10X Genomics Visium Spatial Transcriptomics Service
Understanding the spatial organization of cells within tissues is fundamental to uncovering the mechanisms behind complex diseases. Bulk RNA sequencing blends gene expression signatures, losing the physical context, while single-cell dissociation can destroy critical tumor microenvironment (TME) or neurological structures. Our 10x Genomics Visium Spatial Transcriptomics service provides a comprehensive partnership to map the whole transcriptome directly onto your tissue sections, preserving both morphological and molecular integrity.
- Unbiased whole-transcriptome spatial mapping across intact tissues.
- Multi-platform capabilities including standard V1 and high-density HD arrays.
- Optimized CytAssist-enabled workflows for challenging archival FFPE blocks.
- Comprehensive spatial bioinformatics, from base Space Ranger outputs to advanced clustering.
Unbiased Whole-Transcriptome Spatial Mapping
The true value of the Visium platform lies in its hypothesis-free approach. Instead of relying on pre-selected gene panels, Visium captures poly-A mRNA (or utilizes whole-transcriptome probe sets) across the entire tissue section. This allows researchers to discover unknown biomarkers, map spatially resolved developmental gradients, and visualize the complete transcriptomic landscape of healthy and diseased states.
As your dedicated partner, we manage the entire spatial transcriptomics pipeline. From evaluating the integrity of your tissue blocks to executing complex probe hybridizations and delivering publication-ready data matrices, our laboratory team helps you navigate the operational challenges of spatial biology so you can focus on data interpretation.
Explore Our Specialized Visium Solutions
Because sample conditions and biological questions vary significantly, a "one-size-fits-all" approach to spatial transcriptomics often leads to compromised data. We offer highly specialized sub-services designed to match your exact sample type and resolution requirements. Navigate our focused service tracks below to find the right fit for your project:
- 10x Visium V1 Spatial Transcriptomics Service: The foundational platform utilizing a 55µm spot grid for broad anatomical mapping and whole-transcriptome discovery.
- 10x Visium HD Spatial Transcriptomics Service: The next-generation array featuring a continuous 2µm × 2µm grid, delivering unbiased transcriptome mapping at a near single-cell scale.
- FFPE Spatial Transcriptomics Service: Specialized workflows leveraging the 10x CytAssist instrument to rescue whole-transcriptome data from archival formalin-fixed paraffin-embedded tissue blocks.
- Spatial Transcriptome Sequencing of Frozen Samples: Direct-to-slide optimized protocols for fresh frozen (OCT-embedded) tissues, maximizing RNA capture efficiency.
End-to-End Visium Workflow & QC Checkpoints
Our laboratory implements a strictly validated workflow featuring the 10x Genomics CytAssist instrument to maximize data recovery, especially from archival clinical samples.
End-to-end Visium workflow from sectioning to sequencing.
- Tissue Sectioning & Initial QC: Archival FFPE or Fresh Frozen blocks are sectioned onto standard glass slides. We perform H&E or IF staining to capture high-resolution morphological images.
- RNA Quality Assessment: We assess the RNA integrity (RIN for frozen or DV200 for FFPE) to confirm the sample's suitability for whole-transcriptome profiling.
- Probe Hybridization & Ligation: For FFPE/Fixed tissues, whole-transcriptome probe sets are hybridized directly to the tissue. This ensures high sensitivity even in fragmented samples.
- CytAssist Spatial Transfer: The standard slide is aligned with the Visium capture slide. The CytAssist instrument facilitates the precise transfer of probes/analytes onto the barcoded array.
- Library Preparation & Sequencing: Captured targets are amplified to create Illumina-compatible libraries, followed by high-depth NGS sequencing.
Advanced Spatial Bioinformatics & Deliverables
Transforming massive spatial arrays into actionable biology requires robust computational pipelines. Our bioinformatics team delivers both standard vendor outputs and customized data visualization to support your research objectives.
Standard Data Packages
Comprehensive deliverables including FASTQ files, Space Ranger output matrices, and Loupe Browser visualization files.
Refined Anatomical Mapping
Unsupervised clustering that separates distinct anatomical domains based purely on whole-transcriptome profiles, revealing sub-structures invisible to standard pathology.
Spatial Trajectory Inference
Computational modeling to reconstruct biological trajectories or functional state transitions across the physical tissue space.
Multi-Omics Integration
Specialized bioinformatics to map previously acquired single-cell RNA-seq datasets onto your spatial coordinates for deep cellular deconvolution.
Demo Results: Visualizing Spatial Heterogeneity
Our standard deliverables are designed to support immediate biological interpretation and publication. The following demo results highlight the depth of data captured through our Visium service:
High-resolution spatial heatmaps overlaying morphological images.
- H&E Morphological Overlays: Gene expression clusters are mapped directly onto the high-resolution tissue H&E image, correlating transcriptomic signatures with histology.
- High-Definition 2µm Bin Heatmaps: For Visium HD, we generate gapless 2µm bin heatmaps showing the continuous spatial gradient of specific target genes without the blind spots of traditional arrays.
- TME Immune Exclusion Mapping: Visualization of immune cell markers to isolate specific T-cell states within or excluded from the tumor margin, addressing critical questions in oncology.
- Spatially Resolved UMAP Clustering: Visual UMAP clusters aligned to fine morphological structures via the 8µm/55µm bin arrays, defining clear tissue boundaries.
Sample Submission Requirements
Proper sample preservation and sectioning are the most critical factors dictating the success of a Visium project. We have established clear guidelines to ensure your tissues remain viable for high-resolution capture.
| Sample Type | Preferred Visium Platform | Typical RNA Quality Metric | Sectioning Approach |
|---|---|---|---|
| Fresh Frozen (OCT) | V1 or HD | Recommended RIN > 7.0 | Direct placement or CytAssist |
| Archival FFPE | HD (via CytAssist) | Recommended DV200 > 50% | CytAssist slide transfer |
Critical Submission Notes:
- RNA Integrity: Assessing quality relies on the DV200 metric for FFPE blocks. We prioritize blocks with a DV200 > 50% to ensure optimal hybridization.
- Sectioning Thickness: Optimal thickness is generally 5 µm for FFPE and 10 µm for Fresh Frozen tissues to ensure even permeabilization.
- Block History: Prolonged storage of FFPE blocks can lead to significant RNA degradation. We recommend discussing your sample's history with our experts before shipping.
Visium Platform Comparison: V1 vs. HD vs. Xenium
Choosing the right spatial technology is the most critical decision in your project planning phase. To assist in your evaluation, we compare the core operational metrics of the Visium ecosystem against subcellular in situ technologies.
| Comparison Dimension | Visium V1 | Visium HD | Xenium In Situ |
|---|---|---|---|
| Resolution Strategy | 55 µm spots (Multi-cellular) | 2 µm continuous grid (Near single-cell) | Subcellular (~15 nm) |
| Target Scope | Whole Transcriptome (Unbiased) | Whole Transcriptome (Unbiased) | Targeted Panels (Hundreds of genes) |
| Capture Area | 6.5 mm × 6.5 mm (with physical gaps) | 6.5 mm × 6.5 mm (gapless coverage) | Standard array (~12mm × 24mm) |
| Best Application Phase | Early biomarker discovery; broad anatomical tissue mapping. | High-resolution whole-transcriptome discovery in the TME. | Precise validation of known targets and subcellular cell segmentation. |
Strategic Guidance:
- Start with Visium V1 or Visium HD when you are in the discovery phase and need an unbiased look at the entire transcriptome without prior hypotheses.
- Transition to Xenium for downstream validation when you have identified specific targets and require absolute subcellular imaging resolution across larger sample cohorts.
Case Study: Validating Visium Across Diverse Sample Types
Source: Benchmarking spatial transcriptomics technologies with the multi-sample SpatialBenchVisium dataset (Genome Biology, 2025)
Background
A persistent challenge in spatial biology has been maintaining consistent data quality across different tissue preservation methods—specifically between fresh frozen (FF) tissues and archival formalin-fixed paraffin-embedded (FFPE) blocks. Researchers needed to validate whether probe-based CytAssist workflows could reliably match the transcriptomic profiles of FF tissues.
Methods
The study introduced the "SpatialBenchVisium" dataset, utilizing the 10x Genomics Visium platform to benchmark matched tissue samples. Researchers generated spatial transcriptomic data from both FF and FFPE sections of the same biological origin, employing computational metrics to compare spatial clustering and gene detection sensitivity.
Results
The analysis demonstrated strong correlation in spatial gene expression patterns between the FF and FFPE sections when utilizing optimized probe-based and CytAssist workflows. The platform successfully reconstructed high-fidelity spatial clusters that aligned perfectly with the histological layers identified in matched fresh frozen sections.
Conclusion
The Visium platform, enhanced by CytAssist technology, delivers robust and reproducible whole-transcriptome spatial mapping. This validation confirms the platform's capability to unlock clinical FFPE archives for retrospective spatial biology studies without compromising accuracy.
