10x Genomics
Whole transcriptome spatial discovery at single-cell resolution
Comprehensively characterize tissue sections with Visium HD
Features of Visium HD
Uncover molecular patterns within native tissue environments
Visium HD from 10x Genomics sets a new benchmark in spatial transcriptomics by enabling whole-transcriptome spatial gene expression profiling at a single-cell resolution. Designed for both human and mouse tissue samples, Visium HD empowers researchers to achieve unparalleled spatial detail across entire tissue sections.
At the heart of Visium HD are advanced slides featuring two 6.5 x 6.5 mm Capture Areas, each densely packed with over 11 million barcoded oligonucleotides arranged in continuous 2 × 2 µm squares—a scale that matches single-cell dimensions. This innovative design allows for precise spatial mapping of gene expression across complex tissue architectures.
The CytAssist™ instrument ensures a controlled and consistent RNA transfer process, significantly enhancing spatial accuracy. Coupled with probe-based chemistry, Visium HD delivers exceptional sensitivity and sequencing efficiency, maximizing data quality from each read.
Applications of Visium HD
Cancer Microenvironment Mapping
Visium HD helps visualize how different cell types—like tumor, immune, and stromal cells—are organized in a tumor, revealing spatial patterns that impact progression and treatment response.
Brain Tissue Analysis
High-resolution mapping of gene expression is possible across brain regions and layers, helping researchers study brain function, development, and neurological diseases like Alzheimer's.
Infectious Disease & Immune Response
Visium HD can reveal how immune cells are distributed and activated in tissues during infection, offering insights into host-pathogen interactions and inflammation.
Benefits of Visium HD
Compatible with fixed tissues
Visium HD is compatible with standard histology practices, allowing for the sectioning, staining, and imaging of tissues directly on supported glass slides. Pre-screening is required to find the most biologically significant tissue sections.
Uncover rare cell types
We are able to identify rare cellular phenotypes, cell-cell interactions, and biomarkers providing actionable insights for diagnosis and treatment.
Unified probe chemistry for streamlined analysis
The probe-based chemistry is shared with the Gene Expression Flex technology, allowing FFPE single cell workflows to be combined with the spatial profiling and refine the identification of distinct cell type.
Visium HD workflow
Step 1
Consultation
Every project begins with one or more complimentary consultations, as no two spatial projects are the same. Our experienced PhD-level team discusses your biological question, sample type, planning, data analysis options, and other wishes. This will ensure you select the best method for your project and can hit the ground running.
Step 2
Sample Preparation
Preparing sample for Visium HD involves Embedding and Sectioning. We can work from FFPE tissue blocks or already sectioned material for FFPE, Fresh-Frozen (FF) and Fixed-Frozen (FxF). For sectioning: Cut the tissue into thin sections (typically 5 µm thick) using a microtome or cryotome. Place the sections on glass slides recommended for Visium HD.
Step 3
Processing in Our Lab
Our experienced team performs the Visium HD protocol in our lab involving deparaffinization, staining, decrosslinking, permeabilization, probe-hybridization, probe capture, and library preparation. We sequence the libraries on our Illumina NovaSeq X Plus. We’ll conduct multiple quality control checks and keep you informed of the project's status.
Step 4
Data Analysis
Our data team performs exploratory data analysis using SpaceRanger and checks the data quality. You will receive the raw data files, data report, and guiding explanations. Our data consulting team is ready to provide further guidance or assist with tailored analysis projects, such as pseudotime and gene set enrichment analysis.
Deliverables
As with all of our services, we provide ongoing support from our single-cell sequencing specialists. For each Discovery-seq project, we provide the following.
- Regular updates during processing, including QC reports.
- Raw high resolution images used for the spatial profiling.
- Raw sequencing data (FASTQ files).
- Raw and filtered gene count tables for 2µm, 8µm, and 16µm binned results (including filtered_feature_bc_matrix.h5 object).
- An interactive preliminary analysis report including QC, clustering and differential gene expression analysis
- A Seurat object built from the 8µm binned counts to do your own analysis with the Seurat pipeline
- A cloupe object for easy analysis with the Loupe browser by 10x Genomics
- An explanation from our data team about data quality metrics
- All raw sequencing data, results and reports are processed on EU servers, and securely encrypted using an AES (Advanced Encryption Standard) algorithm with a 256-bit key, before being delivered to the customers and archived
FAQ
Pricing depends on the number of samples, the area to be covered, sequencing depth, and any required protocol modifications. Your account manager can give pricing information specific to your project’s requirements during consultations.
We accept Formalin-Fixed and Parafin-Embedded (FFPE), Fresh-Frozen (FF) and Fixed-Frozen (FxF) samples. Visium HD Spatial Transcriptomics is compatible with human and mouse samples. We only accept tissue sections from FF and FxF samples. For FFPE we accept both tissue sections and tissue blocks.
To be able to assess RNA quality, we will ask you to provide additional 5-10µm sections in a microtube. For large tissues (>6.5mm x 6.5 mm) 1 or 2 sections are enough. For smaller tissues (<6.5mm x 6.5 mm) please provide 4 sections.
We recommend carefully reading the respective 10x Genomics Visium HD tissue preparation Handbook. If there are any questions or doubts about the preparation, do not hesitate to get in touch with your SCD representative.
Check the shipping guidelines for shipping Visium HD samples on our sample requirements page.
Contact Us
Discover our spatial transcriptomic solutions
Connect with our PhD-level scientists to discuss your specific needs, from biological questions to sample types, and customize your single-cell spatial analysis. We'll develop a tailored strategic plan and determine the next steps to help you achieve your goals.