Description

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

Input

name:type
description
pattern

meta:map

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

image:file

Multi-channel image file

*.{tif,tiff}

meta2:map

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

markerfile: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

meta:map

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

*.ome.tif:file

Background corrected pyramidal ome.tif

*.{tif}

markerout

meta2:map

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

*.csv:file

Marker file adjusted to match the background corrected image

*.{csv}

versions

versions.yml:file

File containing software versions

versions.yml

Tools

included in
mcmicro
maintainer
Github user kbestak
get in touch
Ask a question on Slack Open an issue on GitHub