Oct 14, 2025
Loupe Browser Access and Loading Data
- Hannah Aichelman1
- 1University of Rochester
Protocol Citation: Hannah Aichelman 2025. Loupe Browser Access and Loading Data. protocols.io https://dx.doi.org/10.17504/protocols.io.n92ld6qk8g5b/v1
License: This is an open access protocol distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited
Protocol status: Working
We use this protocol and it's working
Created: October 06, 2025
Last Modified: October 14, 2025
Protocol Integer ID: 229183
Keywords: loupe browser access, accessing loupe browser, loupe browser, urmc users on momentum, urmc user, loading data information, access
Abstract
Information for accessing Loupe Browser, particularly for URMC users on Momentum.
Troubleshooting
Loupe Browser Background
Loupe Browser is a tool provided by 10X Genomics for analysis of Chromium and Visium/Visium HD datasets. It is provided as a free download at https://www.10xgenomics.com/support/software/loupe-browser/downloads. For non-URMC users, downloading the software will be the only way to use Loupe Browser. For URMC users, access to this software is provided through the Office of Research IT (ORIT).
Accessing Momentum
Momentum is a platform used to access university hosted softwares made available by ORIT. Upon reasonable request, ORIT is able to host free software for deployment via remote resources.
Opening Loupe Browser
After logging into Momentum, click on the tile for Loupe Browser. You can also use the search bar to locate it. Click the "Connect from Browser" option. The "Connect from Computer" option can be used as a backup option, but we have found it to be less stable than browser access.
If connecting via browser, you will be taken to an Apache Guacamole portal. Log in using your AD credentials. You will then need to perform a duo authentication and then you should have access to the browser.
If connecting via computer, a remote desktop file will be downloaded. When launching this file, you will be prompted for duo authentication and a desktop session will be configured. This may take some time.
Loading in the Data (URMC Users on Momentum)
Once the Loupe Browser window opens, click the 'Open Loupe File' button.
Enter the path to the data you wish to load in Loupe Browser. The file type that Loupe Browser needs is a cloupe file. You can find this file in the delivery directory associated with your project. You can search for this file using the file explorer address bar.
When accessing Loupe Browser from Momentum, you can navigate to your smdnas02 share by typing '\\smdnas02\GRC_' in the address bar, and then select the appropriate share and project folder. Finally, double click the cloupe file to open it.
For Visium data processed with Space Ranger v4 and above, you will have cloupe files associated with both the binned outputs as well as the cell segmentation outputs. There are cloupe files associated with each of these outputs, which you can open and explore in Loupe Browser.
The cloupe file associated with the binned outputs can be found here:
deliv_*_counts/Sample_ID/outs/binned_outputs/square_*um/
The cloupe file associated with the cell segmented outputs can be found here:
deliv_*_counts/Sample_ID/outs/segmented_outputs/
Additional details on understanding Space Ranger Outputs can be found on 10X's website here: https://www.10xgenomics.com/support/software/space-ranger/latest/analysis/outputs/output-overview