JaneliaSciComp/segtools_distributed_mergelabels

module

Merge labels across block boundaries after a 3-D distributed segmentation

dask segmentation cellpose

Module Information

Repository: https://github.com/JaneliaSciComp/nextflow-modules/tree/main/modules/janelia/segtools/distributed/mergelabels
Source: Janelia
Organization: JaneliaSciComp
Authors: @cgoina
Maintainers: @cgoina

Tools

cellpose

A generalist algorithm for cell and nucleus segmentation.

License: ['BSD-3-Clause']

Inputs

Name	Type	Description
meta	map	Groovy map containing: id, input_image_dataset, output_image_name
input_labels	file	Path to the input labels container
input_subpath	string	Relative path to the image dataset if needed (for N5 or zarr containers)
mask	string	Optional path to a mask that can be used to select a subvolume to be segmented with cellpose. If this is not specified pass in as empty list.
mask_subpath	string	The mask subpath.
output_labels	file	Path to the output labels container
output_subpath	string	Relative path to the image dataset if needed (for N5 or zarr containers)
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.
logging_config	file	Optional log config.
cpus	integer	Number of cpus needed to run the main cellpose program
mem_in_gb	integer	Memory needed for the main cellpose program

Outputs

Name	Type	Description
meta	map	Groovy map containing: id, input_image_dataset, output_image_name
input_labels_fullpath	string	Full path to the input labels container
input_subpath	string	Subpath to the input labels dataset
output_labels_fullpath	string	Fullpath to the merged labels container
output_subpath	string	merged labels subpath
versions	file	File containing software versions

Quick Start

Include this module in your Nextflow pipeline:

include { SEGTOOLS_DISTRIBUTED_MERGELABELS } from 'https://github.com/JaneliaSciComp/nextflow-modules/tree/main/modules/janelia/segtools/distributed/mergelabels'

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