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CytAssist Spatial Gene Expression

CytAssist Spatial Gene Expression

What is CytAssist Spatial Gene Expression?

CytAssist Spatial Gene Expression analyzes the whole transcriptome of FFPE, Fresh Frozen, or Fixed Frozen tissue sections in a spatially resolved manner by mapping gene expression over a high resolution microscope image of the tissue.

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Find resources, from protocols to free-to-use analysis tools for processing human or mouse FFPE, Fresh Frozen, and Fixed Frozen tissues.

Frozen Tissue Applications

Documentation for Fresh Frozen and Fixed Frozen Applications.

Experimental Planning & Design

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

Tissue Prep

Best practices for handling FFPE tissue samples and slides before and after sectioning. Guidance for removing hardset coverslips from archived tissue slides.

Tissue Staining

Deparaffinize, stain, image, and decrosslink FFPE 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 CytAssist 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.

Additional Applications


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

View datasets

Videos - CytAssist Spatial Gene Expression

Visium CytAssist Instrument video
How-to series
Visium CytAssist Instrument
Tissue Preparation Guide video
Demonstrated Protocol series
Tissue Preparation Guide
Deparaffinization, H&E Staining, Imaging & Decrosslinking video
Demonstrated Protocol series
Deparaffinization, H&E Staining, Imaging & Decrosslinking
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Find answers to common technical questions, from sample prep through data analysis, about Visium spatial workflows.


Read key peer-reviewed research publications offering greater insights into biology, enabled by 10x Genomics products and technologies.