nf-core/xeniumranger_import_segmentation

module

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

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'
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