modules/ilastik_multicut

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.

multicutsegmentationpixel classification

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

Description

Input

name:type

description

pattern

`meta`
`:map`

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

`h5`
`:file`

h5 file containing image stack to classify file

*.{h5,hdf5}

`probs`
`:file`

Probability map for boundary based segmentation as exported by the pixel classification workflow.

*.{h5,hdf5}

`ilp`
`:file`

Trained ‘Boundary-based Segmentation with Multicut’ .ilp project file

*.{ilp}

Output

name:type

description

pattern

`mask`

`meta`
`:map`

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

`*.tiff`
`:file`

Multicut segmentation mask output.

*.{tiff}

`versions_ilastik`

`${task.process}`
`:string`

The name of the process

`ilastik`
`:string`

The name of the tool

`/opt/ilastik-1.4.0-Linux/run_ilastik.sh --headless --version`
`:eval`

The expression to obtain the version of the tool

Topics

name:type

description

pattern

`versions`

`${task.process}`
`:string`

The name of the process

`ilastik`
`:string`

The name of the tool

`/opt/ilastik-1.4.0-Linux/run_ilastik.sh --headless --version`
`:eval`

The expression to obtain the version of the tool

Tools

ilastik

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_multicut

Description

Input

`meta`
`:map`

`h5`
`:file`

`probs`
`:file`

`ilp`
`:file`

Output

`mask`

`meta`
`:map`

`*.tiff`
`:file`

`versions_ilastik`

`${task.process}`
`:string`

`ilastik`
`:string`

`/opt/ilastik-1.4.0-Linux/run_ilastik.sh --headless --version`
`:eval`

Topics

`versions`

`${task.process}`
`:string`

`ilastik`
`:string`

`/opt/ilastik-1.4.0-Linux/run_ilastik.sh --headless --version`
`:eval`

Tools

ilastik

included in

maintainer

get in touch

modules/ilastik_multicut

Description

Input

meta:map

h5:file

probs:file

ilp:file

Output

mask

meta:map

*.tiff:file

versions_ilastik

${task.process}:string

ilastik:string

/opt/ilastik-1.4.0-Linux/run_ilastik.sh --headless --version:eval

Topics

versions

${task.process}:string

ilastik:string

/opt/ilastik-1.4.0-Linux/run_ilastik.sh --headless --version:eval

Tools

ilastik

included in

maintainer

get in touch

`meta`
`:map`

`h5`
`:file`

`probs`
`:file`

`ilp`
`:file`

`mask`

`meta`
`:map`

`*.tiff`
`:file`

`versions_ilastik`

`${task.process}`
`:string`

`ilastik`
`:string`

`/opt/ilastik-1.4.0-Linux/run_ilastik.sh --headless --version`
`:eval`

`versions`

`${task.process}`
`:string`

`ilastik`
`:string`

`/opt/ilastik-1.4.0-Linux/run_ilastik.sh --headless --version`
`:eval`