CODEX® Support

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