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Release Notes for Xenium Explorer

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

XE v1.3XE v1.2XE v1.1XE v1.0
XA v1.7 - v1.8--
XA v1.3 - v1.6-
XA v1.0 - v1.2
  • 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.