Description

Pixel-by-pixel channel subtraction tool for multiplexed immunofluorescence data.

Input

name:type
description
pattern

meta{:bash}

:map

Groovy Map containing sample information e.g. [ id:‘test’ ]

image{:bash}

:file

Multi-channel image file

*.{tif,tiff}

meta2{:bash}

:map

Groovy Map containing sample information e.g. [ id:‘test’ ]

markerfile{:bash}

:file

Marker file with channel names, exposure times, and specified background to subtract (and remove to exclude channels from output)

*.csv

Output

name:type
description
pattern

backsub_tif{:bash}

meta{:bash}

:map

Groovy Map containing sample information e.g. [ id:‘test’ ]

*.ome.tif{:bash}

:file

Background corrected pyramidal ome.tif

*.{tif}

markerout{:bash}

meta2{:bash}

:map

Groovy Map containing sample information e.g. [ id:‘test’ ]

*.csv{:bash}

:file

Marker file adjusted to match the background corrected image

*.{csv}

versions_backsub{:bash}

${task.process}{:bash}

:string

The name of the process

backsub{:bash}

:string

The name of the tool

backsub --version{:bash}

:eval

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

backsub{:bash}

:string

The name of the tool

backsub --version{:bash}

:eval

The expression to obtain the version of the tool

Tools

included in
mcmicro
maintainer
Github user kbestak
get in touch
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