Article  Google Scholar 

  14. Babaloukas, G., Tentolouris, N., Liatis, S., Sklavounou, A. & Perrea, D. J. Microsc. 244, 320–324 (2011).

    Article  Google Scholar 

  15. Olsen, D. et al. Remote Sens. 2, 464–477 (2010).

    Article  Google Scholar 

  16. Guizar-Sicairos, M., Thurman, S.T. & Fienup, J.R. Opt. Lett. 33, 156–158 (2008).

    Article  Google Scholar 

  17. Liu, D.C. & Nocedal, J. Math. Program. 45, 503–528 (1989).

    Article  Google Scholar 

Download references

Acknowledgements

We thank R. Dechant, T. Schwarz, A. Kaufmann and J. Kusch for data collection; L. Lenherr Smith for help with the manuscript; and our colleagues who completed the survey. This work was funded by SystemsX.ch, the Swiss national initiative for Systems Biology, through the SyBIT project. P.H. acknowledges support from the Finnish TEKES FiDiPro and the Hungarian National Brain Research Programme (MTA-SE-NAP B-BIOMAG).

Author information

Authors and Affiliations

  1. Scientific Center for Optical and Electron Microscopy, ETH Zürich, Zurich, Switzerland

    Kevin Smith, Gabor Csucs & Csaba Balazs

  2. Computer Vision Laboratory, École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland

    Yunpeng Li

  3. Advanced Research Center on Electronic Systems, University of Bologna, Bologna, Italy

    Filippo Piccinini & Alessandro Bevilacqua

  4. Department of Computer Science and Engineering, University of Bologna, Bologna, Italy

    Alessandro Bevilacqua

  5. Institute of Biochemistry, ETH Zürich, Zurich, Switzerland

    Peter Horvath

  6. Synthetic and System Biology Unit, Biological Research Center, Szeged, Hungary

    Peter Horvath

  7. Institute for Molecular Medicine Finland, University of Helsinki, Helsinki, Finland

    Peter Horvath

Authors
  1. Kevin Smith
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  2. Yunpeng Li
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  3. Filippo Piccinini
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  4. Gabor Csucs
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  5. Csaba Balazs
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  6. Alessandro Bevilacqua
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  7. Peter Horvath
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Contributions

P.H., F.P., A.B. and G.C. initiated the project. K.S. and P.H. designed the correction method. K.S. and Y.L. designed the optimization. K.S. and C.B. implemented the software. F.P. and K.S. collected the image data. K.S. performed the analysis and wrote the manuscript.

Corresponding author

Correspondence to Kevin Smith.

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Competing interests

The authors declare no competing financial interests.

Supplementary information

Supplementary Text and Figures

Supplementary Figures 1–3, Supplementary Table 1, Supplementary Notes 1–4 and Supplementary Data 1 and 2 (PDF 18458 kb)

Supplementary Software

Source code for CIDRE illumination correction (Matlab and Java Fiji plugin). License information was corrected on 4 May 2015. (ZIP 300 kb)

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Smith, K., Li, Y., Piccinini, F. et al. CIDRE: an illumination-correction method for optical microscopy. Nat Methods 12, 404–406 (2015). https://doi.org/10.1038/nmeth.3323

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