modules/backsub

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

backgroundcycifautofluorescenceimage_analysismcmicrohighly_multiplexed_imaging

https://github.com/nf-core/modules/[...]/modules/nf-core/backsub

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_backsub`

`${task.process}`
`:string`

The name of the process

`backsub`
`:string`

The name of the tool

`backsub --version`
`:eval`

The expression to obtain the version of the tool

Topics

name:type

description

pattern

`versions`

`${task.process}`
`:string`

The name of the process

`backsub`
`:string`

The name of the tool

`backsub --version`
`:eval`

The expression to obtain the version of the tool

Tools

backsub
MIT licence

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

github.com/SchapiroLabor/Background_subtraction github.com/SchapiroLabor/Background_subtraction/blob/master/README.md https://github.com/SchapiroLabor/Background_subtraction

modules/backsub

Description

Input

`meta`
`:map`

`image`
`:file`

`meta2`
`:map`

`markerfile`
`:file`

Output

`backsub_tif`

`meta`
`:map`

`*.ome.tif`
`:file`

`markerout`

`meta2`
`:map`

`*.csv`
`:file`

`versions_backsub`

`${task.process}`
`:string`

`backsub`
`:string`

`backsub --version`
`:eval`

Topics

`versions`

`${task.process}`
`:string`

`backsub`
`:string`

`backsub --version`
`:eval`

Tools

backsub
MIT licence

included in

maintainer

get in touch

modules/backsub

Description

Input

meta:map

image:file

meta2:map

markerfile:file

Output

backsub_tif

meta:map

*.ome.tif:file

markerout

meta2:map

*.csv:file

versions_backsub

${task.process}:string

backsub:string

backsub --version:eval

Topics

versions

${task.process}:string

backsub:string

backsub --version:eval

Tools

backsub MIT licence

included in

maintainer

get in touch

`meta`
`:map`

`image`
`:file`

`meta2`
`:map`

`markerfile`
`:file`

`backsub_tif`

`meta`
`:map`

`*.ome.tif`
`:file`

`markerout`

`meta2`
`:map`

`*.csv`
`:file`

`versions_backsub`

`${task.process}`
`:string`

`backsub`
`:string`

`backsub --version`
`:eval`

`versions`

`${task.process}`
`:string`

`backsub`
`:string`

`backsub --version`
`:eval`

backsub
MIT licence