Description

Pixel-by-pixel channel subtraction scaled by exposure times of pre-stitched tif images.

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

meta (map)

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

versions (file)

File containing software versions

versions.yml

backsub_tif (file)

Background corrected pyramidal ome.tif

*.{tif}

meta2 (map)

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

markerout (file)

Marker file adjusted to match the background corrected image

*.{csv}
included in
mcmicro
maintainer
Github user kbestak
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Tools