nf-core/xeniumranger_import_segmentation
moduleThe 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.
Module Information
- Repository
- https://github.com/nf-core/modules/tree/master/modules/nf-core/xeniumranger/import-segmentation
- Source
- nf-core
- Organization
- nf-core
- Authors
- @khersameesh24 , @dongzehe
- Maintainers
- @khersameesh24 , @dongzehe
Tools
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.
License: 10x Genomics EULA
Inputs
| Name | Type | Description |
|---|---|---|
| 0 |
Quick Start
Include this module in your Nextflow pipeline:
include { XENIUMRANGER_IMPORT_SEGMENTATION } from 'https://github.com/nf-core/modules/tree/master/modules/nf-core/xeniumranger/import-segmentation'