modules/cellpose

cellpose segments cells in images using GPU-accelerated deep learning

segmentationimagecellposegpuspatial-transcriptomics

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

Description

cellpose segments cells in images using GPU-accelerated deep learning

Input

name:type

description

pattern

`meta`
`:map`

Groovy Map containing sample information (sample id)

`image`
`:file`

tif file ready for segmentation

*.{tif,tiff}

`model`
`:file`

Optional custom cellpose model file. When provided, passed as —pretrained_model to cellpose. Pass [] (empty list) to use the default model (cpsam in cellpose 4).

*

Output

name:type

description

pattern

`mask`

`meta`
`:map`

Groovy Map containing sample information [sample id]

`${prefix}/*masks.tif`
`:file`

labelled mask output from cellpose in tif format

${prefix}/*masks.tif

`flows`

`meta`
`:map`

Groovy Map containing sample information [sample id]

`${prefix}/*flows.tif`
`:file`

cell flow output from cellpose

${prefix}/*flows.tif

`cells`

`meta`
`:map`

Groovy Map containing sample information [sample id]

`${prefix}/*seg.npy`
`:file`

numpy array with cell segmentation data

${prefix}/*seg.npy

`versions_cellpose`

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

The name of the process

`cellpose`
`:string`

The name of the tool

`cellpose --version | sed -n 's/cellpose version:[[:space:]]*//p' | tr -d '[:space:]'`
`: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

`cellpose --version | sed -n 's/python version:[[:space:]]*//p' | tr -d '[:space:]'`
`:eval`

The expression to obtain the version of the tool

`versions_torch`

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

The name of the process

`torch`
`:string`

The name of the tool

`cellpose --version | sed -n 's/torch version:[[:space:]]*//p' | tr -d '[:space:]'`
`:eval`

The expression to obtain the version of the tool

Topics

name:type

description

pattern

`versions`

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

The name of the process

`cellpose`
`:string`

The name of the tool

`cellpose --version | sed -n 's/cellpose version:[[:space:]]*//p' | tr -d '[:space:]'`
`: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

`cellpose --version | sed -n 's/python version:[[:space:]]*//p' | tr -d '[:space:]'`
`:eval`

The expression to obtain the version of the tool

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

The name of the process

`torch`
`:string`

The name of the tool

`cellpose --version | sed -n 's/torch version:[[:space:]]*//p' | tr -d '[:space:]'`
`:eval`

The expression to obtain the version of the tool

Tools

cellpose
BSD 3-Clause

cellpose is an anatomical segmentation algorithm written in Python 3 by Carsen Stringer and Marius Pachitariu

github.com/MouseLand/cellpose cellpose.readthedocs.io/en/latest/command https://github.com/MouseLand/cellpose 10.1038/s41592-022-01663-4

modules/cellpose

Description

Input

meta:map

image:file

model:file

Output

mask

meta:map

${prefix}/*masks.tif:file

flows

meta:map

${prefix}/*flows.tif:file

cells

meta:map

${prefix}/*seg.npy:file

versions_cellpose

${task.process}:string

cellpose:string

cellpose --version | sed -n 's/cellpose version:[[:space:]]*//p' | tr -d '[:space:]':eval

versions_python

${task.process}:string

python:string

cellpose --version | sed -n 's/python version:[[:space:]]*//p' | tr -d '[:space:]':eval

versions_torch

${task.process}:string

torch:string

cellpose --version | sed -n 's/torch version:[[:space:]]*//p' | tr -d '[:space:]':eval

Topics

versions

${task.process}:string

cellpose:string

cellpose --version | sed -n 's/cellpose version:[[:space:]]*//p' | tr -d '[:space:]':eval

${task.process}:string

python:string

cellpose --version | sed -n 's/python version:[[:space:]]*//p' | tr -d '[:space:]':eval

${task.process}:string

torch:string

cellpose --version | sed -n 's/torch version:[[:space:]]*//p' | tr -d '[:space:]':eval

Tools

cellpose BSD 3-Clause

included in

maintainers

get in touch

`meta`
`:map`

`image`
`:file`

`model`
`:file`

`mask`

`meta`
`:map`

`${prefix}/*masks.tif`
`:file`

`flows`

`meta`
`:map`

`${prefix}/*flows.tif`
`:file`

`cells`

`meta`
`:map`

`${prefix}/*seg.npy`
`:file`

`versions_cellpose`

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

`cellpose`
`:string`

`cellpose --version | sed -n 's/cellpose version:[[:space:]]*//p' | tr -d '[:space:]'`
`:eval`

`versions_python`

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

`python`
`:string`

`cellpose --version | sed -n 's/python version:[[:space:]]*//p' | tr -d '[:space:]'`
`:eval`

`versions_torch`

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

`torch`
`:string`

`cellpose --version | sed -n 's/torch version:[[:space:]]*//p' | tr -d '[:space:]'`
`:eval`

`versions`

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

`cellpose`
`:string`

`cellpose --version | sed -n 's/cellpose version:[[:space:]]*//p' | tr -d '[:space:]'`
`:eval`

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

`python`
`:string`

`cellpose --version | sed -n 's/python version:[[:space:]]*//p' | tr -d '[:space:]'`
`:eval`

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

`torch`
`:string`

`cellpose --version | sed -n 's/torch version:[[:space:]]*//p' | tr -d '[:space:]'`
`:eval`

cellpose
BSD 3-Clause