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

Nat Commun. 2017 Jun 8:8:14836. doi: 10.1038/ncomms14836.


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.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Algorithms
  • Artifacts
  • Image Processing, Computer-Assisted / methods
  • Microscopy / methods*
  • Software*
  • Time-Lapse Imaging