Oct 14, 2025
Xenium Explorer Access and Loading Data
- Hannah Aichelman1
- 1University of Rochester
Protocol Citation: Hannah Aichelman 2025. Xenium Explorer Access and Loading Data. protocols.io https://dx.doi.org/10.17504/protocols.io.n2bvjeq7pgk5/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: 229187
Keywords: xenium explorer access, accessing xenium explorer, xenium explorer, urmc users on momentum, loading data information, urmc user, access, data
Abstract
Information for accessing Xenium Explorer, particularly for URMC users on Momentum.
Troubleshooting
Xenium Explorer Background
Xenium Explorer is a tool provided by 10X Genomics for analysis of Xenium datasets. It is provided as a free download at https://www.10xgenomics.com/support/software/xenium-ranger/downloads. For non-URMC users, downloading the software will be the only way to use Xenium Explorer. 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 Xenium Explorer
After logging into Momentum, click on the tile for Xenium Explorer, which should be at the bottom of the page. You can also use the search bar to locate it. Click the "Connect from Browser" option. The "Connect from your computer 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 Xenium Explorer window opens, click the 'Open New File' button.
Enter the path to the data you wish to load in Xenium Explorer. The file type that Xenium Explorer needs is an experiment.xenium file. You can find this experiment file in the delivery directory associated with your project. Note that each ROI has its own experiment file. You can search for this file using the file explorer address bar.
When accessing Xenium Explorer 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. Once you have accessed your shared drive, click the experiment file and open.
Additional details on understanding Xenium Outputs can be found on 10X's website here: