Release Notes for Xenium Explorer

Compatible with all Xenium Onboard Analysis versions (see table).
Supports the visualization of Xenium In Situ Gene and Protein Expression datasets.
For Gene and Protein Expression datasets, view images with multi and single channel views, color cells by protein clustering, and explore protein mean fluorescence intensity within regions and cells of interest.
(Experimental) Load datasets directly from an Amazon Web Services (AWS) S3 bucket.
Import previously created Selections.csv for better analysis continuity and collaboration. The format has been standardized across single and multi-selection files.
The number of recent files displayed has been increased from 10 to 100 to better support large-scale studies.
Improved image visualization with enhanced auto-leveling and fine-tuned intensity slider controls.
General bug fixes and performance improvements.

Compatible with all Xenium Onboard Analysis versions (see table).
Added option to export high resolution images.
Show per-codeword localization plots for custom and boosted genes in Xenium Prime 5K datasets analyzed with XOA v3.2. XOA v3.0 - 3.1 datasets can be relabeled with Xenium Ranger v3.1 to update file formats.
Show boosted genes as their own category in the Transcripts menu.
Enabled lasso selection editing.
Use the cell-feature CSC matrix, in addition to CSR matrix, to improve data processing for displaying transcript and cell information for XOA v3.1 and later datasets with > 200 million unique cell by transcript features.
Improved transcript viewing experience by increasing transcript point size on hover.
Show transcript density map color scale in the Transcripts menu.
To improve app performance, saved views are no longer displayed on the Xenium Explorer home page. They are listed in the Go to location window.
General bug fixes and performance improvements.

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

Compatible with all Xenium Onboard Analysis versions (see table).
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 outputs containing cells with fewer than three vertices.
General bug fixes and performance improvements.

Compatible with all Xenium Onboard Analysis versions, required for Xenium Onboard Analysis v3.y (see table).
New scaled transcript view to visualize spatial transcript distribution for highly and lowly expressed genes at any zoom level.
Export viewport as a transparent PNG.
Sort transcript and cell information in Selections window.
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.
General bug fixes and improvements.

Compatible with all Xenium Onboard Analysis versions, required for Xenium Onboard Analysis v2.y (see table).
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 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.
General bug fixes and improvements.

Compatible with all Xenium Onboard Analysis versions (see table).
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).
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.