Visium Spatial
HD 3’ Gene Expression
Next-generation Visium HD technology–powered assay with whole transcriptome coverage to gather broad information from diverse species.
Recommended Visium assay for expanded spatial discovery applications
Single cell–scale resolution
Why choose HD 3’ Gene Expression
Assay specifications
Species
AgnosticCompatible samples
Fresh frozen tissueMultiomics
3’ Gene expression
Morphology (H&E)
Isoform expression (feasibility)
TCR & BCR sequencing (feasibility)Compatible instruments
Throughput options
Assay components
Each experiment requires Visium HD slides, core reagents, and the Visium CytAssist instrument. If you're unsure what you need, use the experiment builder to find the custom list of items required for your experiment.
Consumables
Index Kit
1000215
Dual Index Kit TT Set A, 96 rxn
Core Slides and Reagents
1000857
Visium HD 3', 6.5 mm, 4 rxns
1000856
Visium HD 3', 6.5 mm, 16 rxns
1000854
Visium HD 3' Reagents - Kit A Small
Starter Kits and Accessories
1000857
Visium HD 3', 6.5 mm, 4 rxns
1000471
Visium CytAssist Tissue Slide Cassette, 4 pk, 6.5 mm
1000886
Visium CytAssist Alignment Aid Kit, 6.5 mm
Optional Accessories
1000499
Visium CytAssist Reagent Accessory Kit
Documents and resources
User guides
Technical notes
Sequencing requirements
The final gene expression library is sequenced at a recommended minimum depth of 550 million read pairs for Capture Areas fully covered by tissue.
View moreResources
Data analysis
Space Ranger Analysis Pipelines
Free analysis pipelines that process the input file types to align Visium sequencing data with the tissue image and perform optional cell segmentation.
Learn about Space Ranger
Loupe Browser
Desktop application for Windows and MacOS that allows you to interactively visualize data.
Download Loupe Browser
Cloud Analysis (coming to HD 3’ in H2 2025)
Cloud Analysis enables quick and easy access to Cell Ranger pipelines from your web browser
Learn more about Cloud AnalysisFeatured datasets
Visium HD 3’ Spatial Gene Expression Library, Mouse Embryo
View datasetVisium HD 3’ Spatial Gene Expression Library, Rhesus Kidney
View datasetVisium HD 3’ Spatial Gene Expression Library, Human/Mouse Xenograft
View datasetRelated products
Visium HD WT Panel
Probe-based spatial gene expression assay for comprehensive differential gene expression at single cell scale.
Visium v2 WT Panel
Probe-based spatial gene expression assay utilizing first-generation slide architecture with a large Capture Area option.
Visium v1 3’
3’ poly(A) capture-based spatial gene expression assay utilizing first-generation slide architecture. Upgrading to HD 3’ is recommended.