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.