Analyzing high-dimensional cytometry data using FlowSOM

Katrien Quintelier, Artuur Couckuyt, Annelies Emmaneel, Joachim Aerts, Yvan Saeys, Sofie Van Gassen*

*Corresponding author for this work

Research output: Contribution to journalReview articleProfessionalpeer-review

66 Citations (Scopus)


The dimensionality of cytometry data has strongly increased in the last decade, and in many situations the traditional manual downstream analysis becomes insufficient. The field is therefore slowly moving toward more automated approaches, and in this paper we describe the protocol for analyzing high-dimensional cytometry data using FlowSOM, a clustering and visualization algorithm based on a self-organizing map. FlowSOM is used to distinguish cell populations from cytometry data in an unsupervised way and can help to gain deeper insights in fields such as immunology and oncology. Since the original FlowSOM publication (2015), we have validated the tool on a wide variety of datasets, and to write this protocol, we made use of this experience to improve the user-friendliness of the package (e.g., comprehensive functions replacing commonly required scripts). Where the original paper focused mainly on the algorithm description, this protocol offers user guidelines on how to implement the procedure, detailed parameter descriptions and troubleshooting recommendations. The protocol provides clearly annotated R code, and is therefore relevant for all scientists interested in computational high-dimensional analyses without requiring a strong bioinformatics background. We demonstrate the complete workflow, starting from data preparation (such as compensation, transformation and quality control), including detailed discussion of the different FlowSOM parameters and visualization options, and concluding with how the results can be further used to answer biological questions, such as statistical comparison between groups of interest. An average FlowSOM analysis takes 1–3 h to complete, though quality issues can increase this time considerably.

Original languageEnglish
Pages (from-to)3775-3801
Number of pages27
JournalNature Protocols
Issue number8
Publication statusPublished - 25 Jun 2021

Bibliographical note

Funding Information:
S.V.G. is an ISAC Marylou Ingram Scholar and supported by an FWO postdoctoral research grant (Research Foundation—Flanders). We thank the VIB Flow Core for training, support and access to the instrument park. This research received funding from the Flemish Government (AI Research program). A.E. is supported by the PID Grand Challenges Program of VIB. This VIB Program received support from the Flemish Government under the Management Agreement 2017–2021 (VR 2016 2312 Doc.1521/4).

Publisher Copyright:
© 2021, The Author(s), under exclusive licence to Springer Nature Limited.


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