Description

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.

Input

name:type
description
pattern

meta{:bash}

:map

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

h5{:bash}

:file

h5 file containing image stack to classify file

*.{h5,hdf5}

probs{:bash}

:file

Probability map for boundary based segmentation as exported by the pixel classification workflow.

*.{h5,hdf5}

ilp{:bash}

:file

Trained ‘Boundary-based Segmentation with Multicut’ .ilp project file

*.{ilp}

Output

name:type
description
pattern

mask{:bash}

meta{:bash}

:map

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

*.tiff{:bash}

:file

Multicut segmentation mask output.

*.{tiff}

versions{:bash}

versions.yml{:bash}

:file

File containing software versions

versions.yml

Tools

ilastik

Ilastik is a user friendly tool that enables pixel classification, segmentation and analysis.

ilastik.org ilastik.org/documentation https://github.com/ilastik/ilastik
included in
mcmicromolkart
maintainer
Github user FloWuenne
get in touch
Ask a question on Slack Open an issue on GitHub