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nf-core/xeniumranger/import-segmentation @ 0.0.0-3fc6d40

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.

spatial segmentation import segmentation nuclear segmentation cell segmentation xeniumranger imaging
Latest version: 0.0.0-3fc6d40
Total downloads: 6
Source: nf-core/modules
Authors: @khersameesh24 @dongzehe
Maintainers: @khersameesh24 @dongzehe

Summary

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.

Get started

Add the following snippet to your workflow script to include this module.

include { XENIUMRANGER_IMPORT_SEGMENTATION } from 'nf-core/xeniumranger/import-segmentation'

License

MIT License

Process
Name XENIUMRANGER_IMPORT_SEGMENTATION
Input 1 channel
#1 tuple
meta map

Groovy Map containing run information e.g. [ id:'xenium_sample' ]
xenium_bundle directory

Path to the Xenium output bundle generated by the Xenium Onboard Analysis pipeline
transcript_assignment file

Transcript assignment CSV with cell assignment, such as from Baysor v0.6, (transcript-based mode). Mutually exclusive with image-based inputs (nuclei, cells). Required when using transcript-based mode. Passed to --transcript-assignment.

 *.csv
viz_polygons file

Cell boundary polygons (GeoJSON) for visualization, such as from Baysor v0.6 (transcript-based mode). Mutually exclusive with image-based inputs (nuclei, cells). Required when using transcript_assignment. Passed to --viz-polygons.

 *.{json,geojson}
nuclei file

Nucleus segmentation input as label mask (TIFF/NPY), polygons (GeoJSON), or Xenium Onboard Analysis cells.zarr.zip (image-based mode). Mutually exclusive with transcript-based inputs (transcript_assignment, viz_polygons). Passed to --nuclei.

 *.{tif,tiff,npy,json,geojson,zarr.zip}
cells file

Cell segmentation input as label mask (TIFF/NPY), polygons (GeoJSON), or Xenium Onboard Analysis cells.zarr.zip (image-based mode). Mutually exclusive with transcript-based inputs (transcript_assignment, viz_polygons). Passed to --cells.

 *.{tif,tiff,npy,json,geojson,zarr.zip}
coordinate_transform file

Image alignment file containing similarity transform matrix (e.g., _imagealignment.csv from Xenium Explorer). Only used with image-based mode inputs (nuclei, cells). units will be automatically set to "microns". Passed to --coordinate-transform.

 *.csv
units string

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.
Output 2 channels
#1 outs tuple
meta map

Groovy Map containing sample information e.g. [ id:'test' ]
${prefix} directory

Directory containing the output xenium bundle of Xenium Ranger

 ${prefix}
#2 versions_xeniumranger tuple
${task.process} string

The process the versions were collected from
xeniumranger string

The tool name
xeniumranger -V | sed -e 's/.*xenium-//' string

The command used to generate the version of the tool
Tool Description Homepage
xeniumranger 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. https://www.10xgenomics.com/support/software/xenium-ranger/latest
Version 0.0.0-3fc6d40
Commit ID 3fc6d40d163d89ae44d40a00b9017d5a9df5170e
Release Date 22 Apr 2026 15:37:01 (UTC)
Download URL https://registry.nextflow.io/api/v1/modules/nf-core%2Fxeniumranger%2Fimport-segmentation/0.0.0-3fc6d40/download
OCI Store URL https://public.cr.seqera.io/v2/nextflow/plugin/modules/nf-core/xeniumranger/import-segmentation/blobs/sha256:7913ca31f4e935864a7e9b8c728a3272b9a102eedc9a741a480f0da11ad97269
Size 3.8 KB
Checksum sha256:7913ca31f4e935864a7e9b8c728a3272b9a102eedc9a741a480f0da11ad97269
Downloads 3