Description

The module prepares the specification JSON file for Vizgen’s post-processing tool cell segmentation workflow.

Input

name:type
description
pattern

meta{:bash}

:map

Groovy Map containing sample information e.g. [ id:‘sample1’, single_end:false ]

input_images{:bash}

:directory

Path to the input images directory to be used for segmentation.

um_to_mosaic_file{:bash}

:file

Path to the micron-to-mosaic pixel transform matrix file.

*.csv

algorithm_json{:bash}

:file

JSON file containing the algorithm specification

*.json

images_regex{:bash}

:string

Can either be blank to match files by MERSCOPE convention, or a python formatting string specifying the file name (e.g., image_{stain}z{z}.tif), or a regular expression matching the tiff files to be used (e.g., mosaic(?P[\w|-]+)_z(?P[0-9]+).tif)

Output

name:type
description
pattern

segmentation_files{:bash}

meta{:bash}

:map

Groovy Map containing sample information e.g. [ id:'sample1', single_end:false ]

${prefix}/*.json{:bash}

:file

Segmentation specification JSON file

*.json

versions{:bash}

versions.yml{:bash}

:file

File containing software versions

versions.yml

Tools

maintainer
Github user mcmero
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