10x Genomics Support/Xenium Ranger/Release Notes/

Release Notes for Xenium Ranger

  • Xenium Ranger v2.0 is required for reanalysis of Xenium Analyzer v2.0 data.
  • The expansion-distance parameter default is now 5 µm instead of 15 µm for the resegment and import-segmentation pipelines.
  • Segmentation model updates:
    • Reanalyze cell segmentation staining workflow data by adjusting the nuclear expansion distance and/or boundary or interior stain used for multimodal cell segmentation, the cell segmentation algorithm introduced in XOA v2.0.
    • Updated nucleus segmentation ML model to match update in XOA v2.0.
  • The import-segmentation pipeline supports importing cell segmentations with zero and multiple nuclei.
  • Interrupted runs can be resumed.
  • Fixed a bug to improve the method to import segmentation results generated from large image files (i.e., from IF or H&E images).
  • Fixed a bug to enable importing segmentation results for smaller regions of the original image data.
  • Supports reanalysis of Xenium Onboard Analysis data up to latest version (see version compatibility table).
  • The image-based import-segmentation --coordinate-transform option is now compatible with segmentation masks (previously limited to polygons).
  • Improved memory usage in the import-segmentation pipeline (see updated system requirements page).
  • Fixed bug where input masks with discontinuous cells or nuclei caused Xenium Ranger to occasionally crash. An analysis summary alert was introduced to flag rare scenarios where discontinuities may lead to splitting of imported cells or nuclei.
  • Several minor bug fixes in the analysis summary user interface.
  • Improved preflight checks.
  • Miscellaneous bug fixes.
  • Initial release.
  • Resegment Xenium data with customizable nucleus expansion distance and the latest 10x cell segmentation algorithm.
  • Import community-developed nucleus and cell segmentations in multiple popular formats (i.e., Baysor).
  • Selected the wrong gene panel when you started the Xenium Analyzer run? Simply fix the mistake by using relabel.
  • All pipelines produce the same output bundle as Xenium Onboard Analysis v1.6, so they are compatible with the same downstream visualization and analysis softwares (e.g., Xenium Explorer).
  • Backwards compatible with all previous Xenium Onboard Analysis versions.