tiff_segmentation_vpt

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

segmentationimagingmerscopevizgentiffspatial

https://github.com/nf-core/modules/[...]/subworkflows/nf-core/tiff_segmentation_vpt

Description

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

Input

name

description

pattern

`ch_input`

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 containing algorithm configuration file
Structure: [ path(algorithm.json) ]

*.json

`ch_images_regex`

Channel containing regex pattern for image matching
Structure: [ val(regex) ]

*

`ch_custom_weights`

Channel containing custom weights for segmentation
Structure: [ path(custom_weights) ]

*

Output

name

description

pattern

`micron_space_segmentation`

Channel containing micron space segmentation results
Structure: [ val(meta), path(parquet) ]

*.parquet

`mosaic_space_segmentation`

Channel containing mosaic space segmentation results
Structure: [ val(meta), path(parquet) ]

*.parquet

`versions`

File containing software versions
Structure: [ path(versions.yml) ]

versions.yml