Dataset and scripts belonging to "Inferring Bacterial Interspecific Interactions from Microcolony Growth Expansion"

Dataset and corresponding analysis scripts underlying the manuscript

Inferring Bacterial Interspecific Interactions from Microcolony Growth Expansion

by

Tania Miguel Trabajo1, Isaline Guex1,2, Manupriyam Dubey1, Elvire Sarton-Lohéac1, Helena Todorov1, Xavier Richard2, Christian Mazza2, Jan Roelof van der Meer1*

Department of Fundamental Microbiology, University of Lausanne

Department of Mathematics, University of Fribourg

Readme - main folder structure

This dataset and corresponding scripts has six main folders. Within the main folders are further Readme-files for the content of the subfolders.

/Colony_segmentation: Contains the python script and instructions on how to segment a TIF set of images from time lapse, and calculate the colony expansion rates, areas and positions from the segmented .npy stack.

/data_processing:Contains the main subfolders for the segmented colonies and derived data from all experiments, the corresponding scripts, output plots or .csv tables with data shown in the paper, and a list per figure, table or supplementary on how those data were derived with the indicated scripts.

/flow_cytometry_data:Has the data and the processing of the flow cytometry quantification of cells washed from the surface of the patches for the relevant experiments shown in the paper.

/Imaging_data:Has subfolders with the individual experiments used for the paper. Subfolder will contain the .npy segmented stacked files and the derived data plus individualized local scripts.

/LCMS_data:Has the data and the processing of the growth of the mono-cultures and the swapped supernatants, and the derived LCMS tables with the peak areas in the different samples, as shown in the paper.

/Surface_model:Has the actual surface model script and the results of the various simulations.