10x Genomics Visium Spatial Software Suite

Overview

Getting Started

Download Center

Analysis

Tutorials

Algorithms

Advanced

Release Notes

Datasets

Loupe Browser

Space Ranger

Set up Space Ranger

Learn how to analyze Fresh Frozen samples with spaceranger

Running spaceranger count (FF)

count for FF

Learn how to analyze FFPE samples with spaceranger

Running spaceranger count (FFPE)

count for FFPE

Learn how to analyze tissue microarray samples with spaceranger

Analyzing CytAssist Tissue Microarray Data with spaceranger count

count 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 more about input files required to Space Ranger

Inputs

Generating FASTQs

Specifying FASTQs

Demultiplexing with Illumina software

Image recommendation

Slide parameters

Slide layout download

Fiducial alignment

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 more about the output files generated by Space Ranger

Outputs

Web Summary

Matrices

Spatial Outputs

Spot Deconvolution Outputs

Molecule Info (H5)

Count Outputs

Aggr Outputs

Space Ranger is a set of analysis pipelines that process Visium Spatial Gene Expression 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 tissues to discover novel insights into normal development, disease pathology, and clinical translational research.

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.