Nextflow Registry | nf-core/ilastik/pixelclassification@0.0.0-0c7146d

nf-core/ilastik/pixelclassification @ 0.0.0-0c7146d

Ilastik is a tool that utilizes machine learning algorithms to classify pixels, segment, track and count cells in images. Ilastik contains a graphical user interface to interactively label pixels. However, this nextflow module will implement the --headless mode, to apply pixel classification using a pre-trained .ilp file on an input image.

pixel_classification segmentation probability_maps

Latest version: 0.0.0-0c7146d

Total downloads: 1

Source: nf-core/modules

Authors: @FloWuenne

Maintainers: @FloWuenne

Summary

Get started

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

include { ILASTIK_PIXELCLASSIFICATION } from 'nf-core/ilastik/pixelclassification'

License

MIT License

Process

`Name`	`ILASTIK_PIXELCLASSIFICATION`

Input 2 channels

#1 tuple

`meta` map	Groovy Map containing sample information for h5 file e.g. [ id:'test' ]
`input_img` file	Input img file containing image stack to classify. Input format is specified within the .ilp project file.
`output_format` string	String specifying the output format passed as the file extension to the output file specified with the `output_filename_format` parameter.
`export_source` string	String passed to the `export_source` parameter - valid options are 'probabilities', '"simple segmentation"', 'uncertainty', 'features', 'labels']

`ilp` file	Trained ilastik pixel classification .ilp project file `*.{ilp}`

Output 2 channels

#1 output tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test' ]
`*.${output_format}` file	Output file from ilastik pixel classification, as specified by the `output_format` parameter.

#2 versions_ilastik tuple

`${task.process}` string	The name of the process
`ilastik` string	The name of the tool
`/opt/ilastik-1.4.0-Linux/run_ilastik.sh --headless --version` eval	The expression to obtain the version of the tool

Tool	Description	Homepage
ilastik	Ilastik is a user friendly tool that enables pixel classification, segmentation and analysis.	https://www.ilastik.org/

Version	0.0.0-0c7146d
Commit ID	0c7146d85582628b5d1034504702fa808632b1af
Release Date	08 Apr 2026 18:48:58 (UTC)
Download URL	https://registry-stage.nextflow.io/api/v1/modules/nf-core%2Filastik%2Fpixelclassification/0.0.0-0c7146d/download
OCI Store URL	https://public.cr.stage-seqera.io/v2/nextflow/plugin-stage/modules/nf-core/ilastik/pixelclassification/blobs/sha256:9d5bccd43cb4789106c6658486eb84478b6c2a8407689206a0224b8dc2a3a36e
Size	2.8 KB
Checksum	sha256:9d5bccd43cb4789106c6658486eb84478b6c2a8407689206a0224b8dc2a3a36e
Downloads	1

Version	Date	Status	Downloads	Size	Diff
0.0.0-0c7146d	08 Apr 2026 18:48:58 (UTC)		1	2.8 KB	-