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descriptor.json
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descriptor.json
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{
"name": "CellDetect_Stardist_HE_ROI",
"container-image": {
"image": "cytomine/s_celldetect_stardist_he_roi",
"type": "singularity"
},
"schema-version": "cytomine-0.1",
"description": "Cell (nuclei) detection using StarDist 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_TERM STARDIST_PROB_T STARDIST_NMS_T STARDIST_NORM_PERC_LOW STARDIST_NORM_PERC_HIGH",
"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_term",
"value-key": "@ID",
"command-line-flag": "--@id",
"name": "Cytomine Cell term ID",
"description": "Ontology term ID for Cell 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": "stardist_prob_t",
"value-key": "@ID",
"command-line-flag": "--@id",
"name": "Stardist Probability Threshold",
"description": "Probability Threshold in range [0.0, 1.0] - higher values lead to fewer segmented objects, but will likely avoid false positives",
"default-value": 0.5,
"set-by-server": false,
"optional": true,
"type": "Number"
},
{
"id": "stardist_nms_t",
"value-key": "@ID",
"command-line-flag": "--@id",
"name": "Stardist Non-Maximum Suppression Overlap threshold",
"description": "Overlap Threshold in range [0.0, 1.0] - higher values allow segmented objects to overlap substantially.",
"default-value": 0.5,
"set-by-server": false,
"optional": true,
"type": "Number"
},
{
"id": "stardist_norm_perc_low",
"value-key": "@ID",
"command-line-flag": "--@id",
"name": "Stardist Image Normalization Percentile Low",
"description": "Percentile low in range [0.0 100.0]",
"default-value": 1,
"set-by-server": false,
"optional": true,
"type": "Number"
},
{
"id": "stardist_norm_perc_high",
"value-key": "@ID",
"command-line-flag": "--@id",
"name": "Stardist Image Normalization Percentile High",
"description": "Percentile high in range [0.0 100.0]",
"default-value": 99.8,
"set-by-server": false,
"optional": true,
"type": "Number"
}
]
}