- 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.tifimages 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.tiffile, 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.tifimage 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.