ConvexGating infers gating strategies from clusters in single cell cytometry data

Vincent D. Friedrich; Karola Mai; Thomas P. J. Hofer; Elfriede Nößner; Lorenzo Bonaguro; Celia L. Hartmann; Aleksej Frolov; Caterina Carraro; Doaa Hamada; Mehrnoush Hadaddzadeh Shakiba; Heidi Theis; Dalila Juliana Silva Ribeiro; Dagmar Wachten; FT Wunderlich; Markus R. Scholz; Fabian Joachim Theis; Matthias Becker; Marc Beyer; Joachim Ludwig Schultze; Maren Büttner

doi:10.1038/s41467-026-77360-z

ImmunologyNature CommunicationsSep 18, 2026

Peer-reviewed journal article

ConvexGating infers gating strategies from clusters in single cell cytometry data

Vincent D. Friedrich iD, Karola Mai iD, Thomas P. J. Hofer iD, Elfriede Nößner, Lorenzo Bonaguro iD, Celia L. Hartmann, Aleksej Frolov iD, Caterina Carraro iD, Doaa Hamada iD, Mehrnoush Hadaddzadeh Shakiba iD, Heidi Theis iD, Dalila Juliana Silva Ribeiro iD, Dagmar Wachten iD, FT Wunderlich iD, Markus R. Scholz iD, Fabian Joachim Theis iD, Matthias Becker iD, Marc Beyer iD, Joachim Ludwig Schultze iD, Maren Büttner iD

Abstract

Manual expert gating remains common practice for the definition of specific cell populations in the analysis of flow cytometry data. The increasing number of measured parameters per individual cell and high inter-rater variability makes manual gating inconsistent in many scenarios such as multi-center studies. Here, we propose ConvexGating, an AI tool that automatically learns gating strategies in an unbiased, fully data-driven, yet interpretable manner. ConvexGating scales efficiently with increasing parameter space, creating proficient strategies with low-contamination in the extracted population for previously known and so far unknown or ill-defined cell populations. The inferred strategies are independent of parent populations, for instance, plasmacytoid dendritic cells (pDCs) can be fully identified as CD45RA- CD123+. In addition to flow cytometry data, ConvexGating derives gating strategies for cyTOF (Cytometry by Time of Flight) and CITEseq (Cellular Indexing of Transcriptomes and Epitopes by Sequencing) data and supports optimal design of marker panels for cell sorting.

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