modules/numorph_3dunet

3DUnet for cell nuclei quantification on 3D microscopy images of the numorph toolkit.

segmentationcell nucleilight-sheet microscopynumorph

https://github.com/nf-core/modules/[...]/modules/nf-core/numorph/3dunet

Description

3DUnet for cell nuclei quantification on 3D microscopy images of the numorph toolkit.

Input

name:type

description

pattern

`meta`
`:map`

Groovy Map containing sample information e.g. [ id:'sample1' ]

`img_directory`
`:directory`

Directory containing stitched image files

*.{tif,tiff}

`parameter_file`
`:file`

File containing parameters for numorph tools

*.{csv}

`model_file`
`:file`

File containing the trained model

*.{h5}

Output

name:type

description

pattern

`cellcounts`

`meta`
`:map`

Groovy Map containing sample information e.g. [ id:'sample1' ]

`${prefix}/`
`:directory`

Directory containing cell count results

${meta.id}/

`versions_numorph_3dunet`

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

The name of the process

`numorph_3dunet`
`:string`

The name of the tool

`numorph_3dunet --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

`numorph_3dunet`
`:string`

The name of the tool

`numorph_3dunet --version`
`:eval`

The expression to obtain the version of the tool

Tools

numorph_3dunet
MIT

This package contains the original 3DUnet for cell nuclei quantification on 3D microscopy images of the numorph toolkit.

github.com/qbic-pipelines/numorph_3dunet

modules/numorph_3dunet

Description

Input

`meta`
`:map`

`img_directory`
`:directory`

`parameter_file`
`:file`

`model_file`
`:file`

Output

`cellcounts`

`meta`
`:map`

`${prefix}/`
`:directory`

`versions_numorph_3dunet`

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

`numorph_3dunet`
`:string`

`numorph_3dunet --version`
`:eval`

Topics

`versions`

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

`numorph_3dunet`
`:string`

`numorph_3dunet --version`
`:eval`

Tools

numorph_3dunet
MIT

maintainer

get in touch

modules/numorph_3dunet

Description

Input

meta :map

img_directory :directory

parameter_file :file

model_file :file

Output

cellcounts

meta :map

${prefix}/ :directory

versions_numorph_3dunet

${task.process} :string

numorph_3dunet :string

numorph_3dunet --version :eval

Topics

versions

${task.process} :string

numorph_3dunet :string

numorph_3dunet --version :eval

Tools

numorph_3dunetMIT

maintainer

get in touch

`meta`
`:map`

`img_directory`
`:directory`

`parameter_file`
`:file`

`model_file`
`:file`

`cellcounts`

`meta`
`:map`

`${prefix}/`
`:directory`

`versions_numorph_3dunet`

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

`numorph_3dunet`
`:string`

`numorph_3dunet --version`
`:eval`

`versions`

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

`numorph_3dunet`
`:string`

`numorph_3dunet --version`
`:eval`

numorph_3dunet
MIT