nf-core/mcquant @ 0.0.0-0c7146d
Summary
Mcquant extracts single-cell data given a multi-channel image and a segmentation mask.
Get started
Add the following snippet to your workflow script to include this module.
include { MCQUANT } from 'nf-core/mcquant'
License
MIT License
Process
Name
|
MCQUANT |
|---|
Input
3 channels
#1
tuple
meta
map
|
Groovy Map containing sample information e.g. [ id:'test', single_end:false ] |
|---|---|
image
file
|
Multi-channel image file *.{tiff,tif,h5,hdf5}
|
#2
tuple
meta2
map
|
Groovy Map containing sample information e.g. [ id:'test', single_end:false ] |
|---|---|
mask
file
|
Labeled segmentation mask for image *.{tiff,tif,h5,hdf5}
|
#3
tuple
meta3
map
|
Groovy Map containing sample information e.g. [ id:'test', single_end:false ] |
|---|---|
markerfile
file
|
Marker file with channel names for image to quantify *.{csv}
|
Output
2 channels
#1
csv
tuple
meta
map
|
Groovy Map containing sample information e.g. [ id:'test', single_end:false ] |
|---|---|
*.csv
file
|
Quantified regionprops_table *.{csv}
|
#2
versions_mcquant
tuple
${task.process}
string
|
The name of the process |
|---|---|
mcquant
string
|
The name of the tool |
1.5.4
string
|
The expression to obtain the version of the tool |
| Tool | Description | Homepage |
|---|---|---|
| mcquant | Module for single-cell data extraction given a segmentation mask and multi-channel image. The CSV structure is aligned with histoCAT output. | https://github.com/labsyspharm/quantification |
| Version | 0.0.0-0c7146d |
|---|---|
| Commit ID | 3fc6d40d163d89ae44d40a00b9017d5a9df5170e |
| Release Date | 08 Apr 2026 19:16:28 (UTC) |
| Download URL | https://registry.nextflow.io/api/v1/modules/nf-core%2Fmcquant/0.0.0-0c7146d/download |
| OCI Store URL | https://public.cr.seqera.io/v2/nextflow/plugin/modules/nf-core/mcquant/blobs/sha256:d475825550569739941dcfc363b4d3db923c5ef1ac62c084946e9e6ca5e7b512 |
| Size | 2.4 KB |
| Checksum | sha256:d475825550569739941dcfc363b4d3db923c5ef1ac62c084946e9e6ca5e7b512 |
| Downloads | 3 |
| Version | Date | Status | Downloads | Size |
|---|---|---|---|---|
| 0.0.0-3fc6d40 | 22 Apr 2026 15:21:09 (UTC) | 3 | 2.5 KB | |
| 0.0.0-0c7146d | 08 Apr 2026 19:16:28 (UTC) | 3 | 2.4 KB |