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:false ]

input_img:file

Input img file containing image stack to classify

output_format:string

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

export_source:string

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

ilp:file

Trained ilastik pixel classification .ilp project file

*.{ilp}

Output

name:type
description
pattern

output

meta:map

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

*.${output_format}:file

Output file from ilastik pixel classification.

versions

versions.yml:file

File containing software versions

versions.yml

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
mcmicro molkart
Github user FloWuenne
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