JaneliaSciComp/bigstream_foregroundmask

module

Generate a foreground mask for a 3-D volume using Bigstream

bigstream foreground-mask segmentation

Module Information

Repository: https://github.com/JaneliaSciComp/nextflow-modules/tree/main/modules/janelia/bigstream/foregroundmask
Source: Janelia
Organization: JaneliaSciComp
Authors: @cgoina , @fleishmang

Tool for creating an alignment pipeline using different ITK algorithms

License: ['BSD-3-Clause']

Name	Type	Description
meta	map	Groovy map containing: id
image	file\|directory	Path to the image (container) for which to generate the foreground mask
image_subpath	string	If the image is a zarr container this is the relative path to the dataset
timeindex	string	Time index to select from the image
channel	string	Channel to select from the image
mask	file\|directory	Path to the output mask (container)
mask_subpath	string	If the output mask is a zarr container this is the relative path to the mask dataset

Name	Type	Description
meta	map	Groovy map containing: id
full_image	string	Full resolved path to the input image
image_subpath	string	Subpath within the input image container
full_mask	string	Full resolved path to the output mask
mask_subpath	string	Subpath within the output mask container

Include this module in your Nextflow pipeline:

include { BIGSTREAM_FOREGROUNDMASK } from 'https://github.com/JaneliaSciComp/nextflow-modules/tree/main/modules/janelia/bigstream/foregroundmask'