A new benchmarking study has set the standard for evaluating high-throughput, subcellular spatial transcriptomics technologies—critical tools for understanding complex tissue biology in cancer and beyond.
"Systematic Benchmarking of High-Throughput Subcellular Spatial Transcriptomics Platforms"
How Did 10x Genomics Platforms Perform Against the Competition?
Visium HD (FFPE and Fresh Frozen): Visium HD from 10x Genomics delivered robust, transcriptome-wide spatial gene expression maps with subcellular resolution. It demonstrated enhanced diffusion control, minimized spatial artifacts, and achieved high concordance with protein-based datasets (CODEX), outperforming other sequencing-based platforms in spatial precision and reproducibility.
While its single-cell segmentation was less precise than imaging-based platforms (sometimes dividing individual cells across multiple spots), Visium HD's ability to capture a broad range of transcripts make it a top choice for studies requiring comprehensive spatial profiling and tissue architecture analysis.
Xenium 5K: Xenium 5K excelled in high-sensitivity detection of lineage marker genes, precise cell segmentation, and reliable cell type annotation, often outperforming other platforms in these areas. Its single-molecule, imaging-based approach enabled accurate mapping of transcripts within individual cells and superior identification of small cell types, such as lymphocytes. Xenium 5K showed higher annotation reliability and spatial concordance with protein data, particularly in colon and ovarian cancer samples, compared to both sequencing- and imaging-based competitors.
While its gene panel was not as broad as sequencing-based platforms, its spatial resolution and cell-level accuracy set a new benchmark for high-throughput spatial transcriptomics.
Overall, 10x Genomics platforms consistently ranked among the top performers for spatial resolution, sensitivity, and cell type annotation.
BonsaiLab: Your 10x Genomics Partner in Spain and Portugal
BonsaiLab is the official distributor of 10x Genomics solutions in Spain and Portugal. If you're interested in bringing the latest spatial transcriptomics technologies—like Visium HD and Xenium 5K—into your research, our expert team is here to help.
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