10x Visium HD Spatial Gene Expression

Spatial Gene Expression

High-resolution spatial transcriptomics for mapping whole-transcriptome gene expression within tissue architecture, morphology and spatial biological context.

Spatial gene expression analysis enables researchers to explore where genes are expressed within tissue, connecting transcriptomic profiles with tissue morphology and spatial organisation. This can reveal tissue architecture, cellular neighbourhoods and region-specific biological patterns that may be missed by dissociated single-cell or bulk RNA-seq methods.

Novogene Europe provides 10x Genomics Visium HD spatial gene expression services using CytAssist-enabled workflows, with both WT Panel and 3′ gene expression options. These complementary approaches support high-resolution spatial profiling across different sample types and research applications, from probe-based analysis of human and mouse tissues to expanded whole-transcriptome discovery across a broader range of species using Visium HD 3′.

Service Highlights

Visium HD Spatial Profiling

High-resolution whole-transcriptome spatial gene expression analysis to explore gene activity within tissue architecture and spatial biological context.

WT Panel & 3′ Gene Expression

Probe-based WT Panel for human and mouse tissues, or 3′ whole-transcriptome profiling for fresh-frozen samples across broader species.

CytAssist-enabled Workflow

10x Genomics CytAssist technology supports probe transfer from tissue slides to Visium slides, helping preserve spatial information during library preparation.

Spatial Bioinformatics Analysis

Analysis outputs can include data QC, mapping, clustering, spatial gene expression visualisation, differential expression and functional enrichment analysis.

Applications

Tissue Architecture Mapping

Profile spatial relationships between tumour, immune and stromal regions to investigate cancer tissue heterogeneity, immune contexture and disease-associated gene expression.

Tumour Microenvironment Studies

Profile spatial relationships between tumour, immune and stromal regions to investigate cancer tissue heterogeneity, immune contexture and disease-associated gene expression.

Development and Disease Models

Study spatial gene expression changes across developmental stages, neurological models, inflammatory disease models or treatment conditions.

Cell Neighbourhood Analysis

Investigate localised gene expression patterns and cellular neighbourhoods, including tumour-immune interfaces and disease-associated tissue regions.

Specifications

Sample Requirements

The quantities listed are provided for reference only. Please download the Sample Requirements for detailed guidance, or Contact us to discuss your project-specific requirements.

Assay	Species	Sample Type (Human/Mouse)	Minimum amount	RNA QC
10x Genomics Visium HD WT Panel	Human/Mouse	FFPE	1 FFPE block Tissue thickness > 1mm	DV200 ≥ 30%
		FFPE	2-4 tissue sections on glass slides and FFPE scrolls (Thickness > 50 µm)	DV200 ≥ 30%
		Fresh (frozen) tisssues (Embedded in OCT blocks)	1 OCT block Tissue thickness > 1mm	RIN ≥ 4
10x Genomics Visium HD 3′	Eukaryotic species (subject to feasibility assessment)	Fresh (frozen) tisssues (Embedded in OCT blocks)	1 OCT block Tissue thickness > 1mm	RIN ≥ 7

Sample Requirements

The quantities listed are provided for reference only. Please download the Sample Requirements for detailed guidance, or Contact us to discuss your project-specific requirements.

Assay	Species	Sample Type (Human/Mouse)	Minimum amount	RNA QC
10x Genomics Visium HD WT Panel	Human/Mouse	FFPE	1 FFPE block Tissue thickness > 1mm	DV200 ≥ 30%
		FFPE	2-4 tissue sections on glass slides and FFPE scrolls (Thickness > 50 µm)	DV200 ≥ 30%
		Fresh (frozen) tisssues (Embedded in OCT blocks)	1 OCT block Tissue thickness > 1mm	RIN ≥ 4
10x Genomics Visium HD 3′	Eukaryotic species (subject to feasibility assessment)	Fresh (frozen) tisssues (Embedded in OCT blocks)	1 OCT block Tissue thickness > 1mm	RIN ≥ 7

Sample Requirements

The quantities listed are provided for reference only. Please download the Sample Requirements for detailed guidance, or Contact us to discuss your project-specific requirements.

Assay	Species	Sample Type (Human/Mouse)	Minimum amount	RNA QC
10x Genomics Visium HD WT Panel	Human/Mouse	FFPE	1 FFPE block Tissue thickness > 1mm	DV200 ≥ 30%
		FFPE	2-4 tissue sections on glass slides and FFPE scrolls (Thickness > 50 µm)	DV200 ≥ 30%
		Fresh (frozen) tisssues (Embedded in OCT blocks)	1 OCT block Tissue thickness > 1mm	RIN ≥ 4
10x Genomics Visium HD 3′	Eukaryotic species (subject to feasibility assessment)	Fresh (frozen) tisssues (Embedded in OCT blocks)	1 OCT block Tissue thickness > 1mm	RIN ≥ 7

Sample Requirements

The quantities listed are provided for reference only. Please download the Sample Requirements for detailed guidance, or Contact us to discuss your project-specific requirements.

Assay	Species	Sample Type (Human/Mouse)	Minimum amount	RNA QC
10x Genomics Visium HD WT Panel	Human/Mouse	FFPE	1 FFPE block Tissue thickness > 1mm	DV200 ≥ 30%
		FFPE	2-4 tissue sections on glass slides and FFPE scrolls (Thickness > 50 µm)	DV200 ≥ 30%
		Fresh (frozen) tisssues (Embedded in OCT blocks)	1 OCT block Tissue thickness > 1mm	RIN ≥ 4
10x Genomics Visium HD 3′	Eukaryotic species (subject to feasibility assessment)	Fresh (frozen) tisssues (Embedded in OCT blocks)	1 OCT block Tissue thickness > 1mm	RIN ≥ 7

Sequencing and Analysis

Recommended data outputs and analysis examples are provided for reference only. For detailed information, please contact us to discuss your project-specific analysis requirements.

	Visium HD
Species	Human, mouse or other eukaryotic species, assay dependent
Capture area	6.5mm x 6.5mm
Sequencing platform	NovaSeq X plus
Read length	PE150
Recommended Data Amount	- Visium HD WT Panel: FFPE: 100 G Fresh Frozen: 210 G - Visium HD 3‘: Fresh Frozen: 165 G
Analysis	Data QC: Mapping and Quantification Space Ranger Analysis (including cell segmentation) Clustering analysis: Graphclust clustering K-means clustering Scanpy Analysis: PCA analysis Spatial variable gene expression analysis Clustering and dimensionality reduction analysis Differential Expression Gene Analysis(DEG): DEGs clustering heatmap Spatial distribution of DEGs Violine plot t-SNE and UMAP dimensional reduction visualization Functional Enrichment Analysis: GO enrichment KEGG enrichment Reactome enrichment

Sequencing and Analysis

Recommended data outputs and analysis examples are provided for reference only. For detailed information, please contact us to discuss your project-specific analysis requirements.

	Visium HD
Species	Human, mouse or other eukaryotic species, assay dependent
Capture area	6.5mm x 6.5mm
Sequencing platform	NovaSeq X plus
Read length	PE150
Recommended Data Amount	- Visium HD WT Panel: FFPE: 100 G Fresh Frozen: 210 G - Visium HD 3‘: Fresh Frozen: 165 G
Analysis	Data QC: Mapping and Quantification Space Ranger Analysis (including cell segmentation) Clustering analysis: Graphclust clustering K-means clustering Scanpy Analysis: PCA analysis Spatial variable gene expression analysis Clustering and dimensionality reduction analysis Differential Expression Gene Analysis(DEG): DEGs clustering heatmap Spatial distribution of DEGs Violine plot t-SNE and UMAP dimensional reduction visualization Functional Enrichment Analysis: GO enrichment KEGG enrichment Reactome enrichment

Sequencing and Analysis

Recommended data outputs and analysis examples are provided for reference only. For detailed information, please contact us to discuss your project-specific analysis requirements.

	Visium HD
Species	Human, mouse or other eukaryotic species, assay dependent
Capture area	6.5mm x 6.5mm
Sequencing platform	NovaSeq X plus
Read length	PE150
Recommended Data Amount	- Visium HD WT Panel: FFPE: 100 G Fresh Frozen: 210 G - Visium HD 3‘: Fresh Frozen: 165 G
Analysis	Data QC: Mapping and Quantification Space Ranger Analysis (including cell segmentation) Clustering analysis: Graphclust clustering K-means clustering Scanpy Analysis: PCA analysis Spatial variable gene expression analysis Clustering and dimensionality reduction analysis Differential Expression Gene Analysis(DEG): DEGs clustering heatmap Spatial distribution of DEGs Violine plot t-SNE and UMAP dimensional reduction visualization Functional Enrichment Analysis: GO enrichment KEGG enrichment Reactome enrichment

Sequencing and Analysis

Recommended data outputs and analysis examples are provided for reference only. For detailed information, please contact us to discuss your project-specific analysis requirements.

	Visium HD
Species	Human, mouse or other eukaryotic species, assay dependent
Capture area	6.5mm x 6.5mm
Sequencing platform	NovaSeq X plus
Read length	PE150
Recommended Data Amount	- Visium HD WT Panel: FFPE: 100 G Fresh Frozen: 210 G - Visium HD 3‘: Fresh Frozen: 165 G
Analysis	Data QC: Mapping and Quantification Space Ranger Analysis (including cell segmentation) Clustering analysis: Graphclust clustering K-means clustering Scanpy Analysis: PCA analysis Spatial variable gene expression analysis Clustering and dimensionality reduction analysis Differential Expression Gene Analysis(DEG): DEGs clustering heatmap Spatial distribution of DEGs Violine plot t-SNE and UMAP dimensional reduction visualization Functional Enrichment Analysis: GO enrichment KEGG enrichment Reactome enrichment

Specifications

Sample Requirements

The quantities listed are provided for reference only. Please download the Sample Requirements for detailed guidance, or Contact us to discuss your project-specific requirements.

Assay	Species	Sample Type (Human/Mouse)	Minimum amount	RNA QC
10x Genomics Visium HD WT Panel	Human/Mouse	FFPE	1 FFPE block Tissue thickness > 1mm	DV200 ≥ 30%
		FFPE	2-4 tissue sections on glass slides and FFPE scrolls (Thickness > 50 µm)	DV200 ≥ 30%
		Fresh (frozen) tisssues (Embedded in OCT blocks)	1 OCT block Tissue thickness > 1mm	RIN ≥ 4
10x Genomics Visium HD 3′	Eukaryotic species (subject to feasibility assessment)	Fresh (frozen) tisssues (Embedded in OCT blocks)	1 OCT block Tissue thickness > 1mm	RIN ≥ 7

Sample Requirements

The quantities listed are provided for reference only. Please download the Sample Requirements for detailed guidance, or Contact us to discuss your project-specific requirements.

Assay	Species	Sample Type (Human/Mouse)	Minimum amount	RNA QC
10x Genomics Visium HD WT Panel	Human/Mouse	FFPE	1 FFPE block Tissue thickness > 1mm	DV200 ≥ 30%
		FFPE	2-4 tissue sections on glass slides and FFPE scrolls (Thickness > 50 µm)	DV200 ≥ 30%
		Fresh (frozen) tisssues (Embedded in OCT blocks)	1 OCT block Tissue thickness > 1mm	RIN ≥ 4
10x Genomics Visium HD 3′	Eukaryotic species (subject to feasibility assessment)	Fresh (frozen) tisssues (Embedded in OCT blocks)	1 OCT block Tissue thickness > 1mm	RIN ≥ 7

Sample Requirements

The quantities listed are provided for reference only. Please download the Sample Requirements for detailed guidance, or Contact us to discuss your project-specific requirements.

Assay	Species	Sample Type (Human/Mouse)	Minimum amount	RNA QC
10x Genomics Visium HD WT Panel	Human/Mouse	FFPE	1 FFPE block Tissue thickness > 1mm	DV200 ≥ 30%
		FFPE	2-4 tissue sections on glass slides and FFPE scrolls (Thickness > 50 µm)	DV200 ≥ 30%
		Fresh (frozen) tisssues (Embedded in OCT blocks)	1 OCT block Tissue thickness > 1mm	RIN ≥ 4
10x Genomics Visium HD 3′	Eukaryotic species (subject to feasibility assessment)	Fresh (frozen) tisssues (Embedded in OCT blocks)	1 OCT block Tissue thickness > 1mm	RIN ≥ 7

Sample Requirements

The quantities listed are provided for reference only. Please download the Sample Requirements for detailed guidance, or Contact us to discuss your project-specific requirements.

Assay	Species	Sample Type (Human/Mouse)	Minimum amount	RNA QC
10x Genomics Visium HD WT Panel	Human/Mouse	FFPE	1 FFPE block Tissue thickness > 1mm	DV200 ≥ 30%
		FFPE	2-4 tissue sections on glass slides and FFPE scrolls (Thickness > 50 µm)	DV200 ≥ 30%
		Fresh (frozen) tisssues (Embedded in OCT blocks)	1 OCT block Tissue thickness > 1mm	RIN ≥ 4
10x Genomics Visium HD 3′	Eukaryotic species (subject to feasibility assessment)	Fresh (frozen) tisssues (Embedded in OCT blocks)	1 OCT block Tissue thickness > 1mm	RIN ≥ 7

Sequencing and Analysis

Recommended data outputs and analysis examples are provided for reference only. For detailed information, please contact us to discuss your project-specific analysis requirements.

	Visium HD
Species	Human, mouse or other eukaryotic species, assay dependent
Capture area	6.5mm x 6.5mm
Sequencing platform	NovaSeq X plus
Read length	PE150
Recommended Data Amount	- Visium HD WT Panel: FFPE: 100 G Fresh Frozen: 210 G - Visium HD 3‘: Fresh Frozen: 165 G
Analysis	Data QC: Mapping and Quantification Space Ranger Analysis (including cell segmentation) Clustering analysis: Graphclust clustering K-means clustering Scanpy Analysis: PCA analysis Spatial variable gene expression analysis Clustering and dimensionality reduction analysis Differential Expression Gene Analysis(DEG): DEGs clustering heatmap Spatial distribution of DEGs Violine plot t-SNE and UMAP dimensional reduction visualization Functional Enrichment Analysis: GO enrichment KEGG enrichment Reactome enrichment

Sequencing and Analysis

Recommended data outputs and analysis examples are provided for reference only. For detailed information, please contact us to discuss your project-specific analysis requirements.

	Visium HD
Species	Human, mouse or other eukaryotic species, assay dependent
Capture area	6.5mm x 6.5mm
Sequencing platform	NovaSeq X plus
Read length	PE150
Recommended Data Amount	- Visium HD WT Panel: FFPE: 100 G Fresh Frozen: 210 G - Visium HD 3‘: Fresh Frozen: 165 G
Analysis	Data QC: Mapping and Quantification Space Ranger Analysis (including cell segmentation) Clustering analysis: Graphclust clustering K-means clustering Scanpy Analysis: PCA analysis Spatial variable gene expression analysis Clustering and dimensionality reduction analysis Differential Expression Gene Analysis(DEG): DEGs clustering heatmap Spatial distribution of DEGs Violine plot t-SNE and UMAP dimensional reduction visualization Functional Enrichment Analysis: GO enrichment KEGG enrichment Reactome enrichment

Sequencing and Analysis

Recommended data outputs and analysis examples are provided for reference only. For detailed information, please contact us to discuss your project-specific analysis requirements.

	Visium HD
Species	Human, mouse or other eukaryotic species, assay dependent
Capture area	6.5mm x 6.5mm
Sequencing platform	NovaSeq X plus
Read length	PE150
Recommended Data Amount	- Visium HD WT Panel: FFPE: 100 G Fresh Frozen: 210 G - Visium HD 3‘: Fresh Frozen: 165 G
Analysis	Data QC: Mapping and Quantification Space Ranger Analysis (including cell segmentation) Clustering analysis: Graphclust clustering K-means clustering Scanpy Analysis: PCA analysis Spatial variable gene expression analysis Clustering and dimensionality reduction analysis Differential Expression Gene Analysis(DEG): DEGs clustering heatmap Spatial distribution of DEGs Violine plot t-SNE and UMAP dimensional reduction visualization Functional Enrichment Analysis: GO enrichment KEGG enrichment Reactome enrichment

Sequencing and Analysis

Recommended data outputs and analysis examples are provided for reference only. For detailed information, please contact us to discuss your project-specific analysis requirements.

	Visium HD
Species	Human, mouse or other eukaryotic species, assay dependent
Capture area	6.5mm x 6.5mm
Sequencing platform	NovaSeq X plus
Read length	PE150
Recommended Data Amount	- Visium HD WT Panel: FFPE: 100 G Fresh Frozen: 210 G - Visium HD 3‘: Fresh Frozen: 165 G
Analysis	Data QC: Mapping and Quantification Space Ranger Analysis (including cell segmentation) Clustering analysis: Graphclust clustering K-means clustering Scanpy Analysis: PCA analysis Spatial variable gene expression analysis Clustering and dimensionality reduction analysis Differential Expression Gene Analysis(DEG): DEGs clustering heatmap Spatial distribution of DEGs Violine plot t-SNE and UMAP dimensional reduction visualization Functional Enrichment Analysis: GO enrichment KEGG enrichment Reactome enrichment

Resources

Example Analysis Output

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Cluster Map

Visualise spatially defined clusters across the tissue section to explore regional organisation and tissue structure.

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UMAP Clustering

Review transcriptional similarity between spots or bins to support cluster interpretation and data exploration.

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Marker Gene Dot Plot

Compare marker gene expression across clusters to support annotation of tissue regions and cell-associated patterns.

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Spatial Gene Expression

Display selected marker genes directly on tissue sections to explore localised expression patterns.

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Tissue Filtering

Review tissue-covered areas used for downstream spatial analysis and quality assessment.

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GO Enrichment

Identify enriched biological processes linked to cluster marker genes or region-specific expression patterns.

Webinars

Getting Started with Spatial Transcriptomics

Looking to get started with spatial transcriptomics? Join this webinar to learn the fundamentals of 10x Genomics Visium HD technology, key applications, sample preparation requirements, and strategies for extracting biological insights from spatial gene expression data.

Learn More

Frequently Asked Questions

What is the difference between Visium HD WT Panel and Visium HD 3′ Gene Expression?

Visium HD WT Panel uses a probe-based approach for spatial gene expression profiling, while Visium HD 3′ uses 3′ gene expression capture for whole-transcriptome discovery. The best option depends on sample type, species and research goals. WT Panel offers broad tissue compatibility for supported species, including human and mouse, while HD 3′ is designed for whole-transcriptome discovery in fresh-frozen tissue and supports a much broader range of eukaryotic species, including human, mouse and other model and non-model organisms.

Which sample types and species are suitable for Visium HD?

How does spatial transcriptomics differ from single-cell RNA sequencing?

Can spatial transcriptomics be combined with single-cell data?

Explore Single-cell & Spatial Resources

Access webinars, brochures and case studies covering sequencing technologies, study planning and data interpretation.

Speak with a Specialist

Have a project in mind?

Send us your enquiry and a Novogene Europe specialist will be in touch.

Spatial Gene Expression

High-resolution spatial transcriptomics for mapping whole-transcriptome gene expression within tissue architecture, morphology and spatial biological context.

Service Highlights

Visium HD Spatial Profiling

High-resolution whole-transcriptome spatial gene expression analysis to explore gene activity within tissue architecture and spatial biological context.

WT Panel & 3′ Gene Expression

Probe-based WT Panel for human and mouse tissues, or 3′ whole-transcriptome profiling for fresh-frozen samples across broader species.

CytAssist-enabled Workflow

10x Genomics CytAssist technology supports probe transfer from tissue slides to Visium slides, helping preserve spatial information during library preparation.

Spatial Bioinformatics Analysis

Analysis outputs can include data QC, mapping, clustering, spatial gene expression visualisation, differential expression and functional enrichment analysis.

Applications

Tissue Architecture Mapping

Profile spatial relationships between tumour, immune and stromal regions to investigate cancer tissue heterogeneity, immune contexture and disease-associated gene expression.

Tumour Microenvironment Studies

Profile spatial relationships between tumour, immune and stromal regions to investigate cancer tissue heterogeneity, immune contexture and disease-associated gene expression.

Development and Disease Models

Study spatial gene expression changes across developmental stages, neurological models, inflammatory disease models or treatment conditions.

Cell Neighbourhood Analysis

Investigate localised gene expression patterns and cellular neighbourhoods, including tumour-immune interfaces and disease-associated tissue regions.

Specifications

Sample Requirements

The quantities listed are provided for reference only. Please download the Sample Requirements for detailed guidance, or Contact us to discuss your project-specific requirements.

Assay	Species	Sample Type (Human/Mouse)	Minimum amount	RNA QC
10x Genomics Visium HD WT Panel	Human/Mouse	FFPE	1 FFPE block Tissue thickness > 1mm	DV200 ≥ 30%
		FFPE	2-4 tissue sections on glass slides and FFPE scrolls (Thickness > 50 µm)	DV200 ≥ 30%
		Fresh (frozen) tisssues (Embedded in OCT blocks)	1 OCT block Tissue thickness > 1mm	RIN ≥ 4
10x Genomics Visium HD 3′	Eukaryotic species (subject to feasibility assessment)	Fresh (frozen) tisssues (Embedded in OCT blocks)	1 OCT block Tissue thickness > 1mm	RIN ≥ 7

Sample Requirements

The quantities listed are provided for reference only. Please download the Sample Requirements for detailed guidance, or Contact us to discuss your project-specific requirements.

Assay	Species	Sample Type (Human/Mouse)	Minimum amount	RNA QC
10x Genomics Visium HD WT Panel	Human/Mouse	FFPE	1 FFPE block Tissue thickness > 1mm	DV200 ≥ 30%
		FFPE	2-4 tissue sections on glass slides and FFPE scrolls (Thickness > 50 µm)	DV200 ≥ 30%
		Fresh (frozen) tisssues (Embedded in OCT blocks)	1 OCT block Tissue thickness > 1mm	RIN ≥ 4
10x Genomics Visium HD 3′	Eukaryotic species (subject to feasibility assessment)	Fresh (frozen) tisssues (Embedded in OCT blocks)	1 OCT block Tissue thickness > 1mm	RIN ≥ 7

Sample Requirements

The quantities listed are provided for reference only. Please download the Sample Requirements for detailed guidance, or Contact us to discuss your project-specific requirements.

Assay	Species	Sample Type (Human/Mouse)	Minimum amount	RNA QC
10x Genomics Visium HD WT Panel	Human/Mouse	FFPE	1 FFPE block Tissue thickness > 1mm	DV200 ≥ 30%
		FFPE	2-4 tissue sections on glass slides and FFPE scrolls (Thickness > 50 µm)	DV200 ≥ 30%
		Fresh (frozen) tisssues (Embedded in OCT blocks)	1 OCT block Tissue thickness > 1mm	RIN ≥ 4
10x Genomics Visium HD 3′	Eukaryotic species (subject to feasibility assessment)	Fresh (frozen) tisssues (Embedded in OCT blocks)	1 OCT block Tissue thickness > 1mm	RIN ≥ 7

Sample Requirements

The quantities listed are provided for reference only. Please download the Sample Requirements for detailed guidance, or Contact us to discuss your project-specific requirements.

Assay	Species	Sample Type (Human/Mouse)	Minimum amount	RNA QC
10x Genomics Visium HD WT Panel	Human/Mouse	FFPE	1 FFPE block Tissue thickness > 1mm	DV200 ≥ 30%
		FFPE	2-4 tissue sections on glass slides and FFPE scrolls (Thickness > 50 µm)	DV200 ≥ 30%
		Fresh (frozen) tisssues (Embedded in OCT blocks)	1 OCT block Tissue thickness > 1mm	RIN ≥ 4
10x Genomics Visium HD 3′	Eukaryotic species (subject to feasibility assessment)	Fresh (frozen) tisssues (Embedded in OCT blocks)	1 OCT block Tissue thickness > 1mm	RIN ≥ 7

Sequencing and Analysis

Recommended data outputs and analysis examples are provided for reference only. For detailed information, please contact us to discuss your project-specific analysis requirements.

	Visium HD
Species	Human, mouse or other eukaryotic species, assay dependent
Capture area	6.5mm x 6.5mm
Sequencing platform	NovaSeq X plus
Read length	PE150
Recommended Data Amount	- Visium HD WT Panel: FFPE: 100 G Fresh Frozen: 210 G - Visium HD 3‘: Fresh Frozen: 165 G
Analysis	Data QC: Mapping and Quantification Space Ranger Analysis (including cell segmentation) Clustering analysis: Graphclust clustering K-means clustering Scanpy Analysis: PCA analysis Spatial variable gene expression analysis Clustering and dimensionality reduction analysis Differential Expression Gene Analysis(DEG): DEGs clustering heatmap Spatial distribution of DEGs Violine plot t-SNE and UMAP dimensional reduction visualization Functional Enrichment Analysis: GO enrichment KEGG enrichment Reactome enrichment

Sequencing and Analysis

Recommended data outputs and analysis examples are provided for reference only. For detailed information, please contact us to discuss your project-specific analysis requirements.

	Visium HD
Species	Human, mouse or other eukaryotic species, assay dependent
Capture area	6.5mm x 6.5mm
Sequencing platform	NovaSeq X plus
Read length	PE150
Recommended Data Amount	- Visium HD WT Panel: FFPE: 100 G Fresh Frozen: 210 G - Visium HD 3‘: Fresh Frozen: 165 G
Analysis	Data QC: Mapping and Quantification Space Ranger Analysis (including cell segmentation) Clustering analysis: Graphclust clustering K-means clustering Scanpy Analysis: PCA analysis Spatial variable gene expression analysis Clustering and dimensionality reduction analysis Differential Expression Gene Analysis(DEG): DEGs clustering heatmap Spatial distribution of DEGs Violine plot t-SNE and UMAP dimensional reduction visualization Functional Enrichment Analysis: GO enrichment KEGG enrichment Reactome enrichment

Sequencing and Analysis

Recommended data outputs and analysis examples are provided for reference only. For detailed information, please contact us to discuss your project-specific analysis requirements.

	Visium HD
Species	Human, mouse or other eukaryotic species, assay dependent
Capture area	6.5mm x 6.5mm
Sequencing platform	NovaSeq X plus
Read length	PE150
Recommended Data Amount	- Visium HD WT Panel: FFPE: 100 G Fresh Frozen: 210 G - Visium HD 3‘: Fresh Frozen: 165 G
Analysis	Data QC: Mapping and Quantification Space Ranger Analysis (including cell segmentation) Clustering analysis: Graphclust clustering K-means clustering Scanpy Analysis: PCA analysis Spatial variable gene expression analysis Clustering and dimensionality reduction analysis Differential Expression Gene Analysis(DEG): DEGs clustering heatmap Spatial distribution of DEGs Violine plot t-SNE and UMAP dimensional reduction visualization Functional Enrichment Analysis: GO enrichment KEGG enrichment Reactome enrichment

Sequencing and Analysis

Recommended data outputs and analysis examples are provided for reference only. For detailed information, please contact us to discuss your project-specific analysis requirements.

	Visium HD
Species	Human, mouse or other eukaryotic species, assay dependent
Capture area	6.5mm x 6.5mm
Sequencing platform	NovaSeq X plus
Read length	PE150
Recommended Data Amount	- Visium HD WT Panel: FFPE: 100 G Fresh Frozen: 210 G - Visium HD 3‘: Fresh Frozen: 165 G
Analysis	Data QC: Mapping and Quantification Space Ranger Analysis (including cell segmentation) Clustering analysis: Graphclust clustering K-means clustering Scanpy Analysis: PCA analysis Spatial variable gene expression analysis Clustering and dimensionality reduction analysis Differential Expression Gene Analysis(DEG): DEGs clustering heatmap Spatial distribution of DEGs Violine plot t-SNE and UMAP dimensional reduction visualization Functional Enrichment Analysis: GO enrichment KEGG enrichment Reactome enrichment

Specifications

Sample Requirements

The quantities listed are provided for reference only. Please download the Sample Requirements for detailed guidance, or Contact us to discuss your project-specific requirements.

Assay	Species	Sample Type (Human/Mouse)	Minimum amount	RNA QC
10x Genomics Visium HD WT Panel	Human/Mouse	FFPE	1 FFPE block Tissue thickness > 1mm	DV200 ≥ 30%
		FFPE	2-4 tissue sections on glass slides and FFPE scrolls (Thickness > 50 µm)	DV200 ≥ 30%
		Fresh (frozen) tisssues (Embedded in OCT blocks)	1 OCT block Tissue thickness > 1mm	RIN ≥ 4
10x Genomics Visium HD 3′	Eukaryotic species (subject to feasibility assessment)	Fresh (frozen) tisssues (Embedded in OCT blocks)	1 OCT block Tissue thickness > 1mm	RIN ≥ 7

Sample Requirements

The quantities listed are provided for reference only. Please download the Sample Requirements for detailed guidance, or Contact us to discuss your project-specific requirements.

Assay	Species	Sample Type (Human/Mouse)	Minimum amount	RNA QC
10x Genomics Visium HD WT Panel	Human/Mouse	FFPE	1 FFPE block Tissue thickness > 1mm	DV200 ≥ 30%
		FFPE	2-4 tissue sections on glass slides and FFPE scrolls (Thickness > 50 µm)	DV200 ≥ 30%
		Fresh (frozen) tisssues (Embedded in OCT blocks)	1 OCT block Tissue thickness > 1mm	RIN ≥ 4
10x Genomics Visium HD 3′	Eukaryotic species (subject to feasibility assessment)	Fresh (frozen) tisssues (Embedded in OCT blocks)	1 OCT block Tissue thickness > 1mm	RIN ≥ 7

Sample Requirements

The quantities listed are provided for reference only. Please download the Sample Requirements for detailed guidance, or Contact us to discuss your project-specific requirements.

Assay	Species	Sample Type (Human/Mouse)	Minimum amount	RNA QC
10x Genomics Visium HD WT Panel	Human/Mouse	FFPE	1 FFPE block Tissue thickness > 1mm	DV200 ≥ 30%
		FFPE	2-4 tissue sections on glass slides and FFPE scrolls (Thickness > 50 µm)	DV200 ≥ 30%
		Fresh (frozen) tisssues (Embedded in OCT blocks)	1 OCT block Tissue thickness > 1mm	RIN ≥ 4
10x Genomics Visium HD 3′	Eukaryotic species (subject to feasibility assessment)	Fresh (frozen) tisssues (Embedded in OCT blocks)	1 OCT block Tissue thickness > 1mm	RIN ≥ 7

Sample Requirements

The quantities listed are provided for reference only. Please download the Sample Requirements for detailed guidance, or Contact us to discuss your project-specific requirements.

Assay	Species	Sample Type (Human/Mouse)	Minimum amount	RNA QC
10x Genomics Visium HD WT Panel	Human/Mouse	FFPE	1 FFPE block Tissue thickness > 1mm	DV200 ≥ 30%
		FFPE	2-4 tissue sections on glass slides and FFPE scrolls (Thickness > 50 µm)	DV200 ≥ 30%
		Fresh (frozen) tisssues (Embedded in OCT blocks)	1 OCT block Tissue thickness > 1mm	RIN ≥ 4
10x Genomics Visium HD 3′	Eukaryotic species (subject to feasibility assessment)	Fresh (frozen) tisssues (Embedded in OCT blocks)	1 OCT block Tissue thickness > 1mm	RIN ≥ 7

Sequencing and Analysis

Recommended data outputs and analysis examples are provided for reference only. For detailed information, please contact us to discuss your project-specific analysis requirements.

	Visium HD
Species	Human, mouse or other eukaryotic species, assay dependent
Capture area	6.5mm x 6.5mm
Sequencing platform	NovaSeq X plus
Read length	PE150
Recommended Data Amount	- Visium HD WT Panel: FFPE: 100 G Fresh Frozen: 210 G - Visium HD 3‘: Fresh Frozen: 165 G
Analysis	Data QC: Mapping and Quantification Space Ranger Analysis (including cell segmentation) Clustering analysis: Graphclust clustering K-means clustering Scanpy Analysis: PCA analysis Spatial variable gene expression analysis Clustering and dimensionality reduction analysis Differential Expression Gene Analysis(DEG): DEGs clustering heatmap Spatial distribution of DEGs Violine plot t-SNE and UMAP dimensional reduction visualization Functional Enrichment Analysis: GO enrichment KEGG enrichment Reactome enrichment

Sequencing and Analysis

Recommended data outputs and analysis examples are provided for reference only. For detailed information, please contact us to discuss your project-specific analysis requirements.

	Visium HD
Species	Human, mouse or other eukaryotic species, assay dependent
Capture area	6.5mm x 6.5mm
Sequencing platform	NovaSeq X plus
Read length	PE150
Recommended Data Amount	- Visium HD WT Panel: FFPE: 100 G Fresh Frozen: 210 G - Visium HD 3‘: Fresh Frozen: 165 G
Analysis	Data QC: Mapping and Quantification Space Ranger Analysis (including cell segmentation) Clustering analysis: Graphclust clustering K-means clustering Scanpy Analysis: PCA analysis Spatial variable gene expression analysis Clustering and dimensionality reduction analysis Differential Expression Gene Analysis(DEG): DEGs clustering heatmap Spatial distribution of DEGs Violine plot t-SNE and UMAP dimensional reduction visualization Functional Enrichment Analysis: GO enrichment KEGG enrichment Reactome enrichment

Sequencing and Analysis

Recommended data outputs and analysis examples are provided for reference only. For detailed information, please contact us to discuss your project-specific analysis requirements.

	Visium HD
Species	Human, mouse or other eukaryotic species, assay dependent
Capture area	6.5mm x 6.5mm
Sequencing platform	NovaSeq X plus
Read length	PE150
Recommended Data Amount	- Visium HD WT Panel: FFPE: 100 G Fresh Frozen: 210 G - Visium HD 3‘: Fresh Frozen: 165 G
Analysis	Data QC: Mapping and Quantification Space Ranger Analysis (including cell segmentation) Clustering analysis: Graphclust clustering K-means clustering Scanpy Analysis: PCA analysis Spatial variable gene expression analysis Clustering and dimensionality reduction analysis Differential Expression Gene Analysis(DEG): DEGs clustering heatmap Spatial distribution of DEGs Violine plot t-SNE and UMAP dimensional reduction visualization Functional Enrichment Analysis: GO enrichment KEGG enrichment Reactome enrichment

Sequencing and Analysis

Recommended data outputs and analysis examples are provided for reference only. For detailed information, please contact us to discuss your project-specific analysis requirements.

	Visium HD
Species	Human, mouse or other eukaryotic species, assay dependent
Capture area	6.5mm x 6.5mm
Sequencing platform	NovaSeq X plus
Read length	PE150
Recommended Data Amount	- Visium HD WT Panel: FFPE: 100 G Fresh Frozen: 210 G - Visium HD 3‘: Fresh Frozen: 165 G
Analysis	Data QC: Mapping and Quantification Space Ranger Analysis (including cell segmentation) Clustering analysis: Graphclust clustering K-means clustering Scanpy Analysis: PCA analysis Spatial variable gene expression analysis Clustering and dimensionality reduction analysis Differential Expression Gene Analysis(DEG): DEGs clustering heatmap Spatial distribution of DEGs Violine plot t-SNE and UMAP dimensional reduction visualization Functional Enrichment Analysis: GO enrichment KEGG enrichment Reactome enrichment

Resources

Example Analysis Output

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Cluster Map

Visualise spatially defined clusters across the tissue section to explore regional organisation and tissue structure.

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UMAP Clustering

Review transcriptional similarity between spots or bins to support cluster interpretation and data exploration.

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Marker Gene Dot Plot

Compare marker gene expression across clusters to support annotation of tissue regions and cell-associated patterns.

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Spatial Gene Expression

Display selected marker genes directly on tissue sections to explore localised expression patterns.

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Tissue Filtering

Review tissue-covered areas used for downstream spatial analysis and quality assessment.

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GO Enrichment

Identify enriched biological processes linked to cluster marker genes or region-specific expression patterns.

Webinars

Getting Started with Spatial Transcriptomics

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Frequently Asked Questions

What is the difference between Visium HD WT Panel and Visium HD 3′ Gene Expression?

Which sample types and species are suitable for Visium HD?

How does spatial transcriptomics differ from single-cell RNA sequencing?

Can spatial transcriptomics be combined with single-cell data?

Explore Single-cell & Spatial Resources

Access webinars, brochures and case studies covering sequencing technologies, study planning and data interpretation.

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