Xenium Onboard Analysis (XOA) data generated by the Xenium Analyzer (XA) instrument can be viewed in the following versions of Xenium Explorer (XE):

• Compatible with all Xenium Onboard Analysis versions (see table above).
• On the Image menu, align and explore an immunofluorescence (IF) image (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 after the image alignment workflow is completed.
• Download and share image alignment 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.

• Compatible with all Xenium Onboard Analysis versions, but required for v1.7 (see table 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 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 "Panel Design ID" and if used, Xenium Ranger metadata.
• On the Cells menu, import a CSV file to view custom clustering results from community-developed tools.
• Use the lasso tool to export Cell IDs 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 must include a column header row ("gene", "group").
• Other bug fixes and improvements.

• Xenium Explorer (XE) v1.1 is required to open datasets generated with Xenium Onboard Analysis v1.3+ 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 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.