nf-core/tiff_segmentation_vpt

subworkflow

Perform segmentation of MERSCOPE TIFF images using the vizgen-postprocessing tool

segmentation imaging merscope vizgen tiff spatial

Module Information

Repository: https://github.com/nf-core/modules/tree/master/subworkflows/nf-core/tiff_segmentation_vpt
Source: nf-core
Organization: nf-core
Authors: @mcmero
Maintainers: @mcmero

This subworkflow uses the following modules:

Name	Type	Description
ch_input	channel	The input channel containing image directory and transformation file Structure: [ val(meta), path(image_dir), path(micron_to_mosaic_pixel_transform.csv) ]
ch_algorithm_json	channel	Channel containing algorithm configuration file Structure: [ path(algorithm.json) ]
ch_images_regex	channel	Channel containing regex pattern for image matching Structure: [ val(regex) ]
ch_custom_weights	channel	Channel containing custom weights for segmentation Structure: [ path(custom_weights) ]

Name	Type	Description
micron_space_segmentation	file	Channel containing micron space segmentation results Structure: [ val(meta), path(parquet) ]
mosaic_space_segmentation	file	Channel containing mosaic space segmentation results Structure: [ val(meta), path(parquet) ]
versions	file	File containing software versions Structure: [ path(versions.yml) ]

Include this subworkflow in your Nextflow pipeline:

include { TIFF_SEGMENTATION_VPT } from 'https://github.com/nf-core/modules/tree/master/subworkflows/nf-core/tiff_segmentation_vpt'