Spatial mapping of cells

Following the Tissue Studio batch processing of all patient tissue samples, a CSV file containing the patient identification, tissue class, cell label class, cell coordinates, and coexpression parameters for all segmented cells was exported and used in subsequent spatial point pattern analysis. For the analysis of cellular spatial distributions, Spatstat, an R package for spatial point pattern analysis (www.spatstat.org), was used together with an ImageJ script for masking tumor and stroma regions.

In general, spatial point patterns for the data were normalized to a corresponding model simulating CSR distribution of cells. Further methodological details on the CSR model, cell cluster analysis, and n-n analysis are provided in Supplementary Materials and Methods.