
<LinkableSection id={"v-3-1-1"} title={"v3.1.1 (October 21, 2024)"}>

- Fixed a bug that caused custom cell groups to be lost after closing Xenium Explorer.

</LinkableSection>

<LinkableSection id={"v-3-1"} title={"v3.1 (September 4, 2024)"}>

- Compatible with all Xenium Onboard Analysis versions (see [table](/support/software/xenium-explorer/latest/getting-started#sw-compat)).
- Improved interactions with the genes and gene categories in the _Transcripts_ menu.
- Changed default density map color palette to Inferno and updated coloring scale for accuracy.
- Increased accuracy of visible gene transcript count in the selected genes list under the _Transcripts_ menu.
- Improved loading time for cells and transcript density map views.
- Fixed bug causing image zooming issues in the image alignment workflow.
- Fixed crash when loading Xenium Ranger [import-segmentation](/support/software/xenium-ranger/latest/analysis/running-pipelines/XR-import-segmentation#xr-transcript) outputs containing cells with fewer than three vertices.
- General bug fixes and performance improvements.

</LinkableSection>

<LinkableSection id={"v-3-0"} title={"v3.0 (June 18, 2024)"}>

- Compatible with all Xenium Onboard Analysis versions, required for Xenium Onboard Analysis v3.y (see [table](/support/software/xenium-explorer/latest/getting-started#sw-compat)).
- New [scaled transcript view](/support/software/xenium-explorer/latest/tutorials/nav-transcripts#scaled-transcripts) to visualize spatial transcript distribution for highly and lowly expressed genes at any zoom level.
- [Export viewport](/support/software/xenium-explorer/latest/tutorials/xe-getting-started-with-xenium-explorer#shortcuts) as a transparent PNG.
- Sort transcript and cell information in [Selections window](/support/software/xenium-explorer/latest/tutorials/xe-selecting-multiple-regions-of-interest).
- Redesigned _Transcripts_ menu to display transcript information by using the search bar to type or select genes listed in the dropdown menu.
- Show the approximate transcript count for selected genes in the _Transcripts_ menu as users zoom in and out of the dataset.
- Implemented a dynamic level of detail rendering for datasets with > 250,000 cells, where the polygons are simplified as you zoom out to improve performance.
- Limited cell and transcript function for datasets with > 200 million unique cell-feature (transcript) entries. Learn more [here](/support/software/xenium-explorer/latest/tutorials/xe-getting-started-with-xenium-explorer#large-matrix-data).
- General bug fixes and improvements.

</LinkableSection>

<LinkableSection id={"v-2-0"} title={"v2.0 (March 19, 2024)"}>

- Compatible with all Xenium Onboard Analysis versions, required for Xenium Onboard Analysis v2.y (see [table](/support/software/xenium-explorer/latest/getting-started#sw-compat)).
- Supports the visualization of multimodal cell segmentation multi-file `ome.tif` images with multi and single channel views, as well as labeling and coloring cells by segmentation method.
- Customize colors across images, cells, and transcripts with a custom hex# color selector. Toggle between uniform and standard color maps for multichannel images.
- Improved visualization for cell boundaries.
- Faster image alignment: automated simultaneous pan and zoom enabled after three keypoints selected in image aligner workflow.
- Supports the import, alignment, and visualization of immunofluorescence (IF) images with more than six channels (display up to six at a time).
- Xenium Onboard Analysis [v2.0](/support/software/xenium-onboard-analysis/latest/release-notes/release-notes-for-xoa) datasets no longer include the `morphology_mip.ome.tif` file, so these datasets will not show "Maximum Intensity Projection" in the _Image options_ drop-down menu.
- Collecting de-identified, non-biological usage data or metadata, see [Sharing usage data](/support/software/xenium-explorer/latest/getting-started#usage).
- General bug fixes and improvements.

</LinkableSection>

<LinkableSection id={"v-1-3"} title={"v1.3 (November 9, 2023)"}>

- Compatible with all Xenium Onboard Analysis versions (see [table](/support/software/xenium-explorer/latest/getting-started#sw-compat)).
- On the Image menu, [align and explore an immunofluorescence (IF) image](/support/software/xenium-explorer/latest/tutorials/xe-image-alignment) (supports up to six channels) from the same section directly on Xenium DAPI image data.
- Import up to two post-Xenium images per sample in the Image menu.
- [Adjust or add more keypoints](/support/software/xenium-explorer/latest/tutorials/xe-image-alignment#adjust-keypoints) after the image alignment workflow is completed.
- [Download and share image alignment](/support/software/xenium-explorer/latest/tutorials/xe-image-alignment#save-share) information in two formats: alignment keypoints coordinates added in addition to affine transformation matrix.
- Gamma correction introduced for all immunofluorescence channels.
- Other bug fixes and improvements.

</LinkableSection>

<LinkableSection id={"v-1-2"} title={"v1.2 (August 17, 2023)"}>

- Compatible with all Xenium Onboard Analysis versions, but required for v1.7 (see [table](/support/software/xenium-explorer/latest/getting-started#sw-compat)).
- The Z-stack `morphology.ome.tif` image is now an optional input to streamline input files required for Xenium Explorer visualization.
- On the Image menu, [align and explore an H&E image](/support/software/xenium-explorer/latest/tutorials/xe-image-alignment) from the same section directly on Xenium DAPI image data.
- In Image options, rotate your data to the preferred orientation.
- The Sample Information window displays [Xenium Gene Expression panel](/support/in-situ-gene-expression/documentation/steps/panel-design) "Panel Design ID" and if used, [Xenium Ranger](/support/software/xenium-ranger/latest) metadata.
- On the Cells menu, [import a CSV file](/support/software/xenium-explorer/latest/tutorials/xe-getting-started-with-xenium-explorer#cell-groups) to view custom clustering results from community-developed tools.
- Use the lasso tool to [export Cell IDs](/support/software/xenium-explorer/latest/tutorials/xe-selecting-multiple-regions-of-interest#sel-cell) from selected regions of interest for further analysis in community-developed tools.
- On the Transcript menu, customize transcript visualization with new icon sizes and shapes. Based on panel source, genes are organized as "Predesigned" or "Custom".
- The [custom gene group CSV file](/support/software/xenium-explorer/latest/tutorials/xe-getting-started-with-xenium-explorer#creating-gene-groups) must include a column header row ("gene", "group").
- Other bug fixes and improvements.

</LinkableSection>

<LinkableSection id={"v-1-1-april-3-2023"} title={"v1.1 (April 3, 2023)"}>

- Xenium Explorer (XE) v1.1 is required to open datasets generated with [Xenium Onboard Analysis v1.3](/support/software/xenium-onboard-analysis/latest/release-notes/release-notes-for-xoa)+ due to a new format for cell IDs.
- In Saved Views, dataset analysis settings, including imported gene groups and their associated transcript icon shape and color changes, can now be saved.
- Point subsampling in Xenium Explorer was reduced for display in the [transcript](/support/software/xenium-explorer/latest/tutorials/xe-getting-started-with-xenium-explorer#transcript-display-options) layer, allowing a fuller view of transcripts when zoomed out.
- Improvements to layer interactions, including the ability to quickly toggle the Image, Cell, and Transcript menus on/off from the sidebar.
- Other bug fixes and improvements.

</LinkableSection>


Release Notes for Xenium Explorer

Explore Xenium In Situ data from the tissue scale down to subcellular resolution with our interactive visualization tool.

Overview

Download Center

Getting Started

Xenium Explorer Demos

Tutorials

Release Notes

Xenium Onboard Analysis

Xenium Ranger

Analysis Guides

Xenium Explorer

List of Xenium Explorer-compatible input files.

Xenium Explorer Inputs

Learn about Xenium Explorer and orient yourself to its interface and features.

Navigate Xenium Explorer

Image Layer

Cells Layer

Learn how to interact with transcript data.

Transcripts Layer

Find tips for examining cell segmentation, cell cluster assignment, and gene expression with Xenium Explorer.

Check Data Quality

Use Xenium Explorer lasso tools to narrow your focus to the cells that matter.

Export Regions of Interest

Save UI settings, transfer configurations to another window, and share settings with others.

Save and Share

Align post-Xenium images or import images aligned with third-party tools.

Image Alignment

Convert post-Xenium images to a format compatible with Xenium Explorer.

Converting Images

Introduction

Learn about Xenium Explorer and get oriented to its interface and features.

Interface and Features

Explore Xenium In Situ data, from tissue macrostructures to subcellular resolution, with our interactive visualization tool. Pinpoint the locations of specific transcripts, check cell segmentation, and inform downstream analysis.

What is Xenium Explorer?

Walk through Xenium Explorer features for investigating your in situ gene expression data.

Getting Started with Xenium Explorer

New to Xenium Explorer?

View the latest updates to Xenium Explorer.

Learn more about Xenium In Situ instrument analysis software.

Reanalyze data from Xenium In Situ solutions.

Browse Q&As from the 10x Genomics support team.

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

Datasets

A collection of introductions, tutorials, and blogs for data analysis beyond 10x Genomics software.