10x Genomics Support/Loupe Browser/

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.