This article provides a systematic evaluation of four advanced, commercially available high-throughput spatial transcriptomics (ST) platforms with subcellular resolution: Stereo-seq v1.3, Visium HD FFPE, CosMx 6K, and Xenium 5K. To establish a robust benchmark, the researchers generated serial tissue sections from human cancer samples (colon adenocarcinoma, hepatocellular carcinoma, and ovarian cancer) and used CODEX protein profiling and single-cell RNA sequencing (scRNA-seq) as orthogonal ground truth datasets. The study comprehensively assesses platform performance across technical metrics such as sensitivity, spatial accuracy, and diffusion control, as well as downstream analytical capabilities including cell segmentation, cell type annotation, and spatial clustering. The resulting multi-omics dataset is publicly accessible via the SPATCH web server, offering a valuable resource for future computational and biological discoveries in the spatial omics field.
References:
- Ren P, Zhang R, Wang Y, et al. Systematic benchmarking of high-throughput subcellular spatial transcriptomics platforms across human tumors[J]. Nature Communications, 2025, 16(1): 9232.
