Description

cellpose segments cells in images

Input

Name (Type)
Description
Pattern

meta (map)

Groovy Map containing sample information
(sample id)

image (file)

tif file for ready for segmentation

*.{tif,tiff}

model (file)

Optional input file. Cellpose 2 model trained by user using human-in-the-loop approach.

Output

Name (Type)
Description
Pattern

meta (map)

Groovy Map containing sample information
[sample id]

versions (file)

File containing software versions

versions.yml

mask (file)

labelled mask output from cellpose in tif format

*.{tif, tiff}

flows (file)

cell flow output from cellpose

*.{tif}

Tools

cellpose
BSD 3-Clause

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