SpatialCCCbench: Standardized Metrics for the Systematic Evaluation of Spatial Cell-Cell Communication Methods

Spatial transcriptomics (ST) enables transcriptome profiling with preserved spatial context, providing spatial dimensions that are essential for understanding complex intercellular signals in tissue architecture. ST-based CCC tools integrate spatial and molecular information to decipher intercellular interactions from a spatially informed perspective. Despite the rapid evolution of many CCC computational tools, a systematic assessment of their performance in handling ST-specific heterogeneity, utilizing spatial information efficiently, and robustness against technical or biological noise is still lacking. To address this gap, SpatialCCCbench incorporates classification accuracy, spatial signal features, robustness, and user-friendliness, aiming to guide the selection of optimal CCC inference tools across diverse spatial biology contexts. SpatialCCCbench systematically evaluates the scenario-specific applicability of ST-based CCC tools. It helps users select tools according to their analytical objectives and provides a practical benchmark for future method development.