cellgeni/tiled_cellpose

subworkflow

A tiled version of CellPose to faciliate processing of large images on HPC

cellpose segmentation instance segmentation deep-learning large-scale image processing

Module Information

Repository: https://github.com/cellgeni/nf-modules/tree/main/subworkflows/sanger-cellgeni/tiled_segmentation
Source: Sanger (cellgeni)
Organization: cellgeni
Authors: @BioinfoTongLI
Maintainers: @BioinfoTongLI

Name	Type	Description
meta	map	Groovy Map containing sample information e.g. `[ id:'test' ]`
images	file	The input channel containing the image files Structure: [ val(meta), path(image) ]
method	string	The method to use for segmentation Options: [ 'cellpose', 'stardist', 'instanseg' ]

Name	Type	Description
wkt	file	2D segmentation polygons in wkt format Structure: [ val(meta), path(wkt) ]
versions	file	File containing software versions Structure: [ path(versions.yml) ]

Include this subworkflow in your Nextflow pipeline:

include { TILED_CELLPOSE } from 'https://github.com/cellgeni/nf-modules/tree/main/subworkflows/sanger-cellgeni/tiled_segmentation'