name: "cellpose"
description: cellpose segments cells in images
keywords:
  - segmentation
  - image
  - cellpose
tools:
  - "cellpose":
      description: "cellpose is an anatomical segmentation algorithm written in Python 3 by Carsen Stringer and Marius Pachitariu"
      homepage: "https://github.com/MouseLand/cellpose"
      documentation: "https://cellpose.readthedocs.io/en/latest/command.html"
      tool_dev_url: "https://github.com/MouseLand/cellpose"
      doi: 10.1038/s41592-022-01663-4
      licence: ["BSD 3-Clause"]
input:
  - meta:
      type: map
      description: |
        Groovy Map containing sample information
        (sample id)
  - image:
      type: file
      description: tif file for ready for segmentation
      pattern: "*.{tif,tiff}"
  - model:
      type: file
      description: Optional input file. Cellpose 2 model trained by user using human-in-the-loop approach.
output:
  - meta:
      type: map
      description: |
        Groovy Map containing sample information
        [sample id]
  - versions:
      type: file
      description: File containing software versions
      pattern: "versions.yml"
  - mask:
      type: file
      description: labelled mask output from cellpose in tif format
      pattern: "*.{tif, tiff}"
  - flows:
      type: file
      description: cell flow output from cellpose
      pattern: "*.{tif}"

authors:
  - "@josenimo"
  - "@FlowWuenne"
maintainers:
  - "@josenimo"
  - "@FlowWuenne"
