SCORPy: Lowering the computational barrier to reproducible multiplexed imaging spatial single-cell proteomics analysis

Spatially resolved single-cell proteomic imaging technologies, including cyclic immunofluorescence (CycIF), generate high-dimensional data, critical for tissue-scale biological analysis. However, single-cell analysis remains computationally demanding, lacks standardization across platforms and is often inaccessible to experimental biologists without programming expertise. Here we present SCORPy (Single-Cell proteOmics Research Platform), a standalone, cross-platform desktop application that provides an end-to-end, code-free workflow for the analysis of single-cell proteomic data extracted from imaging experiments. SCORPy introduces methodological advances for preprocessing multiplexed imaging data: an exposure-aware, cycle-matched background correction strategy, and a normalization framework that harmonizes signal distributions across markers while enabling batch correction across experiments. These approaches are integrated with quality control, interactive thresholding and cell phenotyping using a hierarchical cell reference library, and downstream compositional and spatial analyses within a unified interface. Sample-level metadata can be incorporated throughout the workflow to support integrative analyses and facilitate generation of publication-ready visualizations. By combining robust preprocessing methods with an accessible implementation, SCORPy reduces computational barriers and promotes broader adoption of spatial single-cell proteomics analysis.