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Spatial Gene Expression for FFPE

What is Spatial Gene Expression for FFPE?

Visium Spatial Gene Expression measures the whole transcriptome of FFPE tissue sections in a spatially resolved manner by mapping gene expression over a high-resolution microscope image of the H&E- or IF-stained tissue.

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

Experimental Planning & Design

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

Tissue Prep

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

Tissue Staining

Deparaffinize, stain, image, and decrosslink tissue.

Probe Sets

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

Library Construction

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


Refer to instrument-specific documents for seamless instrument operation.


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


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 for FFPE spatial solutions

View datasets


Videos for Visium CytAssist for FFPE are coming soon.

Visium for FFPE Gene Expression Protocol video
How-to series
Visium for FFPE Gene Expression Protocol
Visium for FFPE Tissue Preparation Guide video
Demonstrated Protocol series
Visium for FFPE Tissue Preparation Guide
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Find answers to common technical questions, from sample prep through data analysis, about Visium spatial workflows.

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

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