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, helping connect transcriptomic profiles with tissue morphology and spatial organisation. This approach can support studies of complex tissues, cellular neighbourhoods and region-specific biological patterns that may be missed by dissociated single-cell or bulk RNA-seq methods.

Novogene Europe provides Visium HD spatial gene expression services using 10x Genomics CytAssist-enabled workflows. The service supports high-resolution, whole-transcriptome spatial profiling for compatible human and mouse tissue samples, including FFPE and fresh frozen tissue, with downstream analysis to visualise gene expression patterns within tissue 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.

FFPE and Fresh Frozen Support

Workflow options for compatible human and mouse FFPE or fresh frozen tissue samples, depending on tissue quality and project requirements.

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.

Sample Type (Human/Mouse)	Minimum amount	RNA QC	Other details
FFPE *block	1 FFPE block Block thickness > 1mm	DV200 ≥ 30%	For optimal capture area usage: Multiple tissue pieces can be embedded into FFPE or OCT blocks 2 FFPE tissue sections can be placed on 1 glass slide, without overlap
FFPE* slide	2-4 tissue sections on glass slides and RNA scrolls (Thickness > 50 µm)	DV200 ≥ 30%	For optimal capture area usage: Multiple tissue pieces can be embedded into FFPE or OCT blocks 2 FFPE tissue sections can be placed on 1 glass slide, without overlap
Fresh (frozen) tisssues (Embedded in OCT blocks)	1 OCT block Block thickness > 1mm	RIN ≥ 4	For optimal capture area usage: Multiple tissue pieces can be embedded into FFPE or OCT blocks 2 FFPE tissue sections can be placed on 1 glass slide, without overlap

Species type - Human/Mouse
*FFPE glass slides must be positive charged glass slides.

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.

Sample Type (Human/Mouse)	Minimum amount	RNA QC	Other details
FFPE *block	1 FFPE block Block thickness > 1mm	DV200 ≥ 30%	For optimal capture area usage: Multiple tissue pieces can be embedded into FFPE or OCT blocks 2 FFPE tissue sections can be placed on 1 glass slide, without overlap
FFPE* slide	2-4 tissue sections on glass slides and RNA scrolls (Thickness > 50 µm)	DV200 ≥ 30%	For optimal capture area usage: Multiple tissue pieces can be embedded into FFPE or OCT blocks 2 FFPE tissue sections can be placed on 1 glass slide, without overlap
Fresh (frozen) tisssues (Embedded in OCT blocks)	1 OCT block Block thickness > 1mm	RIN ≥ 4	For optimal capture area usage: Multiple tissue pieces can be embedded into FFPE or OCT blocks 2 FFPE tissue sections can be placed on 1 glass slide, without overlap

Species type - Human/Mouse
*FFPE glass slides must be positive charged glass slides.

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.

Sample Type (Human/Mouse)	Minimum amount	RNA QC	Other details
FFPE *block	1 FFPE block Block thickness > 1mm	DV200 ≥ 30%	For optimal capture area usage: Multiple tissue pieces can be embedded into FFPE or OCT blocks 2 FFPE tissue sections can be placed on 1 glass slide, without overlap
FFPE* slide	2-4 tissue sections on glass slides and RNA scrolls (Thickness > 50 µm)	DV200 ≥ 30%	For optimal capture area usage: Multiple tissue pieces can be embedded into FFPE or OCT blocks 2 FFPE tissue sections can be placed on 1 glass slide, without overlap
Fresh (frozen) tisssues (Embedded in OCT blocks)	1 OCT block Block thickness > 1mm	RIN ≥ 4	For optimal capture area usage: Multiple tissue pieces can be embedded into FFPE or OCT blocks 2 FFPE tissue sections can be placed on 1 glass slide, without overlap

Species type - Human/Mouse
*FFPE glass slides must be positive charged glass slides.

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.

Sample Type (Human/Mouse)	Minimum amount	RNA QC	Other details
FFPE *block	1 FFPE block Block thickness > 1mm	DV200 ≥ 30%	For optimal capture area usage: Multiple tissue pieces can be embedded into FFPE or OCT blocks 2 FFPE tissue sections can be placed on 1 glass slide, without overlap
FFPE* slide	2-4 tissue sections on glass slides and RNA scrolls (Thickness > 50 µm)	DV200 ≥ 30%	For optimal capture area usage: Multiple tissue pieces can be embedded into FFPE or OCT blocks 2 FFPE tissue sections can be placed on 1 glass slide, without overlap
Fresh (frozen) tisssues (Embedded in OCT blocks)	1 OCT block Block thickness > 1mm	RIN ≥ 4	For optimal capture area usage: Multiple tissue pieces can be embedded into FFPE or OCT blocks 2 FFPE tissue sections can be placed on 1 glass slide, without overlap

Species type - Human/Mouse
*FFPE glass slides must be positive charged glass slides.

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 or Mouse
Capture area	6.5mm x 6.5mm
Sequencing platform	NovaSeq X plus
Read length	PE150
Recommended Data Amount	100 Gb/sample per capture area for FFPE
Analysis	Data QC： Mapping and Quantification Dimensionality Reduction, Clustering, and Differential analysis: Graphclust clustering K-means clustering Seurat 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 or Mouse
Capture area	6.5mm x 6.5mm
Sequencing platform	NovaSeq X plus
Read length	PE150
Recommended Data Amount	100 Gb/sample per capture area for FFPE
Analysis	Data QC： Mapping and Quantification Dimensionality Reduction, Clustering, and Differential analysis: Graphclust clustering K-means clustering Seurat 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 or Mouse
Capture area	6.5mm x 6.5mm
Sequencing platform	NovaSeq X plus
Read length	PE150
Recommended Data Amount	100 Gb/sample per capture area for FFPE
Analysis	Data QC： Mapping and Quantification Dimensionality Reduction, Clustering, and Differential analysis: Graphclust clustering K-means clustering Seurat 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 or Mouse
Capture area	6.5mm x 6.5mm
Sequencing platform	NovaSeq X plus
Read length	PE150
Recommended Data Amount	100 Gb/sample per capture area for FFPE
Analysis	Data QC： Mapping and Quantification Dimensionality Reduction, Clustering, and Differential analysis: Graphclust clustering K-means clustering Seurat 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.

Sample Type (Human/Mouse)	Minimum amount	RNA QC	Other details
FFPE *block	1 FFPE block Block thickness > 1mm	DV200 ≥ 30%	For optimal capture area usage: Multiple tissue pieces can be embedded into FFPE or OCT blocks 2 FFPE tissue sections can be placed on 1 glass slide, without overlap
FFPE* slide	2-4 tissue sections on glass slides and RNA scrolls (Thickness > 50 µm)	DV200 ≥ 30%	For optimal capture area usage: Multiple tissue pieces can be embedded into FFPE or OCT blocks 2 FFPE tissue sections can be placed on 1 glass slide, without overlap
Fresh (frozen) tisssues (Embedded in OCT blocks)	1 OCT block Block thickness > 1mm	RIN ≥ 4	For optimal capture area usage: Multiple tissue pieces can be embedded into FFPE or OCT blocks 2 FFPE tissue sections can be placed on 1 glass slide, without overlap

Species type - Human/Mouse
*FFPE glass slides must be positive charged glass slides.

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.

Sample Type (Human/Mouse)	Minimum amount	RNA QC	Other details
FFPE *block	1 FFPE block Block thickness > 1mm	DV200 ≥ 30%	For optimal capture area usage: Multiple tissue pieces can be embedded into FFPE or OCT blocks 2 FFPE tissue sections can be placed on 1 glass slide, without overlap
FFPE* slide	2-4 tissue sections on glass slides and RNA scrolls (Thickness > 50 µm)	DV200 ≥ 30%	For optimal capture area usage: Multiple tissue pieces can be embedded into FFPE or OCT blocks 2 FFPE tissue sections can be placed on 1 glass slide, without overlap
Fresh (frozen) tisssues (Embedded in OCT blocks)	1 OCT block Block thickness > 1mm	RIN ≥ 4	For optimal capture area usage: Multiple tissue pieces can be embedded into FFPE or OCT blocks 2 FFPE tissue sections can be placed on 1 glass slide, without overlap

Species type - Human/Mouse
*FFPE glass slides must be positive charged glass slides.

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.

Sample Type (Human/Mouse)	Minimum amount	RNA QC	Other details
FFPE *block	1 FFPE block Block thickness > 1mm	DV200 ≥ 30%	For optimal capture area usage: Multiple tissue pieces can be embedded into FFPE or OCT blocks 2 FFPE tissue sections can be placed on 1 glass slide, without overlap
FFPE* slide	2-4 tissue sections on glass slides and RNA scrolls (Thickness > 50 µm)	DV200 ≥ 30%	For optimal capture area usage: Multiple tissue pieces can be embedded into FFPE or OCT blocks 2 FFPE tissue sections can be placed on 1 glass slide, without overlap
Fresh (frozen) tisssues (Embedded in OCT blocks)	1 OCT block Block thickness > 1mm	RIN ≥ 4	For optimal capture area usage: Multiple tissue pieces can be embedded into FFPE or OCT blocks 2 FFPE tissue sections can be placed on 1 glass slide, without overlap

Species type - Human/Mouse
*FFPE glass slides must be positive charged glass slides.

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.

Sample Type (Human/Mouse)	Minimum amount	RNA QC	Other details
FFPE *block	1 FFPE block Block thickness > 1mm	DV200 ≥ 30%	For optimal capture area usage: Multiple tissue pieces can be embedded into FFPE or OCT blocks 2 FFPE tissue sections can be placed on 1 glass slide, without overlap
FFPE* slide	2-4 tissue sections on glass slides and RNA scrolls (Thickness > 50 µm)	DV200 ≥ 30%	For optimal capture area usage: Multiple tissue pieces can be embedded into FFPE or OCT blocks 2 FFPE tissue sections can be placed on 1 glass slide, without overlap
Fresh (frozen) tisssues (Embedded in OCT blocks)	1 OCT block Block thickness > 1mm	RIN ≥ 4	For optimal capture area usage: Multiple tissue pieces can be embedded into FFPE or OCT blocks 2 FFPE tissue sections can be placed on 1 glass slide, without overlap

Species type - Human/Mouse
*FFPE glass slides must be positive charged glass slides.

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 or Mouse
Capture area	6.5mm x 6.5mm
Sequencing platform	NovaSeq X plus
Read length	PE150
Recommended Data Amount	100 Gb/sample per capture area for FFPE
Analysis	Data QC： Mapping and Quantification Dimensionality Reduction, Clustering, and Differential analysis: Graphclust clustering K-means clustering Seurat 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 or Mouse
Capture area	6.5mm x 6.5mm
Sequencing platform	NovaSeq X plus
Read length	PE150
Recommended Data Amount	100 Gb/sample per capture area for FFPE
Analysis	Data QC： Mapping and Quantification Dimensionality Reduction, Clustering, and Differential analysis: Graphclust clustering K-means clustering Seurat 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 or Mouse
Capture area	6.5mm x 6.5mm
Sequencing platform	NovaSeq X plus
Read length	PE150
Recommended Data Amount	100 Gb/sample per capture area for FFPE
Analysis	Data QC： Mapping and Quantification Dimensionality Reduction, Clustering, and Differential analysis: Graphclust clustering K-means clustering Seurat 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 or Mouse
Capture area	6.5mm x 6.5mm
Sequencing platform	NovaSeq X plus
Read length	PE150
Recommended Data Amount	100 Gb/sample per capture area for FFPE
Analysis	Data QC： Mapping and Quantification Dimensionality Reduction, Clustering, and Differential analysis: Graphclust clustering K-means clustering Seurat 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.

1/1

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

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.

FFPE and Fresh Frozen Support

Workflow options for compatible human and mouse FFPE or fresh frozen tissue samples, depending on tissue quality and project requirements.

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.

Sample Type (Human/Mouse)	Minimum amount	RNA QC	Other details
FFPE *block	1 FFPE block Block thickness > 1mm	DV200 ≥ 30%	For optimal capture area usage: Multiple tissue pieces can be embedded into FFPE or OCT blocks 2 FFPE tissue sections can be placed on 1 glass slide, without overlap
FFPE* slide	2-4 tissue sections on glass slides and RNA scrolls (Thickness > 50 µm)	DV200 ≥ 30%	For optimal capture area usage: Multiple tissue pieces can be embedded into FFPE or OCT blocks 2 FFPE tissue sections can be placed on 1 glass slide, without overlap
Fresh (frozen) tisssues (Embedded in OCT blocks)	1 OCT block Block thickness > 1mm	RIN ≥ 4	For optimal capture area usage: Multiple tissue pieces can be embedded into FFPE or OCT blocks 2 FFPE tissue sections can be placed on 1 glass slide, without overlap

Species type - Human/Mouse
*FFPE glass slides must be positive charged glass slides.

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.

Sample Type (Human/Mouse)	Minimum amount	RNA QC	Other details
FFPE *block	1 FFPE block Block thickness > 1mm	DV200 ≥ 30%	For optimal capture area usage: Multiple tissue pieces can be embedded into FFPE or OCT blocks 2 FFPE tissue sections can be placed on 1 glass slide, without overlap
FFPE* slide	2-4 tissue sections on glass slides and RNA scrolls (Thickness > 50 µm)	DV200 ≥ 30%	For optimal capture area usage: Multiple tissue pieces can be embedded into FFPE or OCT blocks 2 FFPE tissue sections can be placed on 1 glass slide, without overlap
Fresh (frozen) tisssues (Embedded in OCT blocks)	1 OCT block Block thickness > 1mm	RIN ≥ 4	For optimal capture area usage: Multiple tissue pieces can be embedded into FFPE or OCT blocks 2 FFPE tissue sections can be placed on 1 glass slide, without overlap

Species type - Human/Mouse
*FFPE glass slides must be positive charged glass slides.

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.

Sample Type (Human/Mouse)	Minimum amount	RNA QC	Other details
FFPE *block	1 FFPE block Block thickness > 1mm	DV200 ≥ 30%	For optimal capture area usage: Multiple tissue pieces can be embedded into FFPE or OCT blocks 2 FFPE tissue sections can be placed on 1 glass slide, without overlap
FFPE* slide	2-4 tissue sections on glass slides and RNA scrolls (Thickness > 50 µm)	DV200 ≥ 30%	For optimal capture area usage: Multiple tissue pieces can be embedded into FFPE or OCT blocks 2 FFPE tissue sections can be placed on 1 glass slide, without overlap
Fresh (frozen) tisssues (Embedded in OCT blocks)	1 OCT block Block thickness > 1mm	RIN ≥ 4	For optimal capture area usage: Multiple tissue pieces can be embedded into FFPE or OCT blocks 2 FFPE tissue sections can be placed on 1 glass slide, without overlap

Species type - Human/Mouse
*FFPE glass slides must be positive charged glass slides.

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.

Sample Type (Human/Mouse)	Minimum amount	RNA QC	Other details
FFPE *block	1 FFPE block Block thickness > 1mm	DV200 ≥ 30%	For optimal capture area usage: Multiple tissue pieces can be embedded into FFPE or OCT blocks 2 FFPE tissue sections can be placed on 1 glass slide, without overlap
FFPE* slide	2-4 tissue sections on glass slides and RNA scrolls (Thickness > 50 µm)	DV200 ≥ 30%	For optimal capture area usage: Multiple tissue pieces can be embedded into FFPE or OCT blocks 2 FFPE tissue sections can be placed on 1 glass slide, without overlap
Fresh (frozen) tisssues (Embedded in OCT blocks)	1 OCT block Block thickness > 1mm	RIN ≥ 4	For optimal capture area usage: Multiple tissue pieces can be embedded into FFPE or OCT blocks 2 FFPE tissue sections can be placed on 1 glass slide, without overlap

Species type - Human/Mouse
*FFPE glass slides must be positive charged glass slides.

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 or Mouse
Capture area	6.5mm x 6.5mm
Sequencing platform	NovaSeq X plus
Read length	PE150
Recommended Data Amount	100 Gb/sample per capture area for FFPE
Analysis	Data QC： Mapping and Quantification Dimensionality Reduction, Clustering, and Differential analysis: Graphclust clustering K-means clustering Seurat 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 or Mouse
Capture area	6.5mm x 6.5mm
Sequencing platform	NovaSeq X plus
Read length	PE150
Recommended Data Amount	100 Gb/sample per capture area for FFPE
Analysis	Data QC： Mapping and Quantification Dimensionality Reduction, Clustering, and Differential analysis: Graphclust clustering K-means clustering Seurat 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 or Mouse
Capture area	6.5mm x 6.5mm
Sequencing platform	NovaSeq X plus
Read length	PE150
Recommended Data Amount	100 Gb/sample per capture area for FFPE
Analysis	Data QC： Mapping and Quantification Dimensionality Reduction, Clustering, and Differential analysis: Graphclust clustering K-means clustering Seurat 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 or Mouse
Capture area	6.5mm x 6.5mm
Sequencing platform	NovaSeq X plus
Read length	PE150
Recommended Data Amount	100 Gb/sample per capture area for FFPE
Analysis	Data QC： Mapping and Quantification Dimensionality Reduction, Clustering, and Differential analysis: Graphclust clustering K-means clustering Seurat 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.

Sample Type (Human/Mouse)	Minimum amount	RNA QC	Other details
FFPE *block	1 FFPE block Block thickness > 1mm	DV200 ≥ 30%	For optimal capture area usage: Multiple tissue pieces can be embedded into FFPE or OCT blocks 2 FFPE tissue sections can be placed on 1 glass slide, without overlap
FFPE* slide	2-4 tissue sections on glass slides and RNA scrolls (Thickness > 50 µm)	DV200 ≥ 30%	For optimal capture area usage: Multiple tissue pieces can be embedded into FFPE or OCT blocks 2 FFPE tissue sections can be placed on 1 glass slide, without overlap
Fresh (frozen) tisssues (Embedded in OCT blocks)	1 OCT block Block thickness > 1mm	RIN ≥ 4	For optimal capture area usage: Multiple tissue pieces can be embedded into FFPE or OCT blocks 2 FFPE tissue sections can be placed on 1 glass slide, without overlap

Species type - Human/Mouse
*FFPE glass slides must be positive charged glass slides.

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.

Sample Type (Human/Mouse)	Minimum amount	RNA QC	Other details
FFPE *block	1 FFPE block Block thickness > 1mm	DV200 ≥ 30%	For optimal capture area usage: Multiple tissue pieces can be embedded into FFPE or OCT blocks 2 FFPE tissue sections can be placed on 1 glass slide, without overlap
FFPE* slide	2-4 tissue sections on glass slides and RNA scrolls (Thickness > 50 µm)	DV200 ≥ 30%	For optimal capture area usage: Multiple tissue pieces can be embedded into FFPE or OCT blocks 2 FFPE tissue sections can be placed on 1 glass slide, without overlap
Fresh (frozen) tisssues (Embedded in OCT blocks)	1 OCT block Block thickness > 1mm	RIN ≥ 4	For optimal capture area usage: Multiple tissue pieces can be embedded into FFPE or OCT blocks 2 FFPE tissue sections can be placed on 1 glass slide, without overlap

Species type - Human/Mouse
*FFPE glass slides must be positive charged glass slides.

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.

Sample Type (Human/Mouse)	Minimum amount	RNA QC	Other details
FFPE *block	1 FFPE block Block thickness > 1mm	DV200 ≥ 30%	For optimal capture area usage: Multiple tissue pieces can be embedded into FFPE or OCT blocks 2 FFPE tissue sections can be placed on 1 glass slide, without overlap
FFPE* slide	2-4 tissue sections on glass slides and RNA scrolls (Thickness > 50 µm)	DV200 ≥ 30%	For optimal capture area usage: Multiple tissue pieces can be embedded into FFPE or OCT blocks 2 FFPE tissue sections can be placed on 1 glass slide, without overlap
Fresh (frozen) tisssues (Embedded in OCT blocks)	1 OCT block Block thickness > 1mm	RIN ≥ 4	For optimal capture area usage: Multiple tissue pieces can be embedded into FFPE or OCT blocks 2 FFPE tissue sections can be placed on 1 glass slide, without overlap

Species type - Human/Mouse
*FFPE glass slides must be positive charged glass slides.

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.

Sample Type (Human/Mouse)	Minimum amount	RNA QC	Other details
FFPE *block	1 FFPE block Block thickness > 1mm	DV200 ≥ 30%	For optimal capture area usage: Multiple tissue pieces can be embedded into FFPE or OCT blocks 2 FFPE tissue sections can be placed on 1 glass slide, without overlap
FFPE* slide	2-4 tissue sections on glass slides and RNA scrolls (Thickness > 50 µm)	DV200 ≥ 30%	For optimal capture area usage: Multiple tissue pieces can be embedded into FFPE or OCT blocks 2 FFPE tissue sections can be placed on 1 glass slide, without overlap
Fresh (frozen) tisssues (Embedded in OCT blocks)	1 OCT block Block thickness > 1mm	RIN ≥ 4	For optimal capture area usage: Multiple tissue pieces can be embedded into FFPE or OCT blocks 2 FFPE tissue sections can be placed on 1 glass slide, without overlap

Species type - Human/Mouse
*FFPE glass slides must be positive charged glass slides.

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 or Mouse
Capture area	6.5mm x 6.5mm
Sequencing platform	NovaSeq X plus
Read length	PE150
Recommended Data Amount	100 Gb/sample per capture area for FFPE
Analysis	Data QC： Mapping and Quantification Dimensionality Reduction, Clustering, and Differential analysis: Graphclust clustering K-means clustering Seurat 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 or Mouse
Capture area	6.5mm x 6.5mm
Sequencing platform	NovaSeq X plus
Read length	PE150
Recommended Data Amount	100 Gb/sample per capture area for FFPE
Analysis	Data QC： Mapping and Quantification Dimensionality Reduction, Clustering, and Differential analysis: Graphclust clustering K-means clustering Seurat 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 or Mouse
Capture area	6.5mm x 6.5mm
Sequencing platform	NovaSeq X plus
Read length	PE150
Recommended Data Amount	100 Gb/sample per capture area for FFPE
Analysis	Data QC： Mapping and Quantification Dimensionality Reduction, Clustering, and Differential analysis: Graphclust clustering K-means clustering Seurat 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 or Mouse
Capture area	6.5mm x 6.5mm
Sequencing platform	NovaSeq X plus
Read length	PE150
Recommended Data Amount	100 Gb/sample per capture area for FFPE
Analysis	Data QC： Mapping and Quantification Dimensionality Reduction, Clustering, and Differential analysis: Graphclust clustering K-means clustering Seurat 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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Explore Single-cell & Spatial Resources

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

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