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

nf-core/cellpose @ 0.0.0-6c4ed3a

cellpose segments cells in images using GPU-accelerated deep learning

segmentation image cellpose gpu spatial-transcriptomics

Latest version: 0.0.0-6c4ed3a

Total downloads: 7

Source: nf-core/modules

Authors: @josenimo @FloWuenne @dongzehe

Maintainers: @josenimo @FloWuenne @kbestak

cellpose segments cells in images using GPU-accelerated deep learning

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

include { CELLPOSE } from 'nf-core/cellpose'

MIT License

Process

`Name`	`CELLPOSE`

Input 2 channels

#1 tuple

`meta` map	Groovy Map containing sample information (sample id)
`image` file	tif file ready for segmentation `*.{tif,tiff}`

`model` file	Optional custom cellpose model file. When provided, passed as --pretrained_model to cellpose. Pass [] (empty list) to use the default model (cpsam in cellpose 4). `*`

Output 6 channels

#1 mask tuple

`meta` map	Groovy Map containing sample information [sample id]
`${prefix}/*masks.tif` file	labelled mask output from cellpose in tif format `${prefix}/*masks.tif`

#2 cells tuple

`meta` map	Groovy Map containing sample information [sample id]
`${prefix}/*seg.npy` file	numpy array with cell segmentation data `${prefix}/*seg.npy`

#3 flows tuple

`meta` map	Groovy Map containing sample information [sample id]
`${prefix}/*flows.tif` file	cell flow output from cellpose `${prefix}/*flows.tif`

#4 versions_torch tuple

`${task.process}` string	The name of the process
`torch` string	The name of the tool
`cellpose --version \| sed -n 's/torch version:[[:space:]]*//p' \| tr -d '[:space:]'` eval	The expression to obtain the version of the tool

#5 versions_python tuple

`${task.process}` string	The name of the process
`python` string	The name of the tool
`cellpose --version \| sed -n 's/python version:[[:space:]]*//p' \| tr -d '[:space:]'` eval	The expression to obtain the version of the tool

#6 versions_cellpose tuple

`${task.process}` string	The name of the process
`cellpose` string	The name of the tool
`cellpose --version \| sed -n 's/cellpose version:[[:space:]]*//p' \| tr -d '[:space:]'` eval	The expression to obtain the version of the tool

Tool	Description	Homepage
cellpose	cellpose is an anatomical segmentation algorithm written in Python 3 by Carsen Stringer and Marius Pachitariu	https://github.com/MouseLand/cellpose

Version	0.0.0-6c4ed3a
Commit ID	6c4ed3a220310b905a1fc9d04f05be2e0837142b
Release Date	23 Apr 2026 15:08:47 (UTC)
Download URL	https://registry.nextflow.io/api/v1/modules/nf-core%2Fcellpose/0.0.0-6c4ed3a/download
OCI Store URL	https://public.cr.seqera.io/v2/nextflow/plugin/modules/nf-core/cellpose/blobs/sha256:61c0a8e1561e6403273b62f549ac69f2bf0c4dd3fcbb79f1d8133cfcb10935d3
Size	4.1 KB
Checksum	sha256:61c0a8e1561e6403273b62f549ac69f2bf0c4dd3fcbb79f1d8133cfcb10935d3