10x Genomics
Visium Spatial Gene Expression
Space Ranger4.1, printed on 12/22/2024
What is Loupe Browser?
Loupe Browser is a desktop application that provides interactive visualization functionality to analyze data from different 10x Genomics solutions. Loupe Browser allows you to easily interrogate different views of your 10x data to quickly gain insights into the underlying biology. Loupe is named for a jeweler's loupe, which is used to magnify and inspect the details of precious gemstones.
Loupe Browser supports the analysis of data from the Visium Spatial Gene Expression solution. This includes the ability to perform the following analysis all within the spatial context of a tissue image:
- Interrogate significant genes.
- Characterize and refine clusters.
- Perform differential expression analysis.
To use Loupe Browser, open any .cloupe file generated by the Space Ranger analysis software. The Space Ranger .cloupe file is embedded with the following information:
- Tiled version of the tissue image that was used as input into Space Ranger to enable zooming.
- Gene expression information for all spots on the slide.
- Information about spot alignment in the image.
- Various gene expression-based clustering information for the spots, including t-SNE and UMAP projections.
Once your data is in Loupe Browser, you can rapidly explore and gain insights from the data without the need to do any programming.
Installing Loupe Browser
To use Loupe Browser, follow the directions on the Installation page to download and install the software on either macOS or Windows.
Navigating the Loupe Browser User Interface
If you are new to Loupe Browser, you can learn more about the user interface in this Navigation Tutorial.
Loupe Browser Spatial Gene Expression Tutorial
Loupe Browser provides many powerful analysis capabilities. To learn how to use Loupe Browser to analyze your Visium Spatial Gene Expression data, review the Spatial Gene Expression Tutorial.