Support homeLoupe Browser
Tutorials

Tutorials

Introduction

Learn about Loupe Browser and get oriented with its interface and features.

Navigation for Single Cell Gene Expression
Navigation for Spatial Gene Expression
LoupeR

LoupeR is an R package developed by 10x Genomics that works with Seurat objects to create a Loupe Browser file.

Assay Analysis

Learn about product-specific analysis capabilities to quickly gain insights from your 10x data.

HD Spatial Gene Expression

New Tutorial: Mapping the Tumor Microenvironment with Visium HD

Spatial Gene Expression (v1/v2)
Single Cell Gene Expression & Flex
Single Cell Immune Profiling
Single Cell ATAC
Single Cell Multiome ATAC + Gene Expression

Manual alignment for Space Ranger

Visium HD manual alignment

Identify fiducials, perform tissue selection and align CytAssist and microscope images for Visium HD. You will then export a JSON file for Space Ranger analysis.

Manual Fiducial Alignment and Tissue Detection (Visium v1/v2)

Manually identify the fiducials in your Visium image and select spots under tissue. You will then export a JSON file for Space Ranger analysis.

Manual CytAssist Image - Microscope Image Alignment (Visium v1/v2)

Align your CytAssist image and microscope image. After you complete this step, you can either export a JSON file for Space Ranger automated fiducial and tissue detection, or continue to Visium Fiducial Alignment.