BioImageTools/cellpose

module

Performs a 3-D segmentation using cellpose distributed on a dask cluster

dask segmentation cellpose

Module Information

Repository: https://github.com/BioImageTools/nextflow-modules/tree/main/modules/bits/cellpose
Source: BioImageTools
Organization: BioImageTools
Authors: @cgoina
Maintainers: @cgoina

A generalist algorithm for cell and nucleus segmentation.

License: ['BSD-3-Clause']

Name	Type	Description
meta	map	Groovy map containing: id, input_image_dataset, output_image_name
image	file	Path to the image
image_subpath	string	Relative path to the image dataset if needed (for N5 or zarr containers)
dask_config	file	Optional path to the dask config. If this is not specified pass in as empty list.
models_path	directory	Optional path to the cellpose models cache directory. If this is not specified pass in as empty list.
outputdir	directory	Directory location of the output image
output_name	string	Name the generated output file(s).
dask_scheduler	string	Dask scheduler IP
cellpose_cpus	integer	Number of cpus needed to run the main cellpose program
cellpose_mem_in_gb	string	Memory needed for the main cellpose program

Name	Type	Description
meta	map	Groovy map containing: id, input_image_dataset, output_image_name
results	directory	Tuple containing meta, input image, output dir
result_names	string	Tuple containing result names and extensions
versions	file	File containing software versions

Include this module in your Nextflow pipeline:

include { CELLPOSE } from 'https://github.com/BioImageTools/nextflow-modules/tree/main/modules/bits/cellpose'