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 for h5 file e.g. [ id:‘test’ ]

input_img{:bash}

:file

Input img file containing image stack to classify. Input format is specified within the .ilp project file.

output_format{:bash}

:string

String specifying the output format passed as the file extension to the output file specified with the output_filename_format parameter.

export_source{:bash}

:string

String passed to the export_source parameter - valid options are ‘probabilities’, ‘“simple segmentation”’, ‘uncertainty’, ‘features’, ‘labels’]

ilp{:bash}

:file

Trained ilastik pixel classification .ilp project file

*.{ilp}

Output

name:type
description
pattern

output{:bash}

meta{:bash}

:map

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

*.${output_format}{:bash}

:file

Output file from ilastik pixel classification, as specified by the output_format parameter.

versions_ilastik{:bash}

${task.process}{:bash}

:string

The name of the process

ilastik{:bash}

:string

The name of the tool

/opt/ilastik-1.4.0-Linux/run_ilastik.sh --headless --version{:bash}

:eval

The expression to obtain the version of the tool

Topics

name:type
description
pattern

versions{:bash}

${task.process}{:bash}

:string

The name of the process

ilastik{:bash}

:string

The name of the tool

/opt/ilastik-1.4.0-Linux/run_ilastik.sh --headless --version{:bash}

:eval

The expression to obtain the version of the tool

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