name: "deepcell_mesmer"
description: Deepcell/mesmer segmentation for whole-cell
keywords:
  - imaging
  - spatial_omics
  - segmentation
tools:
  - "mesmer":
      description: "Deep cell is a collection of tools to segment imaging data"
      homepage: "https://github.com/vanvalenlab/deepcell-tf"
      documentation: "https://github.com/vanvalenlab/intro-to-deepcell/tree/master/pretrained_models"
      tool_dev_url: "https://githu/b.com/vanvalenlab/deepcell-tf"
      doi: 10.1038/s41587-021-01094-0
      licence: ["APACHE2"]
input:
  # Only when we have meta
  - meta:
      type: map
      description: |
        Groovy Map containing sample information
        e.g. [ id:'test', single_end:false ]
  - img:
      type: file
      description: Multichannel image file
      pattern: "*.{tiff,tif,h5,hdf5}"
  - meta2:
      type: map
      description: |
        Groovy Map containing sample information
        e.g. [ id:'test', single_end:false ]
  - membrane_img:
      type: file
      description: Optional membrane image to be provided separately.
      pattern: "*.{tiff,tif,h5,hdf5}"
output:
  #Only when we have meta
  - meta:
      type: map
      description: |
        Groovy Map containing sample information
        e.g. [ id:'test', single_end:false ]
  - mask:
      type: file
      description: File containing the mask.
      pattern: "*.{tif, tiff}"
  - versions:
      type: file
      description: File containing software versions
      pattern: "versions.yml"

authors:
  - "@migueLib"
  - "@chiarasch"
maintainers:
  - "@migueLib"
  - "@chiarasch"
