Nextflow Registry | nf-core/phenoimager2mc@0.0.0-91d94af

nf-core/phenoimager2mc @ 0.0.0-91d94af

Formatting PhenoImager TIFF output files into stacked and normalized OME-TIFF files per cycle, compatible as ASHLAR and MCMICRO input.

imaging registration ome-tif Staging MCMICRO

Latest version: 0.0.0-91d94af

Total downloads: 1

Source: nf-core/modules

Authors: @chiarasch @kbestak

Maintainers: @chiarasch

Formatting PhenoImager TIFF output files into stacked and normalized OME-TIFF files per cycle, compatible as ASHLAR and MCMICRO input.

Add the following snippet to your workflow script to include this module.

include { PHENOIMAGER2MC } from 'nf-core/phenoimager2mc'

MIT License

Process

`Name`	`PHENOIMAGER2MC`

Input 1 channel

#1 tuple

`meta` map	Groovy Map containing sample information e.g. `[ id:'sample1' ]`
`tiles` list	Folder or list with TIFF files of one cycle from PhenoImager

Output 4 channels

#1 tif tuple

`meta` map	Groovy Map containing sample information e.g. `[ id:'sample1' ]`
`*.tif` file	One output .tif file containing concatenated tiles of the cycle. `*.{tif,tiff}`

#2 versions_python tuple

`${task.process}` string	The name of the process
`python` string	The name of the tool
`python --version \| sed -e "s/Python //g"` eval	The expression to obtain the version of the tool

#3 versions_ome_types tuple

`${task.process}` string	The name of the process
`ome_types` string	The name of the tool
`python -m pip show ome_types \| sed -n "s/Version: //p"` eval	The expression to obtain the version of the tool

#4 versions_phenoimager2mc tuple

`${task.process}` string	The name of the process
`phenoimager2mc` string	The name of the tool
`phenoimager2mc --version` eval	The expression to obtain the version of the tool

Tool	Description	Homepage
phenoimager2mc	PhenoImager output conversion into a stacked and normalized OME-TIFF file per cycle.	https://github.com/SchapiroLabor/phenoimager2mc

Version	0.0.0-91d94af
Commit ID	91d94af4aa6e48954670b1485fc729e392a51b43
Release Date	16 Apr 2026 21:15:30 (UTC)
Download URL	https://registry-stage.nextflow.io/api/v1/modules/nf-core%2Fphenoimager2mc/0.0.0-91d94af/download
OCI Store URL	https://public.cr.stage-seqera.io/v2/nextflow/plugin-stage/modules/nf-core/phenoimager2mc/blobs/sha256:ec66d2b3a611938a5d3466d2ad2962ed6c2c48c471e7d1890a8314688f28ecd8
Size	2.6 KB
Checksum	sha256:ec66d2b3a611938a5d3466d2ad2962ed6c2c48c471e7d1890a8314688f28ecd8
Downloads	1

Version	Date	Status	Downloads	Size	Diff
0.0.0-91d94af	16 Apr 2026 21:15:30 (UTC)		1	2.6 KB	-