Single-cell analysis technologies are rapidly improving and will eventually match the performance of their population-level counterparts. RNA transcriptomes can be quantified in thousands of single cells, and analyses of transcriptomes of single cells with spatial resolution in tissues have been reported1,2,3. Mass cytometry has the potential to enable simultaneous detection of up to 50 proteins, protein modifications, such as phosphorylation, and transcripts in single cells4,5,6,7. Recent developments enable highly multiplexed imaging of similar numbers of markers in adherent cells and tissues5,8,9,10. Single-cell data are typically used to identify cell subpopulations that share similar transcript or protein expression or functional markers.