descriptor.json

{
  "name": "NucleiSegmentation-Cellpose",
  "description": "2D nuclei segmentation using Cellpose",
  "container-image": {
    "image": "neubiaswg5/w_nucleisegmentation-cellpose",
    "type": "singularity"
  },
  "command-line": "python wrapper.py CYTOMINE_HOST CYTOMINE_PUBLIC_KEY CYTOMINE_PRIVATE_KEY CYTOMINE_ID_PROJECT CYTOMINE_ID_SOFTWARE DIAMETER PROB_THRESHOLD NUC_CHANNEL",
  "inputs": [
    {
      "id": "cytomine_host",
      "value-key": "@ID",
      "command-line-flag": "--@id",
      "name": "Cytomine host",
      "set-by-server": true,
      "optional": false,
      "type": "String"
    },
    {
      "id": "cytomine_public_key",
      "value-key": "@ID",
      "command-line-flag": "--@id",
      "name": "Cytomine public key",
      "set-by-server": true,
      "optional": false,
      "type": "String"
    },
    {
      "id": "cytomine_private_key",
      "value-key": "@ID",
      "command-line-flag": "--@id",
      "name": "Cytomine private key",
      "set-by-server": true,
      "optional": false,
      "type": "String"
    },
    {
      "id": "cytomine_id_project",
      "value-key": "@ID",
      "command-line-flag": "--@id",
      "name": "Cytomine project ID",
      "set-by-server": true,
      "optional": false,
      "type": "Number"
    },
    {
      "id": "cytomine_id_software",
      "value-key": "@ID",
      "command-line-flag": "--@id",
      "name": "Cytomine software ID",
      "set-by-server": true,
      "optional": false,
      "type": "Number"
    },
    {
      "id": "diameter",
      "value-key": "@ID",
      "command-line-flag": "--@id",
      "name": "Nuclei diameter (if 0 cellpose will estimate for each image)",
      "description": "Nuclei diameter (if 0 cellpose will estimate for each image)",
      "default-value": 0,
      "set-by-server": false,
      "optional": true,
      "type": "Number"
    },
    {
      "id": "prob_threshold",
      "value-key": "@ID",
      "command-line-flag": "--@id",
      "name": "Probability threshold, centered at 0.0",
      "description": "Probability threshold, centered at 0.0",
      "default-value": 0.0,
      "set-by-server": false,
      "optional": true,
      "type": "Number"
    },
    {
      "id": "nuc_channel",
      "value-key": "@ID",
      "command-line-flag": "--@id",
      "name": "Nuclei channel",
	"description": "Use default 0 for grayscale and RGB that should be converted to grayscale based on luminance. Use 1, 2 or 3 to select a specific RGB channel",
      "default-value": 0,
      "set-by-server": false,
      "optional": true,
      "type": "Number"
    }
  ],

  "schema-version": "cytomine-0.1"
}