Zip folder containing set of images (.tif files) analysed in the paper: “The SARS-CoV-2 nucleocapsid protein associates with the replication organelles before viral assembly at the Golgi/ERGIC and lysosome-mediated egress”, doi: 10.1101/2021.06.15.448497. Fixed Vero cells were imaged with confocal microscope (pixel size is 70.6 nm). Zip folder contains images stained for different viral proteins: Spike (S), Envelope (E), Membrane (M), Nucleocapsid (N), lysosomes, ERGIC complex and Golgi apparatus. Images are already automatically cropped around each single cell (see associated article methods for automatic cropping details). Description of colors in each subset is present in txt files which are included in all subsets. These images were analysed for Manders and Spearman coefficients with ColocAnalyzer v.4 https://doi.org/10.17863/CAM.77726 For more details see associated manuscript.