Xenium services: spatial transcriptomics at single-cell resolution
Explicyte is a 10x Genomics Certified Service Provider offering end-to-end Xenium spatial transcriptomics services for academic, biotech and pharmaceutical teams.
With two Xenium Analyzers in Bordeaux, France, we've already processed over 500 samples on Xenium. We support projects from tissue sourcing and QC to data generation, bioinformatics and biological interpretation.
XENIUM CRO SERVICES
Why run Xenium with Explicyte
Fast results: 2 Xenium instruments on-site
Parallel instrument capacity to open slots fast and process large cohorts.
Service provider certified by 10x Genomics
Explicyte is certified by 10x Genomics for Xenium, Visium HD and Chromium X.
In-house bioinformatics & spatial analysis
From raw Xenium data to cell annotation, spatial analysis, biological interpretation and publication-ready deliverables.
HOW WE RUN XENIUM STUDIES
From study design to interpreted Xenium data
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1Objectives, samples, and study design
A PhD study director reviews your biological objectives, available tissue, cohort, timeline and budget, then defines sample eligibility, panel strategy, slide layout, metadata requirements and analysis plan.
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2Sample logistics, preparation, and QC
We provide sample and shipping requirements and can support tissue sourcing when needed. After registration and preparation, tissue suitability is assessed by pathology review and RNA-quality testing, including RNAscope-based qualification where applicable. Only samples meeting the agreed study criteria proceed to Xenium profiling.
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3Xenium data generation on two Analyzers
Qualified samples are processed using the selected Xenium panel, with parallel instrument capacity, harmonized run planning and platform-specific QC across the cohort.
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4Data analysis, post-Xenium imaging & delivery
Our in-house team can preprocess, annotate and analyze the dataset to the depth required by the study, with downstream analyses tailored to the panel and biological question. Where relevant, we can also perform post-Xenium H&E or multiplex IF on the same tissue section and register the resulting images with the Xenium dataset, connecting morphology and protein phenotypes with spatial gene expression.
An in-house workflow to clean and standardize Xenium datasets
After preprocessing
Before preprocessing
Cluster annotation of a Xenium dataset, before and after our preprocessing workflow — ambient RNA, doublets, batch effects, and contaminating populations removed.
Comprehensive Xenium deliverables
- Xenium Analyzer output bundle (transcripts + images)
- Raw + filtered cell-by-gene expression matrix
- Cell segmentation masks (nuclear + cellular)
- Cell-type annotation (curated references + AI-assisted)
- Spatial clustering + neighborhood statistics
- Differential expression + cell-cell communication analysis
- QC report (imaging, segmentation, dataset stats)
- Xenium Explorer bundle for interactive visualization
- Optional post-Xenium H&E or multiplex IF imaging with spatial registration
- Publication-ready figures + report
At a glance
Xenium spatial transcriptomics specifications
- Resolution
- Subcellular transcript localization with cell-level segmentation and analysis in intact tissue, without dissociation.
- Panels
- RNA panels: focused 50–480 gene panels or Xenium Prime 5K, with custom gene options. RNA + protein: Xenium Protein subpanels available with compatible human <500-gene FFPE workflows.
- Imageable area
- Up to 472 mm² per run across 2 slides.
- Sample multiplexing
- Multiple tissue sections or TMA cores can share a slide where tissue dimensions and study design allow, increasing cohort throughput and reducing per-sample run cost.
- Sample types
- Human or mouse FFPE and fresh-frozen tissue specimens (core-needle biopsies, TMAs, surgical sections), organoids, and STAMP-compatible samples (fixed cell cultures).
- Throughput
- Two Xenium instruments on-site — up to 32 samples per week depending on the panel.
- Certification
- 10x Genomics Certified Service Provider
- Post-Xenium imaging
- Same-section H&E or multiplex IF can be added after Xenium profiling, with spatial image registration to the Xenium dataset where included in the study design.
Xenium case studies
Xenium studies and data examples
Paul Marteau, PharmD (study director), Imane Nafia, PhD (CSO), Loïc Cerf, MSc (COO), Alban Bessede, PhD (founder, CEO), Jean-Philippe Guégan, PhD (CTO)
contact our team
Discuss your Xenium project
Have a Xenium project in mind? Tell us the tissue, the genes you care about, and the cohort size — we'll advise on panel and design and scope it with you.
XENIUM FAQ
Frequently asked questions about Xenium services
What is Xenium spatial transcriptomics, and when should I use it?
Xenium is 10x Genomics’ in situ spatial transcriptomics platform for targeted gene-expression profiling at single-cell resolution while preserving tissue architecture. Choose it when you have defined genes of interest and need them resolved cell by cell, in spatial context. For a broader comparison, see our guide to Xenium vs. Visium HD vs. Chromium X.
Which Xenium panels can I run, and can they be customized?
Does Xenium work on FFPE, or only fresh-frozen?
Both. We run Xenium on FFPE and fresh-frozen sections, across indications and species, with specific expertise in FFPE tumor material — biopsies, TMAs, and surgical sections. We work back from the material you have to what’s feasible.
Can Explicyte source tissue for a Xenium study?
Yes, where suitable material is available. Through our network of biobanks, Explicyte can support sourcing of normal and tumor FFPE cohorts for spatial transcriptomics studies. Feasibility depends on the indication, sample criteria, cohort size, required metadata and applicable consent or regulatory requirements.
How do you qualify samples before a Xenium run?
Before profiling, samples undergo study-specific qualification designed to reduce the risk of committing unsuitable tissue to a Xenium run. This typically combines pathology review of tissue morphology and usable tissue area with RNA-quality assessment, including RNAscope-based qualification where applicable. Samples proceed according to the acceptance criteria agreed during study setup.
What cohort sizes can Explicyte support on Xenium?
From a handful of blocks to large cohorts. With two Xenium instruments on-site we run up to 32 samples per week depending on the panel, and the 472 mm² imageable area per run lets small biopsies or a TMA share a slide — so a cohort moves through with consistent QC across the batch. Tell us the number and we’ll scope timeline and capacity.
Can you perform H&E or multiplex IF after Xenium?
Yes. The Xenium workflow leaves the tissue section largely intact, allowing additional staining and imaging after the spatial transcriptomics run. Depending on the study design, Explicyte can perform post-Xenium H&E or multiplex IF on the same section and register the resulting images with the Xenium dataset, allowing morphology or protein phenotypes to be interpreted alongside spatial gene expression. This is distinct from Xenium Protein, which provides integrated RNA and protein detection during compatible human FFPE <500-gene workflows.
Do I get raw data or interpreted results?
Both are available. The standard deliverable is an interpreted dataset — cell-by-gene matrix, segmentation, cell typing, tumor-microenvironment characterization, spatial statistics, QC, and publication-ready figures — from our in-house data-science team. If you only want the primary output plus your own downstream analysis, tell us where you want the handoff.
Are you a certified Xenium provider?
Yes. Explicyte is a 10x Genomics Certified Service Provider for Xenium (and Visium HD and Chromium X).
