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

  • Peng T Department of Computer Science, Chair of Computer Aided Medical Procedure, Technische Universität München, Boltzmannstr. 3, Garching 85748, Germany.
  • Thorn K Department of Biochemistry and Biophysics, University of California, San Francisco, 600 16th Street, San Francisco, California 94158, USA.
  • Schroeder T Department of Biosystems Science and Engineering (D-BSSE), ETH Zurich, Basel 4058, Switzerland.
  • Wang L Department of Computer Science, Chair of Computer Aided Medical Procedure, Technische Universität München, Boltzmannstr. 3, Garching 85748, Germany.
  • Theis FJ Institute of Computational Biology, Helmholtz Zentrum München-German Research Center for Environmental Health, Institute of Computational Biology, Ingolstädter Landstraße 1, Neuherberg 85764, Germany.
  • Marr C Institute of Computational Biology, Helmholtz Zentrum München-German Research Center for Environmental Health, Institute of Computational Biology, Ingolstädter Landstraße 1, Neuherberg 85764, Germany.
  • Navab N Department of Computer Science, Chair of Computer Aided Medical Procedure, Technische Universität München, Boltzmannstr. 3, Garching 85748, Germany.
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  • 2017-06-09
Published in:
  • Nature communications. - 2017
Algorithms
Artifacts
Image Processing, Computer-Assisted
Microscopy
Software
Time-Lapse Imaging
English 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.
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  • English
Open access status
gold
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Persistent URL
https://sonar.ch/global/documents/217395
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