
The Visium Spatial Gene Expression workflow measures mRNA levels in intact, fresh frozen (FF) tissue sections using spatially barcoded oligonucleotides attached to the Visium slide. The workflow begins by first determining the optimal permeabilization time for the tissue. The tissue is stained, imaged, and cell permeabilized to release mRNA. The mRNA binds to the poly(dT) region of spatially barcoded oligonucleotides present on the slide surface. Libraries are generated from the barcoded cDNA of a captured transcript and are sequenced.

<Image src={"https://cdn.10xgenomics.com/image/upload/v1654108033/software-support/Spatial-GEX/SR-v2.0/FF-Workflow-Overview.png"} /> <br />

Resources and additional information are available below:

- [Visium Glossary](/support/software/space-ranger/latest/getting-started/space-ranger-glossary)
- [Running `spaceranger count`](/support/software/space-ranger/latest/analysis/running-pipelines/poly-a-based-assay-count-spatial-gex)
- [Understanding Outputs](/support/software/space-ranger/latest/analysis/outputs/output-overview)
- [Manual Fiducial Alignment in Loupe Browser](/support/software/space-ranger/latest/analysis/inputs/image-fiducial-alignment)


Direct Placement Workflow for FF 

Direct Placement Workflow for Fresh Frozen

10x Genomics Visium Spatial Software Suite

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Space Ranger

Install Space Ranger and perform a test run

Set up Space Ranger

Learn how to analyze fresh frozen (FF) samples with spaceranger count

Running spaceranger count (FF)

Space Ranger for FF

Learn how to analyze formalin fixed paraffin embedded (FFPE) samples with spaceranger count

Running spaceranger count (FFPE)

Space Ranger for FFPE

Learn how to analyze tissue microarray (TMA) samples with spaceranger count

Analyzing CytAssist Tissue Microarray Data with spaceranger count

Space Ranger for CytAssist TMA

Learn how to use protein expression to filter and visualize your data

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Protein Expression and Thresholding

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Spot Deconvolution

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Space Ranger is a set of analysis pipelines that process 10x Genomics Visium data with brightfield or fluorescence microscope images, allowing users to map the whole transcriptome in a variety of tissues. Space Ranger v3.1 now supports Visium HD.

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