modules/xeniumranger_import-segmentation
The xeniumranger import-segmentation module runs xeniumranger import-segmentation
to recompute Xenium Onboard Analysis outputs using external segmentation results.
It supports two execution modes mirroring the Xenium Ranger CLI: an image-based
mode that accepts nuclei and/or cell masks (TIFF/NPY) or GeoJSON polygons together
with optional coordinate transforms and unit definitions, and a transcript-based
mode that ingests Baysor-style transcript assignment CSV files plus visualization
polygons. Use the image-based inputs when providing label masks or polygons, or
switch to the transcript-based inputs when supplying transcript-level assignments
so the appropriate command-line arguments are passed to Xenium Ranger.
Description
The xeniumranger import-segmentation module runs xeniumranger import-segmentation
to recompute Xenium Onboard Analysis outputs using external segmentation results.
It supports two execution modes mirroring the Xenium Ranger CLI: an image-based
mode that accepts nuclei and/or cell masks (TIFF/NPY) or GeoJSON polygons together
with optional coordinate transforms and unit definitions, and a transcript-based
mode that ingests Baysor-style transcript assignment CSV files plus visualization
polygons. Use the image-based inputs when providing label masks or polygons, or
switch to the transcript-based inputs when supplying transcript-level assignments
so the appropriate command-line arguments are passed to Xenium Ranger.
Input
Units for segmentation results. Must be one of two options: “microns” (physical space) or
“pixels” (pixel space). Can be used with both image-based and transcript-based modes.
Default: “pixels”. Must be “microns” if coordinate_transform is used. For Baysor v0.6
inputs, must be “microns”. Passed to --units.
Tools
xeniumranger 10x Genomics EULA
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.
