This study provides an independent evaluation of the Xenium In Situ platform, a high-resolution spatial transcriptomics technology developed by 10x Genomics. By analyzing 25 datasets across various species and tissues, researchers benchmarked Xenium’s performance against several other commercial and open-source platforms. The findings demonstrate that Xenium offers superior sensitivity compared to Visium and achieves a detection efficiency on par with established imaging-based methods. Beyond performance metrics, the authors offer best-practice recommendations for computational workflows, including optimized strategies for cell segmentation and data preprocessing. Their analysis highlights the platform's ability to map subcellular RNA distributions in 3D, allowing for a more nuanced understanding of tissue architecture. Ultimately, the source serves as a comprehensive guide for researchers seeking to maximize the biological insights gained from Xenium's subcellular mapping capabilities.

References:

• Marco Salas S, Kuemmerle L B, Mattsson-Langseth C, et al. Optimizing Xenium In Situ data utility by quality assessment and best-practice analysis workflows[J]. Nature Methods, 2025, 22(4): 813-823.