SpatialBench: Comparative cross-platform benchmarking of high-resolution spatial transcriptomics using matched mouse lymphoid tissue

Abstract

Spatial transcriptomics (ST) has rapidly expanded with the introduction of multiple high-resolution platforms, yet cross-platform benchmarking remains limited and largely focused on technical performance. Here we present SpatialBench, a matched multi-platform resource comprising Visium HD, Xenium and MERSCOPE data together with single-cell and single-nucleus references from a malaria-challenged wild-type and B cell-specific Tbx21 knockout mouse spleen model. In this system, loss of T-bet in B cells disrupts germinal center (GC) polarization and antibody maturation, providing a biologically grounded benchmark for technology comparison. We leveraged this system to systematically evaluate ST platform performance using technical and biological readouts. Across platforms, immune organization and Tbx21-associated programs were consistently recovered, indicating robustness of major biological signals. Platforms instead differed in the level of biological resolution accessible. Visium HD enabled transcriptome-scale GC characterization and, together with Xenium, resolved dark and light zone organization, whereas GC zonation was not resolved in MERSCOPE, consistent with differences in transcript detection sensitivity. SpatialBench provides a biologically defined reference dataset for evaluation of ST technologies, method development, computational benchmarking, and studies of GC spatial organization in lymphoid tissue.