descriptor.json

{
    "name": "NeuronTracing_vaa3d_app2",
    "container-image": {
        "image": "neubiaswg5/w_neurontracing_vaa3d_app2",
        "type": "singularity"
    },
    "schema-version": "cytomine-0.1",
    "description": "trace neuron with vaa3d All-Path-Pruning 2.0 (APP2) algorithm",
    "command-line": "python wrapper.py CYTOMINE_HOST CYTOMINE_PUBLIC_KEY CYTOMINE_PRIVATE_KEY CYTOMINE_ID_PROJECT CYTOMINE_ID_SOFTWARE BKG_THRESH B_256CUBE B_RADIUSFROM2D IS_GSDT IS_GAP LENGTH_THRESH IS_RESAMPLE IS_BRIGHTFIELD IS_HIGH_INTENSITY",
    "inputs": [
        {
            "id": "cytomine_host",
            "value-key": "@ID",
            "command-line-flag": "--@id",
            "name": "Cytomine host",
            "description": "Cytomine server hostname",
            "type": "String",
            "optional": false,
            "set-by-server": true
        },
        {
            "id": "cytomine_public_key",
            "value-key": "@ID",
            "command-line-flag": "--@id",
            "name": "Cytomine public key",
            "description": "Cytomine public key",
            "type": "String",
            "optional": false,
            "set-by-server": true
        },
        {
            "id": "cytomine_private_key",
            "value-key": "@ID",
            "command-line-flag": "--@id",
            "name": "Cytomine private key",
            "description": "Cytomine private key",      
            "type": "String",
            "optional": false,
            "set-by-server": true
        },
        {
            "id": "cytomine_id_project",
            "value-key": "@ID",
            "command-line-flag": "--@id",
            "name": "Cytomine project id",
            "description": "Cytomine project id",
            "type": "String",
            "optional": false,
            "set-by-server": true
        },
        {
            "id": "cytomine_id_software",
            "value-key": "@ID",
            "command-line-flag": "--@id",
            "name": "Cytomine software id",
            "description": "Cytomine software id",
            "type": "String",
            "optional": false,
            "set-by-server": true
        },
        {
          "default-value": 10,
          "name": "bkg_thresh",
          "description": "Default 10 (is specified as AUTO then auto-thresolding)",
          "set-by-server": false,
          "value-key": "@ID",
          "optional": true,
          "id": "bkg_thresh",
          "type": "Number",
          "command-line-flag": "--@id"
        },
        {
          "default-value": 1,
          "name": "b_256cube",
          "description": "Default 10 (is specified as AUTO then auto-thresolding)",
          "set-by-server": false,
          "value-key": "@ID",
          "optional": true,
          "id": "b_256cube",
          "type": "Number",
          "command-line-flag": "--@id"
        },
        {
          "default-value": 1,
          "name": "b_RadiusFrom2D",
          "description": "If estimate the radius of each reconstruction node from 2D plane only (1 for yes as many times the data is anisotropic, and 0 for no. Default 1 which which uses 2D estimation.)",
          "set-by-server": false,
          "value-key": "@ID",
          "optional": true,
          "id": "b_RadiusFrom2D",
          "type": "Number",
          "command-line-flag": "--@id"
        },
        {
          "default-value": 0,
          "name": "is_gsdt",
          "description": "If use gray-scale distance transform (1 for yes and 0 for no. Default 0.)",
          "set-by-server": false,
          "value-key": "@ID",
          "optional": true,
          "id": "is_gsdt",
          "type": "Number",
          "command-line-flag": "--@id"
        },
        {
          "default-value": 0,
          "name": "is_gap",
          "description": "If allow gap (1 for yes and 0 for no. Default 0.)",
          "set-by-server": false,
          "value-key": "@ID",
          "optional": true,
          "id": "is_gap",
          "type": "Number",
          "command-line-flag": "--@id"
        },
        {
          "default-value": 0,
          "name": "length_thresh",
          "description": "Default is 5.)",
          "set-by-server": false,
          "value-key": "@ID",
          "optional": true,
          "id": "length_thresh",
          "type": "Number",
          "command-line-flag": "--@id"
        },
        {
          "default-value": 0,
          "name": "is_resample",
          "description": "If allow resample (1 for yes and 0 for no. Default 1.)",
          "set-by-server": false,
          "value-key": "@ID",
          "optional": true,
          "id": "is_resample",
          "type": "Number",
          "command-line-flag": "--@id"
        },
        {
          "default-value": 0,
          "name": "is_brightfield",
          "description": "If the signals are dark instead of bright (1 for yes and 0 for no. Default 0.)",
          "set-by-server": false,
          "value-key": "@ID",
          "optional": true,
          "id": "is_brightfield",
          "type": "Number",
          "command-line-flag": "--@id"
        },
        {
          "default-value": 0,
          "name": "is_high_intensity",
          "description": "If the image has high intensity background (1 for yes and 0 for no. Default 0.)",
          "set-by-server": false,
          "value-key": "@ID",
          "optional": true,
          "id": "is_high_intensity",
          "type": "Number",
          "command-line-flag": "--@id"
        }
    ]
}