Description

Mcquant extracts single-cell data given a multi-channel image and a segmentation mask.

Input

name:type
description
pattern

meta{:bash}

:map

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

image{:bash}

:file

Multi-channel image file

*.{tiff,tif,h5,hdf5}

meta2{:bash}

:map

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

mask{:bash}

:file

Labeled segmentation mask for image

*.{tiff,tif,h5,hdf5}

meta3{:bash}

:map

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

markerfile{:bash}

:file

Marker file with channel names for image to quantify

*.{csv}

Output

name:type
description
pattern

csv{:bash}

meta{:bash}

:map

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

*.csv{:bash}

:file

Quantified regionprops_table

*.{csv}

versions_mcquant{:bash}

${task.process}{:bash}

:string

The name of the process

mcquant{:bash}

:string

The name of the tool

1.5.4{: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

mcquant{:bash}

:string

The name of the tool

1.5.4{:bash}

:string

The expression to obtain the version of the tool

Tools

mcquant
MIT

Module for single-cell data extraction given a segmentation mask and multi-channel image. The CSV structure is aligned with histoCAT output.

github.com/labsyspharm/quantification github.com/labsyspharm/quantification/blob/master/README.md https://github.com/labsyspharm/quantification 10.1038/s41592-021-01308-y
included in
mcmicro
maintainer
Github user FloWuenne
get in touch
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