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 (map)

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

]

h5 (file)

h5 file containing image stack to classify file

*.{h5,hdf5}

meta2 (map)

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

]

ilp (file)

Trained ilastik .ilp project file

*.{ilp}

meta3 (map)

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

]

probs (file)

Probability map for boundary based segmentation

*.{h5,,hdf5}

Output

Name (Type)
Description
Pattern

meta (map)

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

]

versions (file)

File containing software versions

versions.yml

out_tiff (file)

Multicut segmentation mask output.

*.{tiff}
included in
molkart
author
Github user FloWuenne
get in touch
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Tools

ilastik
GPL3

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

ilastik.org ilastik.org/documentation https://github.com/ilastik/ilastik