modules/deepcell_mesmer

Deepcell/mesmer segmentation for whole-cell

imagingspatial_omicssegmentation

https://github.com/nf-core/modules/[...]/modules/nf-core/deepcell/mesmer

Description

Deepcell/mesmer segmentation for whole-cell

Input

name:type

description

pattern

`meta`
`:map`

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

`img`
`:file`

Multichannel image file

*.{tiff,tif,h5,hdf5}

`meta2`
`:map`

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

`membrane_img`
`:file`

Optional membrane image to be provided separately.

*.{tiff,tif,h5,hdf5}

Output

name:type

description

pattern

`mask`

`meta`
`:map`

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

`*.tif`
`:file`

File containing the mask.

*.{tif, tiff}

`versions_deepcellapplications`

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

The name of the process

`deepcell-applications`
`:string`

The name of the tool

`0.4.1`
`:string`

The expression to obtain the version of the tool

`versions_deepcell`

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

The name of the process

`deepcell`
`:string`

The name of the tool

`pip show 'DeepCell' | sed '2!d;s/Version: //'`
`:eval`

The expression to obtain the version of the tool

`versions_python`

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

The name of the process

`python`
`:string`

The name of the tool

`python --version | sed 's/Python //'`
`:eval`

The expression to obtain the version of the tool

Topics

name:type

description

pattern

`versions`

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

The name of the process

`deepcell-applications`
`:string`

The name of the tool

`0.4.1`
`:string`

The expression to obtain the version of the tool

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

The name of the process

`deepcell`
`:string`

The name of the tool

`pip show 'DeepCell' | sed '2!d;s/Version: //'`
`:eval`

The expression to obtain the version of the tool

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

The name of the process

`python`
`:string`

The name of the tool

`python --version | sed 's/Python //'`
`:eval`

The expression to obtain the version of the tool

Tools

mesmer
APACHE2

Deep cell is a collection of tools to segment imaging data

github.com/vanvalenlab/deepcell-tf github.com/vanvalenlab/intro-to-deepcell[...]pretrained_models https://githu/b.com/vanvalenlab/deepcell-tf 10.1038/s41587-021-01094-0

modules/deepcell_mesmer

Description

Input

`meta`
`:map`

`img`
`:file`

`meta2`
`:map`

`membrane_img`
`:file`

Output

`mask`

`meta`
`:map`

`*.tif`
`:file`

`versions_deepcellapplications`

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

`deepcell-applications`
`:string`

`0.4.1`
`:string`

`versions_deepcell`

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

`deepcell`
`:string`

`pip show 'DeepCell' | sed '2!d;s/Version: //'`
`:eval`

`versions_python`

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

`python`
`:string`

`python --version | sed 's/Python //'`
`:eval`

Topics

`versions`

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

`deepcell-applications`
`:string`

`0.4.1`
`:string`

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

`deepcell`
`:string`

`pip show 'DeepCell' | sed '2!d;s/Version: //'`
`:eval`

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

`python`
`:string`

`python --version | sed 's/Python //'`
`:eval`

Tools

mesmer
APACHE2

included in

maintainers

get in touch

modules/deepcell_mesmer

Description

Input

meta:map

img:file

meta2:map

membrane_img:file

Output

mask

meta:map

*.tif:file

versions_deepcellapplications

${task.process}:string

deepcell-applications:string

0.4.1:string

versions_deepcell

${task.process}:string

deepcell:string

pip show 'DeepCell' | sed '2!d;s/Version: //':eval

versions_python

${task.process}:string

python:string

python --version | sed 's/Python //':eval

Topics

versions

${task.process}:string

deepcell-applications:string

0.4.1:string

${task.process}:string

deepcell:string

pip show 'DeepCell' | sed '2!d;s/Version: //':eval

${task.process}:string

python:string

python --version | sed 's/Python //':eval

Tools

mesmer APACHE2

included in

maintainers

get in touch

`meta`
`:map`

`img`
`:file`

`meta2`
`:map`

`membrane_img`
`:file`

`mask`

`meta`
`:map`

`*.tif`
`:file`

`versions_deepcellapplications`

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

`deepcell-applications`
`:string`

`0.4.1`
`:string`

`versions_deepcell`

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

`deepcell`
`:string`

`pip show 'DeepCell' | sed '2!d;s/Version: //'`
`:eval`

`versions_python`

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

`python`
`:string`

`python --version | sed 's/Python //'`
`:eval`

`versions`

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

`deepcell-applications`
`:string`

`0.4.1`
`:string`

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

`deepcell`
`:string`

`pip show 'DeepCell' | sed '2!d;s/Version: //'`
`:eval`

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

`python`
`:string`

`python --version | sed 's/Python //'`
`:eval`

mesmer
APACHE2