
<LinkableSection id={"Dec2024"} title={"v3.4.6 (December 10, 2024)"}>

- Enabled [gene boosting](/support/software/xenium-panel-designer/latest/tutorials/xenium-panel-design-concepts-terms#gene-boost) for [Xenium Prime 5K panel pre-designed genes](/support/software/xenium-panel-designer/latest/tutorials/pre-designed-xenium-prime-5k) in custom add-on requests.

</LinkableSection>

<LinkableSection id={"v3.1.1"} title={"v3.1.1 (June 18, 2024)"}>

- Incorporated [NUPACK](https://www.nupack.org) to enhance probe design. Panel designer now targets five probe sets per gene for Xenium Prime custom panels.
- Updated BED files to show the codeword and probe set index for each entry.
- Added "xenografts" to the Advanced target list on the "Tell us about your panel" page.
- Added a probe details file (`probe_info.csv.gz`) to "Output files" table for completed panel designs.

</LinkableSection>

<LinkableSection id={"v3.0.21"} title={"v3.0.21 (May 28, 2024)"}>

- Enabled design for Xenium Prime 5K human or mouse custom add-on panels. For more information about the new pre-designed panels and how to request custom designs for them, read the [Pre-designed Xenium Prime Gene Expression Panels page](/support/software/xenium-panel-designer/latest/tutorials/pre-designed-xenium-prime-5k) and the [Xenium Panel Designer Workflow Guide](/support/software/xenium-panel-designer/latest/tutorials/xenium-panel-design-workflow-guide).
- Chemistry version (Xenium v1 or Xenium Prime) is tracked for all custom panel designs
- Updated the Advanced target list on the "Tell us about your panel" page to be more comprehensive. Added "SNVs" to the list. As before, select all that apply for your design request.
- Added three new human kidney reference datasets
- Reduced design build time by optimizing performance
- Updated output JSON filename to improve readability and decrease text length
- Updated advanced custom domain file CSV outputs for simplicity
- Fixed bugs showing wrong panel type selections for pre-existing design IDs

</LinkableSection>

<LinkableSection id={"v1.0"} title={"v1.0.0"}>

_Xenium Panel Designer releases prior to May 28, 2024 are v1.0.0_

</LinkableSection>

<LinkableSection id={"03-13-24"} title={"Mar 13, 2024"} nested={true}>

- 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

</LinkableSection>

<LinkableSection id={"12-18-23"} title={"Dec 18, 2023"} nested={true}>

- 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 [create gene list page](/support/software/xenium-panel-designer/latest/tutorials/create-gene-list#input-gene-list).
- 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.

</LinkableSection>

<LinkableSection id={"11-16-23"} title={"Nov 16, 2023"} nested={true}>

- 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.

</LinkableSection>

<LinkableSection id={"11-14-23"} title={"Nov 14, 2023"} nested={true}>

- 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](/support/in-situ-gene-expression/documentation/steps/panel-design/species-standalone-custom-and-advanced-custom-panel-design-for-xenium-in-situ)).
- 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.

</LinkableSection>

<LinkableSection id={"10-16-23"} title={"Oct 16, 2023"} nested={true}>

- 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.

</LinkableSection>

<LinkableSection id={"10-9-23"} title={"Oct 9, 2023"} nested={true}>

- 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.

</LinkableSection>

<LinkableSection id={"9-27-23"} title={"September 27, 2023"} nested={true}>

- 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.

</LinkableSection>

<LinkableSection id={"9-25-23"} title={"September 25, 2023"} nested={true}>

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

</LinkableSection>

<LinkableSection id={"6-29-23"} title={"June 29, 2023"} nested={true}>

- 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.

</LinkableSection>


Xenium Panel Designer Release Notes

10x Genomics Xenium Panel Designer is an app for designing custom panels.

Overview

Tutorials

Advanced

FAQs

Release Notes

Xenium Analyzer

Xenium Onboard Analysis

Xenium Explorer

Xenium Ranger

Datasets

Xenium Panel Designer

Introduction

Learn about pre-designed and custom panel design options to decide which is best-suited for your research.

Choose Design Option

Enter a list of genes and compare the overlap with available 10x Genomics pre-designed panels.

Compare Panel Genes

Glossary of concepts important for understanding Xenium panel design.

Design Concepts and Terms

Walk through demonstrations of common Xenium Panel Designer use cases

Xenium Panel Designer Examples

Pre-designed Panels

Metadata for pre-designed Xenium v1 panels.

Xenium v1 Panel Info

Metadata for pre-designed Xenium Prime 5K panels.

Xenium Prime 5K Panel Info

Guidance for generating add-on, standalone custom, and advanced custom panel designs with the Xenium Panel Designer tool.

XPD Workflow Guide

Options for creating or selecting a single cell reference for custom panel design.

Create Single Cell Reference

Options for creating a gene list for custom panel design.

Create Gene List

Description of panel design summary HTML.

Interpret Xenium Panel Design Summary

Finalize Panel Design

Panel Part Numbers

Quick reference list for Xenium v1 pre-designed and custom panel part numbers.

Xenium v1 Panel PNs

Quick reference list for Xenium Prime 5K pre-designed and custom panel part numbers.

Xenium Prime 5K Panel PNs

Order a 10x Genomics pre-designed, off-the-shelf panel or design a custom panel with the Xenium Panel Designer app to perform Xenium In Situ Gene Expression analyses. Combine custom targets with pre-designed panels or build a standalone custom panel for maximum flexibility. Sign in to your existing 10x Cloud account or create a new account to get started today.

What is the Xenium Panel Designer?

Use the Xenium Panel Designer app to request custom panel designs. First, choose your custom panel design option. Then read the panel design request workflow guide to follow either the standard or advanced workflow.

Start Panel Request

Tell us about your panel request and enter a design ID if you have one.

Add Sample Info

Add on to a pre-designed panel or design a standalone custom panel. Select the panel type and number of targets.

Select Panel Type

Reference datasets are used to predict highly expressed genes that can cause optical crowding. For optimal results, use a dataset that closely aligns with your sample.

Provide Reference Datasets

Submit a list of custom genes to request for your custom panel design. Genes should be ranked in priority order from most to least important. In the standard workflow, the panel designer app will clean up the custom genes list and then generate a design for you to review.

Add Custom Genes

For advanced target or species standalone custom design requests, submit additional sequence information. This is not necessary for standard workflow design requests.

Advanced Workflow Step

Identify potential issues with your current panel and view the optimized panel design that incorporates all our recommendations.

Review Recommendations

If satisfied with the design, finalize to complete request. Please note that after designs are finalized, no further changes can be made to your panel design.

Review and Finish

Find answers to frequently asked questions about design ID, custom designs, and reference data.

We regularly add new features to the 10x Genomics Xenium Panel Designer. Find details about the updates and improvements on this page.

Access free, publicly available data generated with Xenium In Situ Gene Expression solutions.