Source data for Extended Data 3: stool bacterial cell density, C. difficile abundance - including raw images and raw counts

These data correspond to Extended Data 3 of VanInsberghe et al. To directly count the cell density in mouse fecal samples, we homogenized stool pellets of known mass, mounted on microscope slides, and stained using FITC. These data include: - All of the raw fluorescence images used for counting cells - "cell_counts.csv" contains all of the raw cell counts from our cell counting scripts (also available on github - https://github.com/polzlab/VanInsberghe_2019_Cdiff_colonization) - "extended_data_3_source.xlsx" contains the C. difficile abundance measurements also included in Extended Data 3, including both the 16S rRNA amplicon sequencing measurements, and the rplP qPCR measurements.