nf-core/ilastik/multicut @ 0.0.0-0c7146d
Summary
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.
Get started
Add the following snippet to your workflow script to include this module.
include { ILASTIK_MULTICUT } from 'nf-core/ilastik/multicut'
License
MIT License
Name
|
ILASTIK_MULTICUT |
|---|
meta
map
|
Groovy Map containing sample information e.g. [ id:'test' ] |
|---|---|
h5
file
|
h5 file containing image stack to classify file *.{h5,hdf5}
|
probs
file
|
Probability map for boundary based segmentation as exported by the pixel classification workflow. *.{h5,hdf5}
|
ilp
file
|
Trained 'Boundary-based Segmentation with Multicut' .ilp project file *.{ilp}
|
|---|
mask
tuple
meta
map
|
Groovy Map containing sample information e.g. [ id:'test', single_end:false ] |
|---|---|
*.tiff
file
|
Multicut segmentation mask output. *.{tiff}
|
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 19:10:39 (UTC) |
| Download URL | https://registry.nextflow.io/api/v1/modules/nf-core%2Filastik%2Fmulticut/0.0.0-0c7146d/download |
| OCI Store URL | https://public.cr.seqera.io/v2/nextflow/plugin/modules/nf-core/ilastik/multicut/blobs/sha256:811777495a3f0bc87131ad7cc9a9e7d3287c867e3fe7a3dccc9b7a673b7d8834 |
| Size | 2.5 KB |
| Checksum | sha256:811777495a3f0bc87131ad7cc9a9e7d3287c867e3fe7a3dccc9b7a673b7d8834 |
| Downloads | 4 |
| Version | Date | Status | Downloads | Size |
|---|---|---|---|---|
| 0.0.0-0c7146d | 08 Apr 2026 19:10:39 (UTC) | 4 | 2.5 KB |