US Based · Spatial Transcriptomics
10x Genomics Visium Spatial Transcriptomics Service
Single cell scale spatial profiling with Visium CytAssist HD platform. FFPE, fresh-frozen or fixed-frozen tissue compatibility. Slide placement, capture, sequencing and analysis, all in our SF Bay Area lab.
Assay
Visium CytAssist
Capture area
6.5 mm or 11 mm
Capture
3′ or probe-based
Species
Human, mouse, rat or agnostic
Sequencing
NovaSeq X+ PE50
Turnaround
3 weeks – expedited options
Price
$6,000–15,000 per project
Volume pricing available
Service Highlights
From tissue block to spatial mapping, all in one lab
Every stage runs in-house with defined QC criteria, from sectioning and slide placement through sequencing and spatial analysis. Engage us for end-to-end service, or enter at the stage where you need support.
Tissue Prep & QC
- Sectioning and TMA building
- H&E staining and imaging
- DV200 / RIN QC evaluation
Visium CytAssist
- CytAssist tissue transfer
- 2 x 2 µm barcoded squares
- Probe-based or 3′ poly(A)
Sequencing
- Sequencing depth matched to sample type
- Illumina NovaSeq X+ PE50
- Data QC and FASTQ delivery
Analysis
- Space Ranger outputs & CLOUPE
- Publication-ready figures
- Standard or Advanced packages
Sample & Service Compatibility
Find your sample, find your service
| Sample type | Quality threshold | HD WT Panel | HD 3′ |
|---|---|---|---|
| FFPE blocks | DV200 >30% | ✓ | — |
| FFPE slides | DV200 >30% | ✓ | — |
| Fresh frozen tissue | RIN >7 | ✓ | ✓ |
| Fixed frozen tissue | DV200 >30% | ✓ | — |
| OCT blocks | RIN >7 | ✓ | ✓ |
Service Packages
Match the Visium service best suited for your study
| HD WT Panel | HD 3′ | |
|---|---|---|
| Service | Visium HD Standard (6.5 mm) Visium HD 11×11 (11 mm) | Visium HD 3′ (6.5 mm) |
| Coverage | Protein-coding genes | Whole transcriptome |
| Species | Human, mouse, rat | Species agnostic |
| Chemistry | Probe hybridization | 3′ poly(A) + RT |
Need a different capture or resolution?
Every service includes
- Sample QC
- Slide placement
- Library prep
- Library QC
- Sequencing
- Data QC with FASTQ delivery
Available as add-ons
- Sectioning
- Custom probe panels
- H&E staining and imaging
- TMA construction
- IF staining
- Standard or Advanced analysis
Technical excellence
Three HD slides, one CytAssist instrument
No gaps between features and no spot averaging, so resolution reaches single cell scale. WT Panel offers 6.5 x 6.5 mm and 11 x 11 mm; HD 3′ is 6.5 x 6.5 mm.
Both assays pair gene expression with H&E morphology on the same section so every transcript is read in anatomical context. The WT Panel can add protein immunofluorescence on that same section, giving three readouts from one piece of tissue.
HD WT Panel is probe-based, covering protein-coding genes in human, mouse and rat. Probes hybridize directly to mRNA, which is why fixed and archival FFPE performs well, and it is the most sequencing-efficient Visium HD assay. Custom genes can be spiked in for viral monitoring or xenografts.
HD 3′ Gene Expression uses 3′ poly(A) capture with reverse transcription for whole-transcriptome coverage. It is species agnostic and supports de novo discovery, including feasibility for isoforms and TCR/BCR sequences.
Analysis Packages
Standard or advanced interpretation
Every project delivers FASTQ files and data QC. Add an analysis package for processed outputs and biological interpretation.
Visium Standard Analysis
- Space Ranger sequencing QC metrics
- Space Ranger gene expression and heatmap visualization
- CLOUPE file for use in Loupe Browser
Visium Advanced Analysis
- Advanced filtering of low-quality cells, contamination and multiplets
- Dimensionality reduction and clustering on filtered data
- tSNE / UMAP plots with cluster information
- General cell type annotation
- Differential gene expression for clusters and annotated cell types
- Pathway enrichment analysis
- Group comparison
Service experience
Working with us
Every project is run by scientists, tracked in one portal, and processed entirely in our own lab.
PhD-Level Project Oversight
A PhD scientist owns your project from design through interpretation.
Dedicated Project Manager
One point of contact from quote through delivery.
Easy Ordering
Register samples, track status, and download results in one portal.
100% US-Based
Every stage runs in-house in Foster City, CA. No outsourcing.
Resources & insights
Technical resources
Brochure
Spatial Transcriptomics Brochure
Spatial transcriptomics with Signios Bio: where gene expression meets precision.
BLOG
Choosing the Best Spatial Service for Your Study
Visium HD vs. Xenium Prime vs. Illumina StrataMap — matching platform to study design.
BLOG
Integrating Single-Cell and Spatial Data
Building multimodal maps for translational research.
Frequently asked questions
Planning your spatial project
Samples & tissue prep
What upstream steps can you handle for me?
Sectioning onto charged glass slides, H&E staining and imaging, region-of-interest marking, CytAssist tissue transfer, library prep and QC, sequencing, and data QC. Send FFPE or OCT blocks and we handle sectioning, or send pre-cut serial sections and curls and we start at staining. Send raw tissue and we take it from there, or enter the workflow at whatever step you need.
What sample types are compatible?
FFPE block — ship on dry ice. If the cross section exceeds the capture area, mark your region of interest on the block.
FFPE sections (slides or curls) — four 25 µm curls in a microfuge tube for QC, plus four serial sections at 5–10 µm on charged slides. H&E stain one and mark the region of interest on the back. Slides ship at room temperature; curls in tubes ship on dry ice.
OCT block (frozen or fixed) — ship on dry ice. If the section exceeds the capture area, send a photo of the block with the region of interest marked.
OCT sections (slides or curls) — four 25 µm curls for QC, plus four serial sections at 10–20 µm on charged slides. H&E stain one and mark the region of interest. Ship on dry ice.
No marking is required if the tissue cross section fits within the capture area (6.5 x 6.5 mm or 11 x 11 mm). Follow our spatial transcriptomics sample prep protocol for full detail.
Which species are supported?
The HD WT Panel supports human, mouse and rat via probe-based chemistry. HD 3′ Gene Expression is species agnostic, making it the choice for organisms outside those three.
How large is the capture area?
Two sizes on the HD WT Panel: 6.5 x 6.5 mm and 11 x 11 mm. HD 3′ Gene Expression is 6.5 x 6.5 mm. Every slide carries two capture areas, so paired or replicate samples can run together.
Data & delivery
How many transcripts are profiled?
The WT Panel covers protein-coding genes by probe hybridization. HD 3′ Gene Expression gives whole-transcriptome coverage with de novo discovery, including feasibility for isoforms and TCR/BCR. Both resolve to a continuous lawn of 2 x 2 µm barcoded squares.
What read depth do I get?
What sequencing configuration is used?
What is included in a package?
Sample QC, slide placement, library prep, library QC, sequencing, and data QC with FASTQ delivery.
What is not included?
Sectioning, custom probe panels, and analysis packages are quoted separately. H&E staining, imaging and TMA construction are also available as add-ons.
How is my data delivered?
Demultiplexed FASTQ files and a data QC report via secure FTP, with transfer to your own AWS, Globus or other cloud platform available. Analysis packages add Space Ranger outputs and a CLOUPE file for Loupe Browser.
Ordering & logistics
How do I place an order?
Register your samples in the customer portal to generate your shipping documents, then print and include them in your package. A project manager confirms QC before processing begins.
How do I ship samples?
What is your typical turnaround time?
3 weeks standard from sample receipt to data delivery, with expedited options available. Analysis packages add time depending on scope.
Is there a minimum number of samples?
No order minimums. We recommend at least three biological replicates per condition for statistical power, and per-sample pricing improves with batch size.
Get started with your project
Ready to add spatial context to your study? Contact our team for a technical consultation. We will guide you through assay selection, sample requirements, capture area sizing, and read depth aligned to your analysis goals.
- Volume pricing available on all HD packages
- Data in 3 weeks, expedited available
- Single cell–scale 2 x 2 µm resolution
- 100% in-house at Foster City, CA