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.
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