A Guide on Analyzing Flow Cytometry Data Using Clustering Methods and Nonlinear Dimensionality Reduction (tSNE or UMAP)

Thomas A. Ujas, Veronica Obregon-Perko, Ann M. Stowe

Research output: Contribution to journalArticlepeer-review

17 Scopus citations

Abstract

Flow cytometry has been used for the last two decades to identify which immune cell subsets diapedese from the periphery into the brain parenchyma following injuries, including ischemic and hemorrhagic stroke. Recent developments have moved the analysis of high-parameter flow cytometry data sets from the traditional analysis method of manual gating to using unbiased analyses to improve scientific rigor. This chapter gives a step-by-step guide on using modern computational approaches to analyze complex flow cytometry data sets in FlowJo™ Software v10. The section will describe pre-processing and outline the steps needed to perform unsupervised clustering of your data set in addition to using nonlinear dimensionality reduction for visualizing your analysis. While these methods can identify long-term neuroinflammatory responses after stroke, the methods could be applied to a variety of flow cytometry data sets.

Original languageEnglish
Pages (from-to)231-249
Number of pages19
JournalMethods in Molecular Biology
Volume2616
DOIs
StatePublished - 2023

Bibliographical note

Publisher Copyright:
© 2023. The Author(s), under exclusive license to Springer Science+Business Media, LLC, part of Springer Nature.

Keywords

  • Flow cytometry
  • Flow cytometry analysis
  • FlowJo™
  • Nonlinear dimensionality reduction
  • UMAP
  • tSNE

ASJC Scopus subject areas

  • Molecular Biology
  • Genetics

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