> For the complete documentation index, see [llms.txt](https://help.codex.bio/codex/llms.txt). Markdown versions of documentation pages are available by appending `.md` to page URLs; this page is available as [Markdown](https://help.codex.bio/codex/processor/technical-notes/shading-correction.md).

# Shading Correction

Optical vignetting [\[1\]](https://en.wikipedia.org/wiki/Vignetting)[\[2\]](https://www.edmundoptics.com/resources/application-notes/imaging/sensor-relative-illumination-roll-off-and-vignetting/) is corrected using BaSiC, a retrospective method for estimating flat-field and correcting microscopy images [\[3\]](https://en.wikipedia.org/wiki/Flat-field_correction). This library was developed by Quantitative Single Cell Dynamics group at Helmholtz Zentrum München Institute of Computational Biology. All tiles within a region and z-slice is combined into a single ImagePlus stack and processed to find an estimate flat-field image. The original stack is then divided by resulting flat-field to apply the correction.

![(Left) Ki67 before shading correction. (Right) After](/files/-L_s_H1V0rk3sxs4M6rD)

![(Left) CD7 before shading correction. (Right) After](/files/-L_s_JCfT53TXWJhRwmo)

![(Left) CD34 before shading correction. (Right) after](/files/-L_s_LOgUu2WtF70Vn2z)

[Peng, T., Thorn, K., Schroeder, T., Wang, L., Theis, F. J., Marr, C., & Navab, N. (2017). A BaSiC tool for background and shading correction of optical microscopy images. Nature communications, 8, 14836.](https://www.nature.com/articles/ncomms14836)

[GitHub Link](https://github.com/QSCD/BaSiC)


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