descriptor.json

{
    "name": "NucleiSegmentation3D-ImageJ",
    "container-image": {
        "image": "neubiaswg5/w_nucleisegmentation3d-imagej",
        "type": "singularity"
    },
    "schema-version": "cytomine-0.1",
    "description": "3D nuclei segmentation using 3D gaussian blur thresholding and 3D watershed using MorpholibJ plugin",
    "command-line": "python wrapper.py CYTOMINE_HOST CYTOMINE_PUBLIC_KEY CYTOMINE_PRIVATE_KEY CYTOMINE_ID_PROJECT CYTOMINE_ID_SOFTWARE IJ_RADIUS IJ_MIN_THRESHOLD",
    "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
        },
        {
            "id": "ij_radius",
            "value-key": "@ID",
            "command-line-flag": "--@id",
            "name": "Radius",
            "description": "Radius for Gaussian smoothing",
            "type": "Number",
            "default-value": 4,
            "optional": true
        },
        {
            "id": "ij_min_threshold",
            "value-key": "@ID",
            "command-line-flag": "--@id",
            "name": "Min Threshold",
            "description": "Min Threshold ",
            "type": "Number",
            "default-value": 15,
            "optional": true
}
        
    ]
}