Nextflow Modules
Showing module(s) with keyword "cell segmentation"
| Module | Keywords | Description |
|---|---|---|
| nf-core/xeniumranger/import-segmentation | spatial segmentation import segmentation nuclear segmentation cell segmentation xeniumranger imaging | 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. |