Description of the sub-folders Name, type of data, corresponding Figure in the manuscript 3D view of the LoC model - .tiff image stack, Figure 1. Bacterial Growth Rate Data - .tiff image stacks, .csv files and MATLAB code to extract the fluorescence intensity over time, Figure 2, Figure 2 - figure supplement 2, Figure 2 - figure supplement 4, Figure 3, Figure 3 - figure supplement 2, Figure 4. AT Characterization - .tiff image stacks and MATLAB code to extract the number and volume of lamellar bodies from the stack of confocal images, Figure 1, Figure 1 - figure supplement 1, Figue 1 - figure supplement 2. AT Infection in LoC model - .tiff image stacks, Figure 2 - figure supplement 1. AT Infection in vivo - .tiff image stacks, Figure 1 - figure supplement 3. Simulations of in vivo infections - .dat files of growth rates in macrophages for the WT and ESX-1 deficient populations and MATLAB code to simulate an infection from this data, Figure 4.

Human Frontier Science Program (HFSP): Vivek V Thacker, Long-Term Fellowship,LT000231/2016-L; European Molecular Biology Organization (EMBO): Vivek V Thacker, Long-Term Fellowship,921-2015;