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CIDRE: an illumination-correction method for optical microscopy


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.

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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, 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).

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Authors and Affiliations



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.

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Correspondence to Kevin Smith.

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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).

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