These datasets are associated to the pre-print "High-content high-resolution microscopy and deep learning assisted analysis reveals host and bacterial heterogeneity during *Shigella *infection." Ana T. López-Jiménez, Dominik Brokatzky, Kamla Pillay, Tyrese Williams, Gizem Özbaykal Güler and Serge Mostowy. Briefly, Hela (ATCC CCL-2 cells) were infected by spin inoculation with fluorescent labelled Shigella flexneri M90T. Samples were fixed at 3 h 40 min and immunostained for imaging with a Zeiss CellDiscoverer 7 with Airyscan detectors. For further information on the experimental procedures for each specific dataset, please refer to the Materials and Method sections of the pre-print, and to the provided Dataset_information_experiments.xlsx and Dataset_information_CNN.xlsx files.

Deep learning, HeLa cells, Septins, Shigella flexneri, Biological sciences, Bacterial infection, heterogeneity, High-content microscopy