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