Bartek Rajwa

In cytometry data analysis, a gate functions as a classification boundary, a decision rule that partitions the measurement space into populations of interest [1]. From a decision-theoretic perspective, the geometry of a gate encodes specific assumptions about the statistical relationships among measured parameters [2]. When these assumptions are not explicitly justified, the gate becomes an arbitrary aesthetic choice rather than a principled analytical decision.

1 Introduction The rapid growth of spectral flow cytometry, alongside the proliferation of computational methods for data processing and analysis, has recently introduced considerable terminological confusion. Terms that have long held established meanings in fields such as spectroscopy, spectral imaging, mathematics, and optimization theory are now being redefined (often inappropriately) within the cytometry community.

PC polychromatic cytometry SC spectral cytometry OMIPs optimized multicolor immunofluorescence panels SSM spillover spreading matrix PMT photomultiplier APD avalanche photodiode detector SQI spread quantification index CL cell ontology COG Children's Oncology Group FCS Flow Cytometry Standard tSNE t-distributed stochastic neighbor embedding UMAP uniform manifold approximation projection CE-IVD in vitro diagnostic IVD in vitro diagnostic PI propidium iodide DAPI 4′,6-diamidino-2-phenylindole...