Nextflow Registry | nf-core/stardist@0.0.0-6c4ed3a

nf-core/stardist @ 0.0.0-6c4ed3a

Cell and nuclear segmentation with star-convex shapes

stardist segmentation image gpu spatial-transcriptomics

Latest version: 0.0.0-6c4ed3a

Total downloads: 6

Source: nf-core/modules

Authors: @migueLib @dongzehe

Maintainers: @migueLib

Cell and nuclear segmentation with star-convex shapes

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

include { STARDIST } from 'nf-core/stardist'

MIT License

Process

`Name`	`STARDIST`

Input 2 channels

#1 tuple

`meta` map	Groovy Map containing sample information e.g. `[ id:'sample1' ]`
`image` file	Single channel nuclear image `*.{tiff,tif}`

#2 tuple

`model_name` string	Name of a pretrained StarDist model (e.g. '2D_versatile_fluo', '2D_versatile_he'). Used when model_path is not provided. Pass '' (empty string) if providing a custom model path or passing -m via ext.args.
`model_path` file	Optional path to a custom StarDist model directory. When provided, takes precedence over model_name. Pass [] (empty list) to use a pretrained model name instead. `*`

Output 5 channels

#1 mask tuple

`meta` map	Groovy Map containing sample information e.g. `[ id:'sample1' ]`
`*.stardist.tif` file	labelled mask output from stardist in tif format. `*.{tiff,tif}`

#2 versions_python tuple

`${task.process}` string	The name of the process
`python` string	The name of the tool
`python --version \| sed 's/Python //'` eval	The expression to obtain the version of the tool

#3 versions_stardist tuple

`${task.process}` string	The name of the process
`stardist` string	The name of the tool
`pip show stardist \| sed -n 's/^Version: //p'` eval	The expression to obtain the version of the tool

#4 versions_tifffile tuple

`${task.process}` string	The name of the process
`tifffile` string	The name of the tool
`pip show tifffile \| sed -n 's/^Version: //p'` eval	The expression to obtain the version of the tool

#5 versions_tensorflow tuple

`${task.process}` string	The name of the process
`tensorflow` string	The name of the tool
`pip show tensorflow \| sed -n 's/^Version: //p'` eval	The expression to obtain the version of the tool

Tool	Description	Homepage
stardist	Stardist is an cell segmentation tool developed in Python by Martin Weigert and Uwe Schmidt	https://stardist.net/

Version	0.0.0-6c4ed3a
Commit ID	6c4ed3a220310b905a1fc9d04f05be2e0837142b
Release Date	23 Apr 2026 15:47:29 (UTC)
Download URL	https://registry.nextflow.io/api/v1/modules/nf-core%2Fstardist/0.0.0-6c4ed3a/download
OCI Store URL	https://public.cr.seqera.io/v2/nextflow/plugin/modules/nf-core/stardist/blobs/sha256:2f4b5f51ba578366635800a176b7a44cc50fb0bdb75f2188121ee75280965d03
Size	3.7 KB
Checksum	sha256:2f4b5f51ba578366635800a176b7a44cc50fb0bdb75f2188121ee75280965d03
Downloads	3

Version