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descriptor.json
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descriptor.json
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{
"name": "CellSegmentClassify_HoVerNet_HE_ROI",
"container-image": {
"image": "cellsegmentclassify_hovernet_he_roi",
"type": "singularity"
},
"schema-version": "cytomine-0.1",
"description": "Cell (nuclei) segmentation and classification using HoVer-Net with versatile H&E pre-trained model",
"command-line": "python run.py CYTOMINE_HOST CYTOMINE_PUBLIC_KEY CYTOMINE_PRIVATE_KEY CYTOMINE_ID_PROJECT CYTOMINE_ID_SOFTWARE CYTOMINE_ID_IMAGES CYTOMINE_ID_ROI_TERM CYTOMINE_ID_CELL_NEO_TERM CYTOMINE_ID_CELL_INF_TERM CYTOMINE_ID_CELL_CON_TERM CYTOMINE_ID_CELL_DEAD_TERM CYTOMINE_ID_CELL_NNEPI_TERM HOVERNET_MODEL",
"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": "cytomine_id_images",
"value-key": "@ID",
"command-line-flag": "--@id",
"name": "Cytomine Image IDs",
"description": "Images on which to detect objects",
"set-by-server": false,
"optional": false,
"type": "ListDomain",
"uri": "/api/project/$currentProject$/imageinstance.json",
"uri-print-attribute": "instanceFilename",
"uri-sort-attribute": "instanceFilename"
},
{
"id": "cytomine_id_roi_term",
"value-key": "@ID",
"command-line-flag": "--@id",
"name": "Cytomine ROI term ID",
"description": "Ontology term ID for ROI(s) where to detect cells",
"set-by-server": false,
"optional": false,
"type": "Domain",
"uri": "/api/ontology/$currentOntology$/term.json",
"uri-print-attribute": "name",
"uri-sort-attribute": "name"
},
{
"id": "cytomine_id_cell_neo_term",
"value-key": "@ID",
"command-line-flag": "--@id",
"name": "Neoplastic Epithelial Cell term ID",
"description": "Ontology term ID for Cell of type Neoplastic Epithelial to be detected",
"set-by-server": false,
"optional": false,
"type": "Domain",
"uri": "/api/ontology/$currentOntology$/term.json",
"uri-print-attribute": "name",
"uri-sort-attribute": "name"
},
{
"id": "cytomine_id_cell_inf_term",
"value-key": "@ID",
"command-line-flag": "--@id",
"name": "Inflammatory Cell term ID",
"description": "Ontology term ID for Cell of type Inflammatory to be detected",
"set-by-server": false,
"optional": false,
"type": "Domain",
"uri": "/api/ontology/$currentOntology$/term.json",
"uri-print-attribute": "name",
"uri-sort-attribute": "name"
},
{
"id": "cytomine_id_cell_con_term",
"value-key": "@ID",
"command-line-flag": "--@id",
"name": "Connective Cell term ID",
"description": "Ontology term ID for Cell of type Connective to be detected",
"set-by-server": false,
"optional": false,
"type": "Domain",
"uri": "/api/ontology/$currentOntology$/term.json",
"uri-print-attribute": "name",
"uri-sort-attribute": "name"
},
{
"id": "cytomine_id_cell_dead_term",
"value-key": "@ID",
"command-line-flag": "--@id",
"name": "Dead Cell term ID",
"description": "Ontology term ID for Cell of type Dead to be detected",
"set-by-server": false,
"optional": false,
"type": "Domain",
"uri": "/api/ontology/$currentOntology$/term.json",
"uri-print-attribute": "name",
"uri-sort-attribute": "name"
},
{
"id": "cytomine_id_cell_nnepi_term",
"value-key": "@ID",
"command-line-flag": "--@id",
"name": "Non-Neoplastic Epithelial Cell term ID",
"description": "Ontology term ID for Cell of type Non-Neoplastic Epithelial to be detected",
"set-by-server": false,
"optional": false,
"type": "Domain",
"uri": "/api/ontology/$currentOntology$/term.json",
"uri-print-attribute": "name",
"uri-sort-attribute": "name"
},
{
"id": "hovernet_model",
"value-key": "@ID",
"command-line-flag": "--@id",
"name": "HoVer-Net model",
"description": "The HoVer-Net model to be used. Options here, include hovernet_fast-pannuke, hovernet_fast-monusac, hovernet_original-consep, hovernet_original_kumar.",
"default-value": "hovernet_fast-pannuke",
"set-by-server": false,
"optional": true,
"type": "String"
}
]
}