10x Genomics Visium Spatial Software Suite

Overview

Getting Started

Download Center

Analysis

Tutorials

Algorithms

Advanced

Release Notes

Datasets

Loupe Browser

Space Ranger 2.1

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

Demultiplexing with Illumina software

Image recommendation

Slide parameters

Slide layout download

Manual fiducial alignment

Manual CytAssist image alignment

Running Pipelines

Choosing a pipeline

Computing options

Space Ranger commands

Troubleshooting

count (Spatial GEX)

count (CytAssist GEX)

count (CytAssist GEX + PEX)

Feature Reference

Aggr

Learn about the output files generated by Space Ranger

Outputs

Web Summary

Secondary Analysis

Matrices

Spatial Outputs

Spot Deconvolution Outputs

Molecule Info (H5)

Count Outputs

Aggr Outputs

Space Ranger is a set of analysis pipelines that process Visium data with brightfield and fluorescence microscope images. Space Ranger allows users to map the whole transcriptome in formalin fixed paraffin embedded (FFPE) and fresh frozen (FF) tissues.

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 that allows you to interactively visualize data.