Imaging mass cytometry-derived single cell extraction, transformation and phenotyping to analyze immune tumor...

Spatial technologies have been revolutionary in the analysis of intact tissue samples as they allow for in depth investigation of cellular spatial interactions that cannot be elucidated through conventional single-cell methodologies. Imaging mass cytometry (IMC) is a unique and novel spatial proteomics platform that utilizes metal-conjugated antibodies to generate multi-plex images where spatial information of single cells can be extracted from intact tissue samples, allowing for in depth spatial analyses. However, extracting single cells data and spatial information from IMC multi-plex images can be technically challenging for basic scientists without experience in bioinformatics or computational sciences. In this chapter, we describe how steps on how to extract single cell data and spatial information from multi-plex IMC images of intact tissue samples and tips on performing cell clustering and spatial analyses.