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A BaSiC tool for background and shading correction of optical microscopy images

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  • Tingying Peng

    (Chair of Computer Aided Medical Procedure, Technische Universität München
    Institute of Computational Biology, Helmholtz Zentrum München—German Research Center for Environmental Health, Institute of Computational Biology
    Center for Mathematics, Chair of Mathematical Modeling of Biological Systems, Technische Universität München)

  • Kurt Thorn

    (University of California, San Francisco, 600 16th Street, San Francisco, California 94158, USA)

  • Timm Schroeder

    (ETH Zurich)

  • Lichao Wang

    (Chair of Computer Aided Medical Procedure, Technische Universität München
    Institute of Computational Biology, Helmholtz Zentrum München—German Research Center for Environmental Health, Institute of Computational Biology)

  • Fabian J. Theis

    (Institute of Computational Biology, Helmholtz Zentrum München—German Research Center for Environmental Health, Institute of Computational Biology
    Center for Mathematics, Chair of Mathematical Modeling of Biological Systems, Technische Universität München)

  • Carsten Marr

    (Institute of Computational Biology, Helmholtz Zentrum München—German Research Center for Environmental Health, Institute of Computational Biology)

  • Nassir Navab

    (Chair of Computer Aided Medical Procedure, Technische Universität München
    Chair of Computer Aided Medical Procedure, Johns Hopkins University)

Abstract

Quantitative analysis of bioimaging data is often skewed by both shading in space and background variation in time. We introduce BaSiC, an image correction method based on low-rank and sparse decomposition which solves both issues. In comparison to existing shading correction tools, BaSiC achieves high-accuracy with significantly fewer input images, works for diverse imaging conditions and is robust against artefacts. Moreover, it can correct temporal drift in time-lapse microscopy data and thus improve continuous single-cell quantification. BaSiC requires no manual parameter setting and is available as a Fiji/ImageJ plugin.

Suggested Citation

  • Tingying Peng & Kurt Thorn & Timm Schroeder & Lichao Wang & Fabian J. Theis & Carsten Marr & Nassir Navab, 2017. "A BaSiC tool for background and shading correction of optical microscopy images," Nature Communications, Nature, vol. 8(1), pages 1-7, August.
    • Handle: RePEc:nat:natcom:v:8:y:2017:i:1:d:10.1038_ncomms14836
    DOI: 10.1038/ncomms14836
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    Cited by:

    1. Min Lee & Hyungseok C. Moon & Hyeonjeong Jeong & Dong Wook Kim & Hye Yoon Park & Yongdae Shin, 2024. "Optogenetic control of mRNA condensation reveals an intimate link between condensate material properties and functions," Nature Communications, Nature, vol. 15(1), pages 1-14, December.
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    3. Ilmatar Rooda & Jasmin Hassan & Jie Hao & Magdalena Wagner & Elisabeth Moussaud-Lamodière & Kersti Jääger & Marjut Otala & Katri Knuus & Cecilia Lindskog & Kiriaki Papaikonomou & Sebastian Gidlöf & Ce, 2024. "In-depth analysis of transcriptomes in ovarian cortical follicles from children and adults reveals interfollicular heterogeneity," Nature Communications, Nature, vol. 15(1), pages 1-18, December.
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    6. David Eriksson & Artur Schneider & Anupriya Thirumalai & Mansour Alyahyay & Brice Crompe & Kirti Sharma & Patrick Ruther & Ilka Diester, 2022. "Multichannel optogenetics combined with laminar recordings for ultra-controlled neuronal interrogation," Nature Communications, Nature, vol. 13(1), pages 1-13, December.
    7. Junyoung Seo & Yeonbo Sim & Jeewon Kim & Hyunwoo Kim & In Cho & Hoyeon Nam & Young-Gyu Yoon & Jae-Byum Chang, 2022. "PICASSO allows ultra-multiplexed fluorescence imaging of spatially overlapping proteins without reference spectra measurements," Nature Communications, Nature, vol. 13(1), pages 1-17, December.
    8. Philip Dettinger & Tobias Kull & Geethika Arekatla & Nouraiz Ahmed & Yang Zhang & Florin Schneiter & Arne Wehling & Daniel Schirmacher & Shunsuke Kawamura & Dirk Loeffler & Timm Schroeder, 2022. "Open-source personal pipetting robots with live-cell incubation and microscopy compatibility," Nature Communications, Nature, vol. 13(1), pages 1-12, December.
    9. David R. Ghasemi & Konstantin Okonechnikov & Anne Rademacher & Stephan Tirier & Kendra K. Maass & Hanna Schumacher & Piyush Joshi & Maxwell P. Gold & Julia Sundheimer & Britta Statz & Ahmet S. Rifaiog, 2024. "Compartments in medulloblastoma with extensive nodularity are connected through differentiation along the granular precursor lineage," Nature Communications, Nature, vol. 15(1), pages 1-20, December.

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