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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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).
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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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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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DOI: https://doi.org/10.1038/nmeth.3323
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