nf-core/cellpose

module

cellpose segments cells in images using GPU-accelerated deep learning

segmentation image cellpose gpu spatial-transcriptomics

Module Information

Repository: https://github.com/nf-core/modules/tree/master/modules/nf-core/cellpose
Source: nf-core
Organization: nf-core
Authors: @josenimo , @FloWuenne , @dongzehe
Maintainers: @josenimo , @FloWuenne , @kbestak

cellpose is an anatomical segmentation algorithm written in Python 3 by Carsen Stringer and Marius Pachitariu

License: BSD 3-Clause

Name	Type	Description
0
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).

Include this module in your Nextflow pipeline:

include { CELLPOSE } from 'https://github.com/nf-core/modules/tree/master/modules/nf-core/cellpose'