Imaging Mass Cytometry Dataset of exhausted and non-exhausted breast cancer microenvironments

A cohort of human breast tumor samples were annotated as having an "exhausted" or "non-exhausted" immune environment based on CyTOF characterization of T cell phenotypes (see Wagner et al. 2019). 12 samples (6 exhausted, 6 non-exhausted) were then selected for further analysis by Imaging Mass Cytometry (IMC) with the goal to compare the two immune environment types and to comprehensively characterize exhaustion-associated spatial features of the tumor microenvironment. For IMC, two consecutive FFPE sections of each sample were stained with two different antibody panels (Protein Panel and RNAscope Panel), and 4-10 regions of interest (ROIs, 1mm x 1mm) were measured on each section. ROIs on consecutive sections were registered manually to be as spatially close as possible.