- Required for reanalysis of Xenium Onboard Analysis v3.0 data (see table).
- Reanalyze pre-v3.0 data to convert to XOA v3.0 file formats that support scaled transcript view in Xenium Explorer v3.0. When reanalyzing XOA v3.0+ data, Xenium Ranger recomputes the transcript clusters in a different order so the scaled transcript view may look slightly different.
- New
xeniumranger rename
subcommand for editing the region name and cassette name specified on instrument. - When only importing cell segmentations, Xenium Ranger no longer produces synthetic nucleus segmentations because visualization of a single polygon set is now supported in Xenium Explorer v3.0.
- Importing transcript-based segmentation results with transcript assignments and boundaries will produce only one polygon set in the
cells.zarr.zip
. - Importing image-based segmentation results with cells will produce two polygon sets and masks in the
cells.zarr.zip
file, where the polygon set and mask that are usually reserved for nuclei will be empty. - Nuclear transcripts per 100 µm2 will be
NaN
because the nuclei boundaries are not defined. Use cellular transcripts per 100 µm2 instead to estimate transcript density.
- Importing transcript-based segmentation results with transcript assignments and boundaries will produce only one polygon set in the
- Output format changes (will be added to upcoming XOA v3.1 release):
- The
cell_feature_matrix.zarr.zip
is zstd compressed and includes a compressed sparse column (CSC) matrix representation for enhanced performance of certain features in future Xenium Explorer releases. - Upgraded
experiment.xenium
version to v5.1 with new fields:panel_designer_version
,num_transcripts
,num_transcripts_high_quality
, andnon_zero_matrix_entries
metrics_summary.csv
values truncated to 15 decimal places.
- The
- General bug fixes and improvements:
- Cell segmentation: Fixed a bug to guarantee every nucleus and cell segmentation mask is a single connected component. Cell segmentation algorithm matches algorithm in XOA v3.0.
- Robust to transcript-assignment data where one or more cells have no > Q20 transcripts. This fixes a bug in XR v2.0.1 that could result in erroneous transcript assignment to cells when the transcript-assignment CSV included cells with only low-quality transcripts (see this Knowledge Base article for help).
- Fixed a bug that caused
cell_ids
to be misassigned intranscripts.csv.gz
andtranscripts.parquet
when importing transcript assignments (e.g. from Baysor) withimport-segmentation
. This bug also resulted in erroneous cell-feature matrix files and erroneous counts incells.csv.gz
. Any datasets that were segmented with transcript-based methods, such as Baysor or Proseg, and used Xenium Ranger v2.0 to import transcript assignments, should re-run the analysis using Xenium Ranger v2.0.1. - Fixed a bug to ensure interior stain-based expansion extends all the way to the neighboring cell's boundary in
resegment
.
- The expansion-distance parameter default is now 5 µm instead of 15 µm for the
resegment
andimport-segmentation
pipelines. - Segmentation algorithm updates for the
resegment
pipeline:- 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. Suboptimal or unsuitable stains can be excluded from the segmentation algorithm by specifying the
interior-stain
orboundary-stain
arguments. - Updated nucleus segmentation ML model to match update in XOA v2.0.
- 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. Suboptimal or unsuitable stains can be excluded from the segmentation algorithm by specifying the
- Updates for
import-segmentation
pipeline:- The
xeniumranger resegment --resegment-nuclei
option is deprecated and will be removed in future releases.resegment
will always resegment nuclei from the input DAPI image. To use the nuclei segmentation from input data and adjust expansion distance, the preferred method is to runxeniumranger import-segmentation
with--expansion-distance
and--nuclei=cells.zarr.zip
, which will use the nucleus segmentation masks fromcells.zarr.zip
file. - The
--nuclei
argument no longer needs to be used with--cells
. - The
--cells
and--nuclei
arguments supportcells.zarr.zip
format and will use the cell and nucleus masks for transcript assignment. - New metrics provided in
metrics_summary.csv
: "Number of cell non-simple polygons", "Number of cell multipolygons", "Number of nucleus non-simple polygons", "Number of nucleus multipolygons", "Segmented cell imported fraction", and "Segmented cell imported count". The "Number of cells from imported segmentation" is also reported in theanalysis_summary.html
Segmentation Methods table. - The "Percentage of cells without a nucleus" metric has been removed.
- The
- Interrupted runs can be resumed. Issuing the same
xeniumranger
command will now resume execution of the pipestance from the stage that originally failed. See troubleshooting page. - Fixed a bug where Xenium Ranger
import-segmentation
errored if GeoJSON inputs had theMultiPolygon
type orPolygon
type with holes. If Xenium Ranger encounters a polygon with a hole, it will remove the hole and retain only the exterior of the polygons (interior edges/segments are removed.) If typeMultiPolygon
is present, they will be ignored and will not be included in the analysis.
- 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.