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

Visium

Gene Expression

Protein co-detection

Visium Spatial Gene Expression is a next-generation molecular profiling solution for classifying tissue based on total mRNA. Map the whole transcriptome with morphological context in FFPE or fresh frozen tissues to discover novel insights into normal development, disease pathology, and clinical translational research.

Immunofluorescence protein co-detection

Visium CytAssist Gene and Protein Expression

Map the whole transcriptome within the <em>tissue context</em>

Visium CytAssist

Compact instrument designed to simplify the Visium workflow by facilitating the transfer of analytes from standard glass slides to Visium slides.

Spatial Gene Expression

Spatial gene expression profiling and imaging data of fresh frozen or FFPE tissues.

Analyze your Visium Spatial data with microscope images.

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

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?

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.