• ⸻ 2026-09-07

Extracting single-cell morphology and subcellular protein localisation from Xenium data with scPortrait

• Sophia C. Mädler, Niklas A. Schmacke

Spatial transcriptomics measures RNA abundance and spatial localization in tissue and is routinely complemented by fluorescence microscopy imaging. Here, we show how to extract single-cell images from this data with the Python-based toolkit scPortrait. We then embed the single-cell images with a neural network to identify cells with distinct morphologies and intracellular protein distributions. We further characterize these cells by inspecting their gene expression, finding a morphologically defined subpopulation that expresses the collagen gene COL5A1.