# 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](https://1268872846-files.gitbook.io/~/files/v0/b/gitbook-legacy-files/o/assets%2F-LWT7bo4Xbl2jOnmH1yB%2F-L_sZICy-PnYYccqFEtG%2F-L_s_H1V0rk3sxs4M6rD%2Fshading-correction-1-Ki67.png?alt=media\&token=9243e3b3-a1fd-4add-885f-c154dde27e89)

![(Left) CD7 before shading correction. (Right) After](https://1268872846-files.gitbook.io/~/files/v0/b/gitbook-legacy-files/o/assets%2F-LWT7bo4Xbl2jOnmH1yB%2F-L_sZICy-PnYYccqFEtG%2F-L_s_JCfT53TXWJhRwmo%2Fshading-correction-2-CD7.png?alt=media\&token=ca2450a9-43c1-465f-9843-8f1063e60706)

![(Left) CD34 before shading correction. (Right) after](https://1268872846-files.gitbook.io/~/files/v0/b/gitbook-legacy-files/o/assets%2F-LWT7bo4Xbl2jOnmH1yB%2F-L_sZICy-PnYYccqFEtG%2F-L_s_LOgUu2WtF70Vn2z%2Fshading-correction-3-CD34.png?alt=media\&token=d527f9cd-075e-44bd-a5f5-0109d0ead197)

[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)





