Description

performs shading correction and intensity normalization between tile stacks

Input

name:type
description
pattern

meta{:bash}

:map

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

img_directory{:bash}

:directory

Directory containing image files

*.{tif,tiff}

parameter_file{:bash}

:file

File containing parameters for numorph tools

*.{csv}

Output

name:type
description
pattern

variables{:bash}

meta{:bash}

:map

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

results/variables/{:bash}

:directory

Directory containing tile normalization factors and intensity thresholds

/{results}/variables/*

samples{:bash}

meta{:bash}

:map

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

results/samples/{:bash}

:directory

Directory containing QC images for tile normalization and intensity adjusted example images

/{results}/samples/*

NM_variable{:bash}

meta{:bash}

:map

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

results/NM_variables.mat{:bash}

:file

File containing processing parameters and varaiables in .mat format

/{results}/NM_variables.mat

versions_numorph_intensity{:bash}

${task.process}{:bash}

:string

The name of the process

numorph_intensity{:bash}

:string

The name of the tool

1.0.0{:bash}

:string

The expression to obtain the version of the tool

Topics

name:type
description
pattern

versions{:bash}

${task.process}{:bash}

:string

The name of the process

numorph_intensity{:bash}

:string

The name of the tool

1.0.0{:bash}

:string

The expression to obtain the version of the tool

Tools

numorph
MIT

A toolkit for processing and analysis of light-sheet microscopy images

github.com/qbic-pipelines/Numorph-toolkit
included in
lsmquant
maintainer
Github user CaroAMN
get in touch
Ask a question on Slack Open an issue on GitHub