After all cells have been assigned a phenotype, we are now ready to perform spatial analysis of the different cell types. Essentially, the various spatial analyses modules are used to determine if there are patterns in the spatial organization of various cell types. At this point, there are three types of spatial analyses supported on the Enable Medicine Platform: (1) Cell-Cell Interactions, which look at which cell types border other cell types; (2) Spatial Nearest Neighbor Analysis, which finds the distances between cells of one phenotype to the nearest cell of a second phenotype; and (3) Neighborhood Analysis, which looks at larger groups of cells located in the same spatial area.
Cell-Cell Interactions are automatically calculated once phenotyping analysis has been completed, which generates a new Explorer Version, accessed under Applications in the Analysis Toolkit. Spatial Nearest Neighbor Analysis and Neighborhood Analysis both have their own Extensions which can be accessed through the Analysis Toolkit.