10x Genomics
Spatial Gene Expression

Space Ranger, printed on 10/31/2024

What's New in Loupe Browser 4.0

Loupe Browser 4.0 has been updated to allow users to easily analyze data generated with the Visium Spatial Gene Expression Solution, while still allowing users to easily explore single-cell gene expression, immunology, and ATAC data. It is compatible with Space Ranger 1.0, and remains compatible with .cloupe files generated by all versions of Cell Ranger after v1.3.

Spatial Gene Expression Analysis

Loupe Browser 4.0 allows users to analyze spatial gene expression data within the context of a high-resolution microscope image:

Loupe Browser's fluid, responsive user interface allows users to quickly label morphological structure, explore the relation between underlying tissue structure and gene expression and identify regions of the tissue with unique gene expression. A variety of graphical settings and a wider range of color palettes will allow users to export the ideal graphics for their experiment. Finally, Loupe Browser 4.0 comes preloaded with a mouse brain tutorial, so existing single-cell users can explore a spatial gene expression dataset.

To find out how to use Loupe Browser 4.0 to analyze spatial gene expression, please consult the Loupe Browser documentation.

Visium Manual Slide Alignment

Though Space Ranger comes with reliable automatic image detection algorithms, Loupe Browser 4.0 can also be used to override the pipeline's decisions, or provide finer-grained control over tissue labeling for diverse samples.

The Visium Manual Alignment Wizard allows users to easily line up their microscope image with a slide layout file, and to precisely label tissue and background spots for processing by the Space Ranger pipeline.

Improvements For All Applications

Added Expression Color Palettes

Enjoy a variety of new color palettes for feature expression, including inverted color scales, Turbo, Viridis and Plasma. The heatmap color scheme should also make it easier to see differences in differential gene patterns between clusters.

Lifted Limits

Loupe Browser will warn, but not prevent you from doing the following:

• Differential expression on datasets over 100,000 cells
• SVG export on datasets over 100,000 cells

Bugfixes

• Better behavior in split view.
• Do not grey out ATAC motif expression levels outside the default range.
• Notarized for warning-free distribution on macOS Mojave and Catalina.