# 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) --- # Agent Instructions: Querying This Documentation If you need additional information that is not directly available in this page, you can query the documentation dynamically by asking a question. Perform an HTTP GET request on the current page URL with the `ask` query parameter: ``` GET https://help.codex.bio/codex/processor/technical-notes/shading-correction.md?ask= ``` The question should be specific, self-contained, and written in natural language. The response will contain a direct answer to the question and relevant excerpts and sources from the documentation. Use this mechanism when the answer is not explicitly present in the current page, you need clarification or additional context, or you want to retrieve related documentation sections.