Description

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

Input

Name (Type)
Description
Pattern

meta (map)

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

]

image (file)

Multi-channel image file

*.{tiff,tif,h5,hdf5}

meta2 (map)

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

]

mask (file)

Labeled segmentation mask for image

*.{tiff,tif,h5,hdf5}

meta3 (map)

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

]

markerfile (file)

Marker file with channel names for image to quantify

*.{csv}

Output

Name (Type)
Description
Pattern

meta (map)

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

]

versions (file)

File containing software versions

versions.yml

csv (file)

Quantified regionprops_table

*.{csv}

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.