Spatial transcriptomics helps researchers see where genes are active in tissue. The Xenium In Situ platform is one of the leading tools used for high-plex, single-cell spatial profiling. As more labs offer Xenium services, picking the right provider matters more than ever.
Certification is just the starting point, not the whole story
Xenium certification means a service provider has the right setup and basic skills. But certification does not explain much about he scientific depth, tissue handling skills, or analytical sophistication. When evaluating a Xenium certified service provider, it is a minimum requirement, not proof of quality. You still need to look deeper.
Tissue handling and sample preparation expertise
Spatial transcriptomics results are highly sensitive to the quality of tissue. Fresh frozen and FFPE tissues behave differently. Each needs the right approach. A solid provider should know how to check section quality, assess RNA integrity, and adjust protocols for different tissue types. If the tissue is poorly handled early on, there’s no fix later. And that affects data quality and interpretability.
Panel design and scientific support
Xenium studies require a thoughtful gene panel design because it shapes the whole study. If the wrong targets are chosen, the data won’t answer your question. Experienced providers help at this stage. They offer scientific consultation with you to prioritize genes that match your goals and the biology of your tissue. This step improves the interpretative value ot the resulting dataset.
Image acquisition and quality standards
Xenium data includes both images and transcript detection. Image quality affects how well cells are identified and how transcripts are mapped.
Providers should have provided clear quality control standards. They should track things like signal strength, noise, and tissue coverage. And they need to be transparent about how they control these factors.
Bioinformatics and analytical capabilities
Raw Xenium data is not ready to use. It needs processing and analysis. This includes cell segmentation, transcript mapping, clustering and visualization. Evaluating a provider’s bioinformatics capabilities, which includes their ability to integrate Xenium data with complementary single-cell RNA-seq datasets. This is essential for research teams that need more than data delivery. Providers offering end-to-end analytical support can accelerate the path from tissue to biological insight.
Conclusion
Choosing a Xenium-certified service provider takes more than verifying certification. Look at how they handle tissue, support study design, manage the quality of the image, and analyze data.
Investing time in provider evaluation upfront pays dividends in data quality and scientific impact downstream.
Image from freepik by freepik
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