Studying intestinal immunity is critical to understanding the residential characteristics and interaction of immune and non-immune cells. A clear understanding of immune regulation and microenvironment often provides a clue to the resolution of the digestive disease. This collection recruits a series of methods developed to investigate local mechanisms using in vitro and in vivo approaches. Each method has its specific aspect, such as enabling the description of cell phenotype and function with surface and intracellular markers, exhibiting detailed spatial and temporal information about tissue in vivo, or simulating the cell-cell interaction in a local artificial environment.

Some methods are used for high-throughput transcriptome sequencing or delineating spatial distributions, while others show a more limited but precise detection. Organoid is a splendid cell-cell interaction in vitro model arranged similarly to the cells in the digestive organ. Intravital imaging is used in temporal cell-cell interaction methods in conjunction with microscopy.

Methods to be included are animal model, intestinal immune cell, non-immune cell, and bacteria isolation and culture, residential cell detection with flow cytometry, organoid forming, organoid and immune cell coculture, intestinal bacteria isolation and culture, fluorescence microscopy (e.g., immunofluorescence, multiplex immunohistochemistry, and intravital imaging), and microarray-based techniques (i.e., tissue and spatial transcription arrays).