72: Evaluate Cell–cell and Cell–extracellular Marker Interactions Based on Imaging Mass Cytometry Data

Thomas M. Menino Convention & Exhibition Center 

Spatial context is essential for interpreting cell behavior in tissues, yet linking local microenvironments to cell phenotypes in Imaging Mass Cytometry (IMC) remains challenging. We present scalable methods to quantify two spatial feature sets around each cell. For cell–extracellular marker interactions, we aggregate pixel-level marker intensities within concentric rings surrounding each cell. For cell–cell interactions, we estimate the composition of neighboring cell types within increasing radii, enabling fixed-radius summaries and multi-scale interaction curves.

We use spatial indexing for fast queries of marker pixels and neighbors. Extracellular features are analyzed with mixed-effects models to estimate condition-specific marginal means while accounting for image-to-image variability. Cell–cell enrichment or depletion is assessed by comparing local neighborhood composition to overall image abundances across radii.

We implement these methods in the R package CytoHalo and demonstrate them on Collagen I–macrophage associations and macrophage-centered cell–cell interactions.

IMC spatial analysis

Cell–cell interactions

Extracellular markers 

Section on Statistics in Imaging