Nextflow Registry | nf-core/vizgenpostprocessing/preparesegmentation@0.0.0-0c7146d

nf-core/vizgenpostprocessing/preparesegmentation @ 0.0.0-0c7146d

The module prepares the specification JSON file for Vizgen's post-processing tool cell segmentation workflow.

vpt vizgen segmentation microscopy spatial transcriptomics

Latest version: 0.0.0-0c7146d

Total downloads: 1

Source: nf-core/modules

Authors: @mcmero

Maintainers: @mcmero

The module prepares the specification JSON file for Vizgen's post-processing tool cell segmentation workflow.

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

include { VIZGENPOSTPROCESSING_PREPARESEGMENTATION } from 'nf-core/vizgenpostprocessing/preparesegmentation'

MIT License

Process

`Name`	`VIZGENPOSTPROCESSING_PREPARESEGMENTATION`

Input 3 channels

#1 tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'sample1', single_end:false ]
`input_images` directory	Path to the input images directory to be used for segmentation.
`um_to_mosaic_file` file	Path to the micron-to-mosaic pixel transform matrix file. `*.csv`

`algorithm_json` file	JSON file containing the algorithm specification `*.json`

`images_regex` string	Can either be blank to match files by MERSCOPE convention, or a python formatting string specifying the file name (e.g., image_{stain}z{z}.tif), or a regular expression matching the tiff files to be used (e.g., mosaic(?P[\w\|-]+)_z(?P[0-9]+).tif)

Output 2 channels

#1 versions

`versions.yml` file	File containing software versions `versions.yml`

#2 segmentation_files tuple

`meta` map	Groovy Map containing sample information e.g. `[ id:'sample1', single_end:false ]`
`${prefix}/*.json` file	Segmentation specification JSON file `*.json`

Tool	Description	Homepage
vizgenpostprocessing	Vizgen's post-processing tool	https://github.com/Vizgen/vizgen-postprocessing

Version	0.0.0-0c7146d
Commit ID	4e8e48c04e24c2159a5589a36bae0f038809cd48
Release Date	08 Apr 2026 19:22:51 (UTC)
Download URL	https://registry-stage.nextflow.io/api/v1/modules/nf-core%2Fvizgenpostprocessing%2Fpreparesegmentation/0.0.0-0c7146d/download
OCI Store URL	https://public.cr.stage-seqera.io/v2/nextflow/plugin-stage/modules/nf-core/vizgenpostprocessing/preparesegmentation/blobs/sha256:e1f91b61283577a1d68a6a646dcc0ae56dcfc0c2dc7acb3184f4c0087ca30ba8
Size	2.9 KB
Checksum	sha256:e1f91b61283577a1d68a6a646dcc0ae56dcfc0c2dc7acb3184f4c0087ca30ba8
Downloads	1

Version	Date	Status	Downloads	Size	Diff
0.0.0-0c7146d	08 Apr 2026 19:22:51 (UTC)		1	2.9 KB	-