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Significance Multimarker cytometry technologies, including cytometry by time of flight, are rapidly advancing and will soon produce large sets of rich immunoprofiling data. Here, we introduce X-Cyt, an automated cytometric data analysis tool for large-scale studies. Unlike existing software intended for exploratory analysis, it specializes in identifying populations of interest in large sample numbers. X-Cyt incorporates user guidance to allow customizable and targeted analysis, as well as template-guided partitioning to enable rapid batch processing. In this study, we demonstrate its performance in three data sets. With its versatility, reproducibility, and speed of analysis, as well as user-customized flexible analytical scheme, X-Cyt will certainly become a valuable tool for future cytometry-based profiling studies.

Application of user-guided automated cytometric data analysis to large-scale immunoprofiling of invariant natural killer T cells