Systematic analysis of cell phenotypes and cellular social networks in tissues using the multiplexed image cytometry analysis toolbox (miCAT)

Single-cell, spatially resolved 9omics analysis of tissues is poised to transform biomedical research and clinical practice. We have developed a computational multiplexed image cytometry analysis toolbox (miCAT) to enable the interactive, quantitative, and comprehensive exploration of phenotypes of individual cells, cell-to-cell interactions, microenvironments, and morphological structures within intact tissues. miCAT will be useful in all areas of tissue-based research. We highlight the unique abilities of miCAT by analysis of highly multiplexed mass cytometry images of human breast cancer tissues.