modules/ilastik_pixelclassification

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.

pixel_classificationsegmentationprobability_maps

https://github.com/nf-core/modules/[...]/modules/nf-core/ilastik/pixelclassification

Description

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

`output`

`meta:map`

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

]

`*.${suffix}: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

modules/ilastik_pixelclassification

Description

Input

`meta:map`

`input_img:file`

`meta2:map`

`ilp:file`

Output

`output`

`meta:map`

`*.${suffix}:file`

`versions`

`versions.yml:file`

Tools

ilastik
GPL3

included in

maintainer

get in touch

modules/ilastik_pixelclassification

Description

Input

meta:map

input_img:file

meta2:map

ilp:file

Output

output

meta:map

*.${suffix}:file

versions

versions.yml:file

Tools

ilastik GPL3

included in

maintainer

get in touch

`meta:map`

`input_img:file`

`meta2:map`

`ilp:file`

`output`

`meta:map`

`*.${suffix}:file`

`versions`

`versions.yml:file`

ilastik
GPL3