Description

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

Input

name:type
description
pattern

meta

:map

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

input_images

:directory

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

um_to_mosaic_file

:file

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

*.csv

algorithm_json

:file

JSON file containing the algorithm specification

*.json

images_regex

: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

meta

:map

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

${prefix}/*.json

:file

Segmentation specification JSON file

*.json

versions_vpt

${task.process}

:string

The name of the process

vpt

:string

The name of the tool

pip show vpt | sed -n 's/Version: //p'

:eval

The expression to obtain the version of the tool

versions_vptplugincellpose2

${task.process}

:string

The name of the process

vpt-plugin-cellpose2

:string

The name of the tool

pip show vpt-plugin-cellpose2 | sed -n 's/Version: //p'

:eval

The expression to obtain the version of the tool

Topics

name:type
description
pattern

versions

${task.process}

:string

The name of the process

vpt

:string

The name of the tool

pip show vpt | sed -n 's/Version: //p'

:eval

The expression to obtain the version of the tool

${task.process}

:string

The name of the process

vpt-plugin-cellpose2

:string

The name of the tool

pip show vpt-plugin-cellpose2 | sed -n 's/Version: //p'

:eval

The expression to obtain the version of the tool

Tools

maintainer
Github user mcmero
get in touch
Ask a question on Slack Open an issue on GitHub