Spatial biology CRO services — spatial transcriptomics & digital pathology
Explicyte designs and executes spatial biology studies across FFPE and fresh-frozen tissue using Atera, Xenium, Visium HD, GeoMx DSP and multiplex IHC/IF.
We help select the right platform, qualify samples, generate the data and deliver in-house bioinformatics and biological interpretation.
Recently published with our spatial platforms
END-TO-END SPATIAL BIOLOGY SUPPORT
Is Explicyte the right fit for your study?
What samples?
FFPE and fresh-frozen tissue, across indications and species. Tell us what you have — we work back from the material to what's feasible.
Which platform?
Not sure which technology or panel fits your question? We advise on the most cost- and time-effective plan for your samples and objectives.
Quality standards?
Explicyte is a 10x Genomics Certified Service Provider, and our digital pathology workflow is certified ISO 9001 and ISO 13485.
What output?
Beyond raw data, our in-house bioinformatics team delivers custom spatial analysis — from data cleaning to publication-ready figures.
Our spatial biology platforms
Spatial technologies for every depth and scale
Whole transcriptome · single-cell
Atera
10x’s in-situ whole-transcriptome platform pairs single-cell sensitivity with cohort-scale throughput for human samples. First runs available Q4 2026 / Q1 2027.
Single-cell · targeted panels
Xenium
Single-cell spatial transcriptomics in intact human and mouse tissues, with targeted panels (5K or focused panels). 2 Xenium instruments on-site to process large cohorts.
Whole transcriptome · Morphology-anchored
Visium HD
Whole-transcriptome coverage across an entire section, registered to the histology, in human, mouse, and rat samples.
Region-based · whole transcriptome
GeoMx DSP
Digital spatial profiling of regions of interest in mouse and human samples — whole-transcriptome, plus protein panels available.
Whole-slide · multiplex protein
Digital pathology (mIF/IHC)
In-house multiplex immunofluorescence or IHC on rodent or human samples — stained, scanned, and analyzed end to end.
SPATIAL BIOLOGY PROJECTS
Sponsor stories
Why Explicyte
Why run your spatial study with Explicyte
Scientific advice to optimize your spatial study
Each study begins with scientific review of the biological question, tissue, cohort and required readout so that platform and panel selection are driven by the study objectives rather than by a predefined technology.
The whole spatial stack, one team
We run the different spatial approaches in-house, so the recommendation isn’t skewed toward the one instrument we happen to own. You get the approach that fits the biology — including combinations across platforms on the same cohort.
Slots open, cohorts delivered fast
Slot availability and lead time on large cohorts are what stall spatial projects. We keep both in check with high-throughput or redundant instruments and, where applicable, sample-multiplexing strategies that cut cost and lead times.
Bioinformatics, not just raw data
Too often a dataset sits on a server waiting to be analyzed. Our in-house bioinformatics team takes it from there — from cleaning and annotation through to in-depth statistics and publication-grade deliverables.
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 project
Tell us your biological question, tissue type, cohort size and preferred platform if known. We'll help define the most appropriate spatial workflow, sample requirements, analysis plan, timeline and budget.
Answers about spatial biology CRO services
FAQs about spatial biology services
How do I choose between Atera, Xenium, Visium HD, GeoMx and digital pathology?
The right platform depends on the biological question, gene or protein breadth, spatial resolution, tissue area and cohort size. Atera combines whole-transcriptome in situ profiling with single-cell sensitivity and high tissue throughput; Xenium provides targeted high-plex in situ profiling at single-cell resolution; Visium HD provides sequencing-based whole-transcriptome spatial profiling anchored to tissue morphology; GeoMx DSP profiles selected regions of interest for RNA or protein; and multiplex IHC/IF provides spatial protein phenotyping across tissue sections. We can recommend a single platform or a complementary cross-platform strategy after reviewing your samples and objectives.
What sample types do you work with?
We work with FFPE and fresh-frozen tissue across multiple indications and species, depending on platform compatibility. Tissue suitability, morphology and RNA quality are reviewed where required during study setup, and we recommend the platform and workflow that best fit the available material.
What cohort size can you handle?
From a handful of blocks to large cohorts. The workflow is built for consistent QC across a batch, so scaling up doesn’t mean the later blocks are handled differently from the first. Tell us the number and we’ll scope capacity and timeline around it.
What are your turnaround times?
Turnaround depends on the platform, the cohort size, and the depth of analysis you need, so we quote it per project rather than posting a single number. After a short intake call you get a scope with a timeline attached, before any work starts.
Is bioinformatics included, or do I just get raw data?
Bioinformatics is performed in house. Depending on study scope, deliverables can include platform-specific QC, cell or region annotation, spatial-domain and neighborhood analyses, differential expression, pathway analysis, interactive outputs and publication-ready figures. Raw or minimally processed data can also be supplied when preferred.
I'm based outside France — how does sample logistics work?
We routinely receive cohorts from across Europe and beyond. We’ll send shipping and documentation guidance for your material up front, coordinate on customs paperwork where it’s needed, and confirm receipt and QC on arrival before the run begins.
Who owns the data and the results?
You do. Under our standard service agreement the sponsor owns the data and the results generated from their cohort; the specifics are set out in that agreement before the project starts.
Are your spatial transcriptomics services certified?
Explicyte is a 10x Genomics Certified Service Provider for Xenium and Visium HD. In parallel, our ISO 13485:2016 and ISO 9001:2015-certified QMS covers defined tissue-biomarker development and testing activities. GeoMx and Atera are not currently covered by these certifications.
Can you combine platforms on the same cohort?
Yes — that’s often the point. A common pattern is whole-transcriptome discovery on one platform followed by single-cell or region-level confirmation on another, all on the same cohort and analyzed together. Because it’s one team, the cross-platform dataset comes back integrated rather than as separate deliverables.
