Previous Versions Xenium Explorer - Official 10x Genomics Support

Previous Versions

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Improved interactions with the genes and gene categories in the Transcripts menu.
Improved loading time for cells and transcript density map views.
Fixed crash when loading Xenium Ranger import-segmentation outputs containing cells with < 3 vertices.
And more - see full release notes.

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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.
Sorting of transcripts and cells in Selections window.
And more - see full release notes.

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Supports the visualization of multimodal cell segmentation, including coloring cells by segmentation method.
Customize colors across images, cells, and transcripts with a custom hex# color selector.
Supports the import, alignment, and visualization of immunofluorescence (IF) images with >6 channels.
And more - see full release notes.

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Align and explore an immunofluorescence image from the same section directly on the Xenium data.
Adjust, add, or download and share keypoints after the image alignment workflow is completed.
Import up to two post-Xenium images per sample.
And more - see full release notes.

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Align and explore an H&E image from the same section directly on the Xenium data.
Import a CSV file and view clustering results from community-developed tools.
Use the lasso tool to export Cell IDs for further analysis in community-developed tools.
Streamline files for Xenium Explorer visualization - Z-stack morphology.ome.tif image is now optional.

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Explore Xenium image-based in situ data with intuitive controls.
Organize markers of interest and visualize 3D localized transcripts at any scale.
Examine segmented cells colored by transcript density or clustering result.
Compare gene expression profiles and cell type proportions across tissue regions with a versatile lasso tool.
New: Save imported gene groups across sessions with Saved Views.
New: Compatible with all Xenium Onboard Analysis versions, but required for v1.3+.

Download is unavailable on mobile devices.

Initial release of Xenium Explorer!
Explore Xenium image-based in situ data with intuitive controls.
Organize markers of interest and visualize 3D localized transcripts at any scale.
Examine segmented cells colored by transcript density or clustering result.
Compare gene expression profiles and cell type proportions across tissue regions with a versatile lasso tool.