
Xenium Onboard Analysis ([XOA](/support/in-situ-gene-expression/documentation/steps/onboard-analysis)) data generated by the Xenium Analyzer (XA) instrument can be viewed in the following versions of Xenium Explorer (XE):

 |  | XE v1.2 | XE v1.1 | XE v1.0 |
 | --- | --- | --- | --- | 
 | XA v1.7 - v1.8 | <Check /> | - | - 
 | XA v1.3 - v1.6 | <Check />|<Check />| - 
 | XA v1.0 - v1.2 | <Check />|<Check />|<Check />|

Software compatibility

* Compatible with all Xenium Onboard Analysis versions (see [table](#sw-compat) above).
* On the Image menu, [align and explore an immunofluorescence (IF) image](/support/software/xenium-explorer/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/tutorials/xe-image-alignment#adjust-keypoints) after the image alignment workflow is completed.
* [Download and share image alignment](/support/software/xenium-explorer/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.

v1.3 (November 9, 2023)

* Compatible with all Xenium Onboard Analysis versions, but required for v1.7 (see [table](#sw-compat) above).
* 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/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) metadata.
* On the Cells menu, [import a CSV file](/support/software/xenium-explorer/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/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/tutorials/xe-getting-started-with-xenium-explorer#creating-gene-groups) must include a column header row ("gene", "group").
* Other bug fixes and improvements.

v1.2 (August 17, 2023)

* Xenium Explorer (XE) v1.1 is required to open datasets generated with [Xenium Onboard Analysis v1.3](/support/in-situ-gene-expression/documentation/steps/onboard-analysis/release-notes-xenium-analyzer-instrument-sw)+ 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/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.

v1.1 (April 3, 2023)

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

Tutorials

Release Notes

Xenium Onboard Analysis

Xenium Ranger

Datasets

Analysis Guides

Xenium Explorer

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.

Multiple Selections

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

Saving and Sharing

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.

Post-Xenium Image Format

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?

We provide resources from protocols, user guides, and free-to-use analysis tools.

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.

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