IDEAS home Printed from https://ideas.repec.org/a/nat/natcom/v8y2017i1d10.1038_ncomms14836.html
   My bibliography  Save this article

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

Author

Listed:
  • 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
    as

    Download full text from publisher

    File URL: https://www.nature.com/articles/ncomms14836
    File Function: Abstract
    Download Restriction: no
    File URL: https://libkey.io/10.1038/ncomms14836?utm_source=ideas
    LibKey link: if access is restricted and if your library uses this service, LibKey will redirect you to where you can use your library subscription to access this item
    ---><---

    Citations

    Citations are extracted by the CitEc Project, subscribe to its RSS feed for this item.
    as


    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.
    2. Shu Wang & Xiaoxiang Liu & Yueying Li & Xinquan Sun & Qi Li & Yinhua She & Yixuan Xu & Xingxin Huang & Ruolan Lin & Deyong Kang & Xingfu Wang & Haohua Tu & Wenxi Liu & Feng Huang & Jianxin Chen, 2023. "A deep learning-based stripe self-correction method for stitched microscopic images," Nature Communications, Nature, vol. 14(1), pages 1-15, December.
    3. Ceren Pajanoja & Jenny Hsin & Bradley Olinger & Andrew Schiffmacher & Rita Yazejian & Shaun Abrams & Arvydas Dapkunas & Zarin Zainul & Andrew D. Doyle & Daniel Martin & Laura Kerosuo, 2023. "Maintenance of pluripotency-like signature in the entire ectoderm leads to neural crest stem cell potential," Nature Communications, Nature, vol. 14(1), pages 1-17, December.
    4. 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.
    5. 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.
    6. 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.
    7. 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.

    More about this item

    Statistics

    Access and download statistics

    Corrections

    All material on this site has been provided by the respective publishers and authors. You can help correct errors and omissions. When requesting a correction, please mention this item's handle: RePEc:nat:natcom:v:8:y:2017:i:1:d:10.1038_ncomms14836. See general information about how to correct material in RePEc.

    If you have authored this item and are not yet registered with RePEc, we encourage you to do it here. This allows to link your profile to this item. It also allows you to accept potential citations to this item that we are uncertain about.

    We have no bibliographic references for this item. You can help adding them by using this form .

    If you know of missing items citing this one, you can help us creating those links by adding the relevant references in the same way as above, for each refering item. If you are a registered author of this item, you may also want to check the "citations" tab in your RePEc Author Service profile, as there may be some citations waiting for confirmation.

    For technical questions regarding this item, or to correct its authors, title, abstract, bibliographic or download information, contact: Sonal Shukla or Springer Nature Abstracting and Indexing (email available below). General contact details of provider: http://www.nature.com .

    Please note that corrections may take a couple of weeks to filter through the various RePEc services.

    IDEAS is a RePEc service. RePEc uses bibliographic data supplied by the respective publishers.