JaneliaSciComp/cellpose

module

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

dask segmentation cellpose

Module Information

Repository: https://github.com/JaneliaSciComp/nextflow-modules/tree/main/modules/janelia/cellpose
Source: Janelia
Organization: JaneliaSciComp
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 container
image_subpath	string	Relative path to the image dataset if needed (for N5 or zarr containers)
models_path	directory	Optional path to the cellpose models cache directory. If this is not specified pass in as empty list.
model_name	string	The name of the cellpose model.
output_dir	directory	Directory location of the output image container
labels	string	Name of the labels container created at the location specified by output_dir
labels_subpath	string	Relative labels dataset subpath
working_dir	directory	Location of the temporary files created during the segmentation. This must have enough space to hold the temporary labels before they are reassigned during the merge process
dask_scheduler	string	Dask scheduler IP
dask_config	file	Optional path to the dask config. If this is not specified pass in as empty list.
preprocessing_config	file	Optional YAML file holding the configuration parameters for various preprocessing operations. So far the only preprocessing available is a gaussian filter but there may be more in the future
logging_config	file	Optional log config.
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
input_image_fullpath	directory	Full path to the input image container
image_subpath	string	Subpath to the input image dataset
output_label_images	string	One or more image names containing segmentation results. If the output is a zarr or N5 container there's only one output_label_image, but if the output type is a tiff and the segmented image is large there can be multiple tiff files
output_labels_subpath	string	this is the labels dataset if the output is a zarr or N5 container
versions	file	File containing software versions

Include this module in your Nextflow pipeline:

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