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This is the optical microscopy raw data and processed data to our published manuscript. Our code used for analysis has been published in the supporting information of the manuscript, but can also be found here. The data here can be used to test the code and reproduce the published results. The dataset is best viewed in tree mode, because it contains 1000 files, which are organized in folders. The following items are in the root folder: GO, GOe, GOw folders: data from three different samples as discussed in the manuscript ParticleAnalysis-Histograms_and_Data.qti: analyzed histograms and derived plots, as used in the manuscript (QtiPlot format) Each of the three folders with sample data has subfolders Raw images (PNG format) and Processed images (TIFF and ASCII formats). The latter folder contains files of different stages of the processing process: Averaged: Average of raw images EmptySubstrateDivided: Image after division by empty substrate EmptySubstrateDivided-GwyddionExport: Same as previous, but in Gwyddion text (ASCII) image format ExtractedBackground: Fitted plane in Gwyddion text (ASCII) format Final: Image after division by fitted plan Final-Inverted: Final image after inversion (may not be present if inversion not required)