
Tissue biogeography, defined as the study of spatial distribution and interaction of cell types within a given tissue, is essential for the investigation of pathological conditions. Cancerous, scarred, injured, or inflamed tissues are described by cellular composition, cell-to-cell-interaction, paracrine signals, and extracellular matrix structure. In this proposed collection, we aim to assemble various techniques aimed to characterize the evolution of a tissue in different phases, specifically in the study of the same cohort of cells but from different area of research. It is known that otherwise disparate diseases are connected by the presence or appearance of the same type of cells, and the expression of the same markers or paracrine signals. The dissemination of protocols for single cell isolation, single cell sequencing, lineage tracing, and in vitro phenotype derivation will allow researchers in different fields to investigate the same population of cells with respect to their particular areas of study. With this collection, we aim to gather protocols on the in vitro derivation of activated cells isolated from tissue, methods for studying how specific cell types switch phenotype or acquire specific markers, and techniques for the in vitro reproduction of disease-specific cells isolated from animals. Understanding the composition and cell communication occurring in diseased tissue is essential for the study of tissue regeneration, to reduce inflammation, and to avoid the formation of detrimental and nonfunctional tissue structure.