10x Visium HD Spatial Transcriptomics Service
As a premier 10x Visium HD spatial transcriptomics service provider, we deliver unbiased, whole-transcriptome mapping across intact FFPE sections at a continuous 2µm resolution. By combining an optimized CytAssist workflow with deep computational deconvolution, we solve spatial resolution limits, enabling you to pinpoint cellular neighborhoods within complex tissues.
- Gapless 2µm × 2µm continuous grid for single-cell scale resolution.
- Optimized CytAssist workflow strictly validated for archived human and mouse FFPE blocks.
- Advanced bioinformatics utilizing Space Ranger for precise cellular segmentation.
Single-Cell Scale Spatial Resolution with Visium HD
A historical limitation of spatial transcriptomics has been the physical resolution of the capture arrays. Earlier iterations relied on 55µm spots separated by 100µm intervals, which inherently left physical gaps where tissue was not profiled, and grouped transcripts from multiple cells into a single data point.
The 10x Genomics Visium HD platform completely reconstructs this architecture. The HD array consists of 2µm × 2µm contiguous barcoded squares, ensuring gapless tissue coverage across the entire capture area. Because a typical mammalian cell is approximately 10 to 20 µm in diameter, a single cell spans multiple 2µm bins. This fundamental hardware upgrade allows researchers to profile the transcriptome at single-cell scale.
Each standard Visium HD capture area is 6.5mm × 6.5mm, providing a massive spatial canvas that accommodates standard microtome tissue sections. By leveraging a high-density probe chemistry (utilizing multiple probe pairs per target gene), the platform provides exceptional sensitivity, recovering whole-transcriptome data even from historically difficult sample types.
Diverse Applications in Translational Research
For translational research programs and therapeutic development, the transition to 2µm continuous spatial profiling opens new avenues for target discovery and mechanism-of-action studies. Integrating our spatial transcriptomics services into your pipeline allows for precise biological inquiries across diverse fields.
Tumor Microenvironment (TME) Mapping
In oncology, evaluating the exact spatial distribution of tumor-infiltrating lymphocytes (TILs) relative to the tumor boundary is critical. Visium HD allows for the precise mapping of immune exclusion zones, identifying where cytotoxic T cells are physically halted by physical or chemical barriers in the stroma. The 2µm resolution ensures that thin, single-cell wide invasive fronts or micro-capillaries are accurately profiled rather than averaged into the surrounding tissue signal.
Developmental Biology & Lineage Tracing
Understanding embryogenesis and organogenesis requires tracking gene expression across highly stratified, developing tissues. Visium HD enables the assignment of localized transcriptomic profiles to distinct developmental layers. Researchers can map morphogen gradients without physical microdissection, preserving the delicate native architecture required to understand tissue maturation.
Neurobiology and Pathology
The mammalian cortex and specific brain structures operate based on highly organized, layered architectures. The continuous 2µm grid allows researchers to map pathological markers—such as localized microglial activation or astrogliosis—directly adjacent to microscopic amyloid-beta plaques or tau tangles in neurodegenerative disease models, isolating the exact transcriptomic response of the immediate cellular niche.
CytAssist-Enabled Workflow & Strict QC Checkpoints
Working with archival clinical samples requires a specialized approach. Standardizing the transfer of RNA from glass slides to spatial arrays minimizes tissue handling errors. Our laboratory utilizes the 10x Genomics CytAssist instrument to facilitate a highly controlled, optimized workflow for FFPE samples.
End-to-end Visium HD workflow featuring CytAssist integration.
- Sectioning and RNA Quality Control (DV200)
Projects begin with the reception of archival FFPE blocks. Assessing RNA quality in FFPE tissue relies on the DV200 metric, which measures the percentage of RNA fragments longer than 200 nucleotides, rather than the RNA Integrity Number (RIN), which is often inaccurate for highly fragmented samples. We mandate a strict DV200 > 30% cutoff for FFPE samples to ensure optimal probe hybridization and sequencing depth.
- Section Placement and Staining
Tissue sections are placed directly onto standard glass slides, rather than the specialized capture arrays. This allows our histopathology team to perform standard H&E or Immunofluorescence (IF) staining and high-resolution imaging to capture the precise tissue morphology before any transcriptomic processing begins.
- Probe Hybridization and Ligation
Visium HD utilizes highly specific transcriptomic probes designed to bind to human and mouse protein-coding genes. These probes are hybridized directly to the permeabilized tissue on the standard glass slide. Following hybridization, the probes are ligated to create full-length spatial templates.
- CytAssist Transfer and Sequencing
The standard glass slide is loaded into the CytAssist instrument alongside the Visium HD capture slide (containing the 2µm barcoded grid). The instrument precisely aligns the tissues and facilitates the spatial transfer of the ligated probes from the tissue onto the barcoded array. Libraries are then amplified, quality-checked for fragment size, and sequenced on high-throughput Illumina platforms.
FFPE Sample Submission Guidelines
Proper sample preservation and sectioning are the most critical factors dictating the success of a Visium HD project. We have established clear guidelines to ensure your tissues remain viable for high-resolution capture.
| Sample Type | Preservation Method | Max Capture Area | Recommended Thickness | RNA Quality QC |
|---|---|---|---|---|
| Human/Mouse Tissue Block | FFPE | 6.5mm × 6.5mm | 5 µm | DV200 > 30% |
| Fresh Frozen Tissue | OCT Embedded | 6.5mm × 6.5mm | 10 µm | RIN > 7 |
Important Considerations:
- Thickness: FFPE sections must be cut at precisely 5 µm to ensure even permeabilization and accurate probe hybridization.
- Tissue Tiling: Please consult our technical support prior to submitting multiplexed or tiled tissue sections. Attempting to tile multiple small biopsies onto a single 6.5mm × 6.5mm capture area can introduce a high risk of tissue detachment during the deparaffinization and antigen retrieval phases.
Advanced Bioinformatics: From 2µm Bins to Cell Segmentation
Generating massive amounts of sequencing data is only the first phase. The continuous 2µm grid generates an unprecedented volume of data points per sample. Processing massive 2µm spatial matrices requires immense high-performance computing infrastructure, which our analytical team fully provides, ensuring your data is translated into actionable biological insights.
ioinformatics pipeline for processing high-density 2µm spatial data.
Standard Space Ranger Processing
Our baseline data processing utilizes the latest 10x Genomics analytical pipelines.
- Sequence Alignment: Mapping reads to the reference genome and assigning them to specific spatial barcodes.
- Bin Aggregation: Space Ranger outputs count matrices at the raw 2µm × 2µm level, while also generating aggregated 8µm × 8µm bins to help users balance spatial resolution with increased transcript counts per bin for initial exploratory analysis.
- Basic Clustering: Unsupervised clustering of the aggregated spatial bins, overlaid directly onto your H&E image to define broad anatomical domains.
High-Resolution Spatial Data Mining (Segmentation)
To achieve true biological meaning, transcriptomic data must be mapped to distinct cells, not just physical squares.
- Cellular Segmentation: Using the high-resolution H&E image, advanced algorithms identify nuclear boundaries and draw polygonal boundaries around individual cells. The 2µm bins falling within these boundaries are aggregated, allowing us to generate a highly accurate, single-cell scale gene expression matrix.
- Spatial Trajectory Inference: Reconstructing pseudotime trajectories to trace cellular development or functional state transitions across the physical tissue space.
- Ligand-Receptor Networks: Inferring active communication pathways specifically between physically adjacent segmented cells, providing strong evidence for localized cellular interactions.
Demo Results: Unprecedented Detail in the TME
Our standard deliverables are designed to support immediate biological interpretation and grant applications. The visual outputs clearly communicate the value of the 2µm continuous resolution.
High-resolution spatial clustering and cell abundance mapping.
- Continuous Spatial Clustering: High-resolution UMAP clusters perfectly aligned to fine morphological structures via the 2µm/8µm bin arrays, separating distinct histological layers.
- Inferred Cell Segmentation Maps: Polygonal boundaries identifying individual cells drawn directly over the tissue image, mapped with their corresponding transcriptomic identities.
- High-Definition Tumor Boundaries: Spatial heatmaps providing a sharp interface mapping of immune infiltration precisely at the tumor margin.
- Spatially Resolved Differential Gene Expression: Volcano plots paired with spatial distribution maps that define specific micro-niches.
- Ligand-Receptor Networks: Interaction diagrams mapped over physical tissue architecture showing exactly where communication is occurring.
Platform Selection: Visium HD vs. Visium V1 vs. Xenium
Selecting the correct spatial platform dictates the type of biological questions you can answer. Use the following guide to navigate your technology selection.
| Parameter | 10x Visium V1 | 10x Visium HD | Xenium In Situ |
|---|---|---|---|
| Resolution Grid | 55µm spots (100µm pitch) | 2µm × 2µm continuous | Subcellular imaging |
| Transcriptome Coverage | Whole Transcriptome | Whole Transcriptome | Targeted Panel (Hundreds of Genes) |
| Tissue Coverage | 6.5mm × 6.5mm (with gaps) | 6.5mm × 6.5mm (gapless) | ~12mm × 24mm |
| Sample Processing | Direct on slide (Fresh Frozen/FFPE) | CytAssist Transfer (FFPE/Fresh Frozen) | In Situ Hybridization |
Strategic Platform Selection:
- Choose Visium HD for unbiased, whole-transcriptome discovery at near single-cell scale in archival FFPE tissues. It provides the perfect balance of massive target discovery and high spatial resolution.
- Choose Xenium In Situ if you require absolute subcellular imaging resolution and already have a targeted panel of known genes you wish to validate.
- Choose Visium V1 if ultra-high resolution is not biologically required and you need broad anatomical mapping of fresh frozen samples.
Case Study: Cell-Level Reconstruction in Lung Cancer TME
Source: STCS: A Platform-Agnostic Framework for Cell-Level Reconstruction in Sequencing-Based Spatial Transcriptomics (bioRxiv, 2026)
High-resolution Visium HD spatial mapping of a human lung cancer FFPE section, demonstrating cell-level segmentation.
Background
Translating the massive volume of 2µm continuous bin data generated by Visium HD into biologically meaningful single-cell information is a major computational challenge. Researchers needed to accurately reconstruct individual cells within the complex tumor microenvironment (TME) of human lung cancer to study localized immune interactions.
Methods
The study utilized a human lung cancer FFPE dataset generated via the 10x Visium HD platform. To process the 2µm spatial grid, the team applied an advanced computational framework designed for cell-level reconstruction. This approach integrated the high-resolution H&E morphological image with the continuous transcriptomic bin data to accurately delineate true cellular boundaries.
Results
The advanced segmentation successfully reconstructed single-cell spatial profiles from the Visium HD grid. This cell-level resolution clearly identified distinct tumor and immune cell populations, revealing intricate spatial arrangements and sharp tumor boundaries that standard bin-level aggregation might obscure.
Conclusion
Coupling Visium HD's 2µm continuous capture technology with robust cell segmentation algorithms enables true single-cell spatial transcriptomics. This validates the platform's capability to deeply profile the TME and identify precise, localized therapeutic targets in archival FFPE tissues.
Frequently Asked Questions (FAQs)
References
- High-definition spatial transcriptomic profiling of immune cell populations in colorectal cancer (PMC, 2025)
- Visium Sample Submission Guidelines | GENEWIZ from Azenta
- Getting Started with Visium HD Spatial Transcriptomics | Omics Empower
- Bin2cell reconstructs cells from high resolution Visium HD data (Oxford Academic, 2024)
- STCS: A Platform-Agnostic Framework for Cell-Level Reconstruction in Sequencing-Based Spatial Transcriptomics (bioRxiv, 2026)
