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phenotyping

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Assign cell types from marker expression in IMC/MIBI data using clustering (PhenoGraph/FlowSOM/Leiden/Pixie), marker-based probabilistic classifiers (Astir), or image-context CNNs (CellSighter), covering the double-positive segmentation artifact, lineage-vs-state markers, the two spillover types, and why a "cell type" in imaging is conditioned on a segmentation guess. Use when phenotyping segmented IMC cells, choosing clustering vs classification, diagnosing implausible double-positive populations, separating lineage from functional markers, or transferring labels across a cohort.

When to use

• phenotyping segmented IMC cells
• choosing clustering vs classification
• diagnosing implausible double-positive populations
• separating lineage from functional markers
• transferring labels across a cohort

When not to use

• differential analysis
• statistical-unit choice

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