Multidimensional profiling of cancer microenvironments in FFPE tissues by imaging mass cytometry

In recent years, significant advancements have been achieved in the development of multiplex imaging methodologies for immunophenotyping, enabling a comprehensive characterization of the complexity of tumor microenvironments. Imaging mass cytometry combines the detection of over 40 cellular targets with spatial information, enabling the identification of not only which cells are present in a tissue but also their localization relative to each other. Here, we present an easy-to-implement imaging mass cytometry workflow that ranges from antibody selection and testing to running a full panel. Additionally, we discuss the standard steps of IMC analysis and the currently available tools. Overall, the protocols proposed here are directly applicable to characterize immune contextures in a variety of tissues.