Shading Correction

Optical vignetting [1][2] is corrected using BaSiC, a retrospective method for estimating flat-field and correcting microscopy images [3]. 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

(Left) CD7 before shading correction. (Right) After

(Left) CD34 before shading correction. (Right) after

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.

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