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 for h5 file
e.g. [ id:‘test’, single_end

]

input_img (file)

Input img file containing image stack to classify

meta2 (map)

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

]

ilp (file)

Trained ilastik pixel classification .ilp project file

*.{ilp}

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

output (file)

Output file from ilastik pixel classification.

included in
molkart
author
Github user FloWuenne
get in touch
Ask a question on Slack Open an issue on GitHub

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