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

Protein Expression Visualization and Thresholding with Loupe Browser

Protein Expression and Thresholding

Learn how to perform reference-free spot deconvolution using a public mouse brain dataset

Spot Deconvolution

View all tutorials

Learn about input files required to run Space Ranger

Inputs

Generating FASTQs

Specifying FASTQs

Image Recommendations

Slide Parameters

Manual Alignment

Feature Reference

Running Pipelines

Computing Options

Space Ranger Commands

Count

Aggr

Troubleshooting

Learn about the output files generated by Space Ranger

Outputs

Web Summary

Secondary Analysis

Matrices

Spatial Outputs

Molecule Info (H5)

Feature Slice (H5)

Protein Expression

Metrics Summary

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.

What is Space Ranger?

We provide resources from protocols, user guides, and free-to-use analysis tools.

Algorithms overview

Advanced pipeline content for Space Ranger

Browse Q&As from the 10x Genomics support team

Access free public Visium data from 10x Genomics

A collection of introductions, tutorials, and blogs for data analysis beyond software

Analysis Guides

Loupe Browser is a desktop application for interactive data visualization