10x Genomics
Visium Spatial Gene Expression

Space Ranger6.3, printed on 12/30/2024

Sharing Results

Saving .cloupe files

Loupe Browser files are self contained, so if you want to share a dataset with a colleague, you can send them the .cloupe file. You can save your dataset workspace, including the custom groups that were created and any gene lists created or imported, by clicking onin Toolbox.

We strongly recommend any dataset changes in Loupe Browser be saved by creating a new version of the .cloupe file. Changes made to the pipeline generated .cloupe file are irreversible; to regenerate the original file, you would have to re-run the pipeline. You can save .cloupe under a new name by:

• Choose Save As from the File menu

• Press Command-Shift-S if on macOS

• If on Windows, press Ctrl-Shift-S

This will prompt you to create a new .cloupe file in a desired location in your file system.

Exporting data and plots

Loupe Browser also provides the ability to export individual plots and data tables. These options are summarized below. For more details refer to the Navigation tutorial.

• Use to export the plot in the main window in PNG or SVG format. Plots will include the legend if there is an active coloring. We recommend centering the plot by clickingon Mode Selector andon Data Panel Selector to minimize the panels prior to export.

• For the Data Panel Selector:

  • Use to export the Heat Map in PNG format
  • Use to export the Feature Table and Spatial Enrichment results in CSV format. Note that you can modify the contents of this file using the option.
  • Use to export the Violin Plots in either SVG or PNG formats

• From the View Selector use to export the projection's barcodes and coordinates in CSV format

• For each of the modes in Mode Selector use to export

  • [Name of Category] in CSV format
  • Active Feature list in CSV format
  • Filters in JSON format

Next steps and support

This concludes the Loupe Browser spatial gene expression tutorial. Now you are ready to analyze and visualize your own data. Read about how to generate your own .cloupe files with the Space Ranger pipeline.

Reporting Issues

If you encounter any errors in the program, you can send a bug report by clicking on Generate Bug Report from the Help menu. A .tar.gz file containing logs from your most recent Loupe Browser session will be created, and you can send that file to [email protected]. Add the subject line Loupe Browser Error to your message.

You can also submit general feedback and feature requests by clicking on Send Feedback in the Help menu.

We hope this tutorial has made you familiar with the capabilities of Loupe Browser, and that you find it to be the easiest, fastest way to interpret your Visium Spatial Gene Expression data.