10x Genomics Support/In Situ Gene Expression/Documentation/Panel Design/

Release Notes: Xenium Panel Designer

Table of contents

  • Mar 13, 2024
  • Dec 18, 2023
  • Nov 16, 2023
  • Nov 14, 2023
  • Oct 16, 2023
  • Oct 9, 2023
  • Sept 27, 2023
  • Sept 25, 2023
  • June 29, 2023

Mar 13, 2024

  • Added support for design of add-on panels for the newly released Human Immuno-Oncology Profiling Panel
  • Added support for CLOUPE format reference files in addition to H5 and MEX matrices
  • Enabled accepting and rejecting recommendations when modifying the gene list and probe set counts while iterating on a Xenium custom panel design

Dec 18, 2023

  • Improved probe set coverage for many human and mouse genes, reducing the likelihood that a gene has fewer than eight probe sets available when being included in a Xenium custom design. Read more about our gene coverage in our Getting Started guide.
  • Improved communication regarding the impact of finalizing a panel design when you enter a design ID that was given to you by a 10x Genomics sales representative.
  • Added support for .tar.gz reference datasets.

Nov 16, 2023

  • Building a design has been sped up significantly by improving the performance of our probe screening algorithm. This will resolve issues where some users encountered timeouts when designing 480-plex panels with large reference datasets.
  • When cleaning up your gene list, the Xenium Panel Designer now differentiates between genes that have been removed because we cannot find a match in the Ensembl reference and genes that have been removed because we have zero probes available.
  • The design summary file now uses reference 'nicknames' rather than reference filenames in the dropdown selectors.
  • Fixed a bug where reference files that were compressed on macOS led to design errors.

Nov 14, 2023

  • If you are inputting a request for an advanced design, you are now given the option to provide your RNA binding sequences CSV file via the Xenium Panel Designer application (CSV format described in the Technical Note).
  • When modifying your gene list after a design is generated, the Xenium Panel Designer now displays the reason that we recommend modifying your gene list at the top of the page.
  • Fixed a bug where you could not navigate back to previous page if the panel designer encountered a timeout when designing your panel.
  • Fixed a bug where the total number of genes displayed on the panel review page did not update based on your selected finalization choice.

Oct 16, 2023

  • Provide BED files for each panel design iteration.
  • Introduce limit of 500 MB for uploaded reference datasets in order to improve reliability of the designer. The Xenium Panel Designer computes a pseudobulk matrix from the reference and only requires that all cell types of interest are well represented. Our testing indicates that the end result of 50,000 cell and 1 million cell reference matrices will be very similar.

Oct 9, 2023

  • Enable design of non-advanced human and mouse panels with an existing design ID.
  • Additional public single cell reference datasets from CELLxGENE are available in the Xenium Panel Designer. We have updated existing reference datasets to ensure all selected single cell references are consistently processed and of high quality.

September 27, 2023

  • Add support for design of up to 480-plex standalone custom panels.
  • Add support for design of add-on panels for the newly released human skin and human colon base panels.

September 25, 2023

  • Enable design of human and mouse add-on and standalone custom panels (up to 300 targets) without involvement of 10x Genomics Support team.

June 29, 2023

  • Initial release of the Xenium Panel designer, enabling input of design requests for Xenium Custom Panels by providing a gene list and reference single cell transcriptomics datasets.
Document Type
Panel Information

Last Modified
March 13, 2024