descriptor.json

{
  "command-line": "python wrapper.py CYTOMINE_HOST CYTOMINE_PUBLIC_KEY CYTOMINE_PRIVATE_KEY CYTOMINE_ID_PROJECT CYTOMINE_ID_SOFTWARE GBLURRAD MEANBOX OFFSET ",
  "inputs": [
    {
      "name": "Cytomine host",
      "description": "Cytomine server hostname",
      "set-by-server": true,
      "value-key": "@ID",
      "optional": false,
      "id": "cytomine_host",
      "type": "String",
      "command-line-flag": "--@id"
    },
    {
      "name": "Cytomine public key",
      "description": "Cytomine public key",
      "set-by-server": true,
      "value-key": "@ID",
      "optional": false,
      "id": "cytomine_public_key",
      "type": "String",
      "command-line-flag": "--@id"
    },
    {
      "name": "Cytomine private key",
      "description": "Cytomine private key",
      "set-by-server": true,
      "value-key": "@ID",
      "optional": false,
      "id": "cytomine_private_key",
      "type": "String",
      "command-line-flag": "--@id"
    },
    {
      "name": "Cytomine project id",
      "description": "Cytomine project id",
      "set-by-server": true,
      "value-key": "@ID",
      "optional": false,
      "id": "cytomine_id_project",
      "type": "Number",
      "command-line-flag": "--@id"
    },
    {
      "name": "Cytomine software id",
      "description": "Cytomine software id",
      "set-by-server": true,
      "value-key": "@ID",
      "optional": false,
      "id": "cytomine_id_software",
      "type": "Number",
      "command-line-flag": "--@id"
    },
    {
      "default-value": 3,
      "name": "Gaussian Blur Radius",
      "description": "Gaussian Blur Radius pre-filter",
      "set-by-server": false,
      "value-key": "@ID",
      "optional": true,
      "id": "gblurrad",
      "type": "Number",
      "command-line-flag": "--@id"
    },
    {
      "default-value": 101,
      "name": "Mean Box",
      "description": "Size of the box used to perform local mean for local thresholding",
      "set-by-server": false,
      "value-key": "@ID",
      "optional": true,
      "id": "meanbox",
      "type": "Number",
      "command-line-flag": "--@id"
    },
    {
      "default-value": 2,
      "name": "Threshold offset",
      "description": "Local theshold offset level",
      "set-by-server": false,
      "value-key": "@ID",
      "optional": true,
      "id": "offset",
      "type": "Number",
      "command-line-flag": "--@id"
    }
  ],
  "name": "ObjectTracking-Octave",
  "description": "Nuclei tracking in 2D time-lapse with Octave tracker (adapted from Matlab LOBSTER version: https://github.com/SebastienTs/LOBSTER)",
  "schema-version": "cytomine-0.1",
  "container-image": {
    "image": "neubiaswg5/w_objecttracking-octave",
    "type": "singularity"
  }
}