Nextflow Modules
Showing module(s) with keyword "spatial"
| Module | Kind | Keywords | Description |
|---|---|---|---|
| nf-core/proseg/proseg | Process | segmentation spatial transcriptomics | Proseg (probabilistic segmentation) is a cell segmentation method for in situ spatial transcriptomics. |
| nf-core/proseg/proseg2baysor | Process | segmentation spatial transcriptomics | Convert proseg outputs to baysor format for import to Xenium explorer |
| nf-core/rami2d/register | Process | registration imaging multiplex spatial | offers 3 pre-defined registration schemes 1) Rigid, 2) Rigid+Affine 3) Rigid+Affine+Bsplines, each of them providing more geometrical adaptability and thus more control in the final outcome. |
| nf-core/scimap/mcmicro | Process | sort spatial single cell | SCIMAP is a suite of tools that enables spatial single-cell analyses |
| nf-core/spaceranger/count | Process | align count spatial spaceranger imaging | Module to use the 10x Space Ranger pipeline to process 10x spatial transcriptomics data |
| nf-core/spotiflow | Process | imaging image microscopy transcriptomics spatial spot detection | Spotiflow, accurate and efficient spot detection with stereographic flow. |
| nf-core/tiff_segmentation_vpt | Workflow | segmentation imaging merscope vizgen tiff spatial | Perform segmentation of MERSCOPE TIFF images using the vizgen-postprocessing tool |
| nf-core/xeniumranger/importsegmentation | Process | spatial segmentation import segmentation nuclear segmentation cell segmentation xeniumranger imaging | The xeniumranger importsegmentation 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. |
| nf-core/xeniumranger/relabel | Process | spatial relabel gene labels transcripts xeniumranger | The xeniumranger relabel module allows you to change the gene labels applied to decoded transcripts. |
| nf-core/xeniumranger/rename | Process | spatial rename gene labels transcripts xeniumranger | The xeniumranger rename module allows you to change the sample region_name and cassette_name throughout all the Xenium Onboard Analysis output files that contain this information. |
| nf-core/xeniumranger/resegment | Process | spatial resegment morphology segmentation xeniumranger | The xeniumranger resegment module allows you to generate a new segmentation of the morphology image space by rerunning the Xenium Onboard Analysis (XOA) segmentation algorithms with modified parameters. |