1292 A reproducible pipeline for analysis of multiplex imaging (MIBI) data with application to uncovering novel features of the tumor-immune microenvironment

Background Although immune checkpoint inhibition (ICI) has been transformational, tumor-associated factors regulating response have not been elucidated. High-dimensional spatial profiling technologies have enabled simultaneous investigation of many protein targets on individual cells within the spatial context of the tumor microenvironment (TME). Analysis of these data to uncover immune and tumor profiles relies on identification of individual cells and characterization of their specific marker expression to classify lineage and functional state. However, robust automated cell type assignment remains a key challenge in multiplex image data analysis. Here, we describe a reproducible pipeline for single cell identification and typing from multiplex ion beam imaging (MIBI) data uti-lizing lineage protein expression, which has applications in the context of precision immunotherapy and beyond.