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HD Spatial Gene Expression

HD Spatial Gene Expression

This assay requires CytAssist instrument Firmware v2.0.0 or higher. Refer to the Visium CytAssist with Readiness Test User Guide (CG000542) for details.
What is Visium HD Spatial Gene Expression?

Visium HD Spatial Gene Expression is a single cell scale, high resolution, CytAssist-enabled, whole transcriptome probe-based assay compatible with mouse or human FFPE tissue sections placed on glass slides.

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Find resources, from protocols to free-to-use analysis tools.

Experimental Planning and Design

Plan ahead by referring to the list of equipment, kits, and reagents needed for the Visium HD Spatial Gene Expression protocols.

Tissue Prep & Staining

Best practices for handling FFPE tissue samples and generating tissue slides. Protocol outlines deparaffinization, staining, and decrosslinking of tissue sections.


For imaging hardware, general image acquisition and analysis guidelines, and example images.

Probe Sets

Find a list of probes targeting protein-coding genes in human or mouse transcriptome for the Visium HD Spatial Gene Expression assay.

Library Construction

Construct a sequencing-ready Visium spatial library from your FFPE tissue sections.


Refer to instrument-specific documents for seamless instrument operation.


Sequence your Visium spatial library as per our provided recommendations.

Software Analysis

Analyze your Visium spatial data using our pipelines and visualization tools.


Access free, publicly available data from a number of different sample types generated with Visium Spatial solutions

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Find answers to common technical questions, from sample prep through data analysis, about Visium spatial workflows.