3D Imaging for the Quantification of Spatial Patterns in Microbiota of the Intestinal Mucosa

Please scroll down to see download links. Data and scripts for "3D Imaging for the Quantification of Spatial Patterns in Microbiota of the Intestinal Mucosa" submitted as a preprint to bioRxiv and accepted to PNAS (doi pending). Contents (see also DataList document in download): ***Confocal imaging of bacteria, mucus and murine epithelium in the proximal colon of a specific-pathogen free mouse (Fig. 3A-F) Raw multi-color confocal imaging of bacteria embedded in mucus over folds in the epithelium of the proximal colon. ***Multiplexed, spectral confocal imaging of bacterial communities in the cecal crypts of a specific-pathogen free mouse (Fig. 5C-Q) Raw spectral imaging Linear unmixing of spectral imaging Processing and analysis of unmixed spectral imaging in arivis Vision4D 3.0 ***Raw spectral confocal imaging of cecum Spectral confocal imaging of cecum after linear unmixing Confocal imaging of cecum after linear unmixing, and processed in arivis Vision4D 3.0 ***Spectral and standard confocal imaging of bacterial communities in cecal crypts at different stages of antibiotic exposure: unexposed (2 mice), antibiotic (3 mice), and recovery (3 mice). (Figs. 6-7) Raw spectral imaging Linear unmixing of spectral imaging Processing and analysis of unmixed spectral imaging in arivis Vision4D 3.0 ***Mouse unexposed to ciprofloxacin #1 Raw spectral confocal imaging of cecum Spectral confocal imaging of cecum after linear unmixing Confocal imaging of cecum after linear unmixing, and processed in arivis Vision4D 3.0 ***Mouse unexposed to ciprofloxacin #2 Raw spectral confocal imaging of cecum Spectral confocal imaging of cecum after linear unmixing Confocal imaging of cecum after linear unmixing, and processed in arivis Vision4D 3.0 ***Mouse exposed to ciprofloxacin #1 Raw spectral confocal imaging of cecum Spectral confocal imaging of cecum after linear unmixing Confocal imaging of cecum after linear unmixing, and processed in arivis Vision4D 3.0 ***Mouse exposed to ciprofloxacin #2 Standard confocal imaging of cecum Confocal imaging of cecum processed in arivis Vision4D 3.0 ***Mouse exposed to ciprofloxacin #3 Raw spectral confocal imaging of cecum Spectral confocal imaging of cecum after linear unmixing Confocal imaging of cecum after linear unmixing, and processed in arivis Vision4D 3.0 ***Mouse that recovered from ciprofloxacin for 10 days #1 Raw spectral confocal imaging of cecum Spectral confocal imaging of cecum after linear unmixing Confocal imaging of cecum