10x Genomics Support/Loupe Browser/Analysis/

Tutorials for Spatial Gene Expression

Tutorial Dataset Introduction
Get oriented with the Spatial mouse brain tutorial dataset and learn about sharing usage data
Interface and Navigation
Learn how to navigate the Loupe Browser interface with a pre-loaded mouse brain dataset
Evaluate Gene Markers
Evaluate the expression profiles of known gene markers of interest in the context of tissue morphology using Loupe Browser
Manual Fiducial Alignment
For fluorescence images, or when fiducial markers are obstructed or tissue boundaries are unclear
Manual Visium CytAssist Image Alignment
For shape or stain mismatches with the Visium CytAssist instrument
Explore Spatial Clusters
Evaluating image data and clustering in the spatial view with Loupe Browser
Characterize Substructure
Find subgroups within the clusters and perform differential gene expression with Loupe Browser
Spatial Reclustering
Interactive filtering and reclustering workflow for spatial datasets
Sharing Results
Share a dataset with colleagues
Protein Expression and Thresholding
Learn how to use protein expression to filter and visualize your data
Spot Deconvolution
Learn how to perform reference-free spot deconvolution using a public mouse brain dataset