AUTHOR=Patel Ravi K. , Jaszczak Rebecca G. , Im Kwok , Carey Nicholas D. , Courau Tristan , Bunis Daniel G. , Samad Bushra , Avanesyan Lia , Chew Nayvin W. , Stenske Sarah , Jespersen Jillian M. , Publicover Jean , Edwards Austin W. , Naser Mohammad , Rao Arjun A. , Lupin-Jimenez Leonard , Krummel Matthew F. , Cooper Stewart , Baron Jody L. , Combes Alexis J. , Fragiadakis Gabriela K. TITLE=Cyclone: an accessible pipeline to analyze, evaluate, and optimize multiparametric cytometry data JOURNAL=Frontiers in Immunology VOLUME=14 YEAR=2023 URL=https://www.frontiersin.org/journals/immunology/articles/10.3389/fimmu.2023.1167241 DOI=10.3389/fimmu.2023.1167241 ISSN=1664-3224 ABSTRACT=

In the past decade, high-dimensional single-cell technologies have revolutionized basic and translational immunology research and are now a key element of the toolbox used by scientists to study the immune system. However, analysis of the data generated by these approaches often requires clustering algorithms and dimensionality reduction representation, which are computationally intense and difficult to evaluate and optimize. Here, we present Cytometry Clustering Optimization and Evaluation (Cyclone), an analysis pipeline integrating dimensionality reduction, clustering, evaluation, and optimization of clustering resolution, and downstream visualization tools facilitating the analysis of a wide range of cytometry data. We benchmarked and validated Cyclone on mass cytometry (CyTOF), full-spectrum fluorescence-based cytometry, and multiplexed immunofluorescence (IF) in a variety of biological contexts, including infectious diseases and cancer. In each instance, Cyclone not only recapitulates gold standard immune cell identification but also enables the unsupervised identification of lymphocytes and mononuclear phagocyte subsets that are associated with distinct biological features. Altogether, the Cyclone pipeline is a versatile and accessible pipeline for performing, optimizing, and evaluating clustering on a variety of cytometry datasets, which will further power immunology research and provide a scaffold for biological discovery.