Description
The xeniumranger import-segmentation module allows you to specify 2D nuclei and/or cell segmentation results for assigning transcripts to cells and recalculate all Xenium Onboard Analysis (XOA) outputs that depend on segmentation. Segmentation results can be generated by community-developed tools or prior Xenium segmentation result.
Input
Nuclei boundary expansion distance in µm. Only for use when nucleus segmentation provided as input. Default-5 (accepted range 0 - 100)
Image alignment file containing similarity transform matrix e.g., the _imagealignment.csv file exported from Xenium Explorer
Label mask (TIFF or NPY), polygons of nucleus segmentations (GeoJSON FeatureCollection), or Xenium Onboard Analysis cells.zarr.zip (the nucleus masks as input). --nuclei will use nucleusGeometry polygon if it exists in the GeoJSON (i.e., for QuPath-like GeoJSON files), or geometry if it does not. Error if --transcript-assignment argument is used.
Label mask (TIFF or NPY), polygons of cell segmentations (GeoJSON FeatureCollection), or Xenium Onboard Analysis cells.zarr.zip (the cell masks as input). Features with a non-cell objectType will be ignored. Error if --transcript-assignment argument is used. In Xenium Ranger v2.0, --nuclei no longer needs to be used with --cells.
Transcript CSV with cell assignment from Baysor v0.6. Error if --cells or --nuclei arguments are used.
Tools
xeniumranger Documentation
Xenium Ranger is a set of analysis pipelines that process Xenium In Situ Gene Expression data to relabel, resegment, or import new segmentation results from community-developed tools. Xenium Ranger provides flexible off-instrument reanalysis of Xenium In Situ data. Relabel transcripts, resegment cells with the latest 10x segmentation algorithms, or import your own segmentation data to assign transcripts to cells.
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