Shapes for two-photon fluorescence imaging

modules/experiment/src/main/resources/schemas/neurosciencegraph/experiment/cranialwindow/v0.1.0.json

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+{
+    "@context": [
+      "{{base}}/contexts/neurosciencegraph/core/schema/v0.1.0",
+      {
+        "this": "{{base}}/schemas/neurosciencegraph/experiment/cranialwindow/v0.1.1/shapes/"
+      }
+    ],
+    "@type": "nxv:Schema",
+    "imports": [
+      "{{base}}/schemas/neurosciencegraph/commons/entity/v0.1.0",
+      "{{base}}/schemas/neurosciencegraph/commons/brainlocation/v0.1.1",
+      "{{base}}/schemas/neurosciencegraph/commons/quantitativevalue/v0.1.2"
+    ],
+    "shapes": [
+      {
+        "@id": "this:CranialWindowShape",
+        "@type": "sh:NodeShape",
+        "label": "Cranial window shape definition",
+        "targetClass": "nsg:CranialWindow",
+        "nodeKind": "sh:BlankNodeOrIRI",
+        "and": [
+          {
+            "node": "{{base}}/schemas/neurosciencegraph/commons/entity/v0.1.0/shapes/EntityShape"
+          },
+          {
+            "property": [
+              {
+                "path": "nsg:brainLocation",
+                "name": "Brain location",
+                "description": "Brain location information of the cranial window",
+                "node": "{{base}}/schemas/neurosciencegraph/commons/brainlocation/v0.1.1/shapes/BrainLocationShape"
+              },
+              {
+                "path": "nsg:windowType",
+                "name": "Window type",
+                "in": [
+                    "open window",
+                    "thinned skull",
+                    "chronically implanted glass window"
+                ],
+                "description": "The type of window."
+              },
+              {
+                "path": "nsg:diameter",
+                "name": "Diameter",
+                "description": "Diameter of the window",
+                "node": "{{base}}/schemas/neurosciencegraph/commons/quantitativevalue/v0.1.2/shapes/QuantitativeValueShape"
+              },
+              {
+                "path": "nsg:labellingMethod",
+                "name": "Fluorescence labelling",
+                "datatype": "xsd:string",
+                "description": "Details of the labelling method (for example, injection of a viral construct)."
+              }
+            ]
+          }
+        ]
+      }
+    ]
+  }

modules/experiment/src/main/resources/schemas/neurosciencegraph/experiment/craniotomy/v0.1.0.json

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+{
+    "@context": [
+      "{{base}}/contexts/neurosciencegraph/core/schema/v0.1.0",
+      {
+        "this": "{{base}}/schemas/neurosciencegraph/experiment/craniotomy/v0.1.0/shapes/"
+      }
+    ],
+    "imports": [
+      "{{base}}/schemas/neurosciencegraph/commons/activity/v0.1.4"
+    ],
+    "@type": "nxv:Schema",
+    "shapes": [
+      {
+        "@id": "this:CraniotomyShape",
+        "@type": "sh:NodeShape",
+        "label": "Craniotomy shape definition",
+        "description": "Surgical procedure to give optical access through the skull to the brain (dura).",
+        "nodeKind": "sh:BlankNodeOrIRI",
+        "targetClass": "nsg:Craniotomy",
+        "and": [
+          {
+            "node": "{{base}}/schemas/neurosciencegraph/commons/activity/v0.1.4/shapes/ActivityShape"
+          },
+          {
+            "property": [
+              {
+                "path": "prov:used",
+                "description": "The subject used",
+                "class": "nsg:Subject",
+                "minCount": 1,
+                "maxCount": 1
+              },
+              {
+                "path": "prov:generated",
+                "description": "The cranial window(s) generated",
+                "class": "nsg:CranialWindow",
+                "minCount": 1
+              },
+              {
+                "path": "nsg:anesthesia",
+                "name": "Anesthesia",
+                "description": "Anaesthesia used during the procedure.",
+                "datatype": "xsd:string"
+              }
+            ]
+          }
+        ]
+      }
+    ]
+  }

modules/experiment/src/test/resources/data/neurosciencegraph/experiment/cranialwindow/v0.1.0/example.json

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+{
+    "@context": [
+      "{{base}}/contexts/neurosciencegraph/core/data/v0.1.0"
+    ],
+    "@type": [
+      "prov:Entity",
+      "nsg:CranialWindow"
+    ],
+    "name": "Window1",
+    "nsg:windowType": "thinned skull",
+    "nsg:diameter": {
+        "unitText": "mm",
+        "value": "3.0"
+    },
+    "nsg:labellingMethod": "injection of the viral construct AAV1.Syn.GCaMP6m.WPRE.SV40"
+}

modules/experiment/src/test/resources/data/neurosciencegraph/experiment/craniotomy/v0.1.0/example.json

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+{
+    "@context": [
+      "{{base}}/contexts/neurosciencegraph/core/data/v0.1.0"
+    ],
+    "@type": [
+      "nsg:Craniotomy",
+      "prov:Activity"
+    ],
+    "generated": {
+      "@id": "{{base}}/data/neurosciencegraph/experiment/cranialwindow/v0.1.1/87a00313-e95b-4282-8a84-94afc639d47e",
+      "@type": [
+        "nsg:CranialWindow",
+        "prov:Entity"
+      ]
+    },
+    "used": {
+      "@id": "{{base}}/data/neurosciencegraph/experiment/subject/v0.1.0/c33d5541-ac7a-4214-8928-f4edc48e893e",
+      "@type": [
+        "nsg:Subject",
+        "prov:Entity"
+      ]
+    },
+    "nsg:anesthesia": "1–2% isoflurane"
+  }

modules/optophysiology/src/main/resources/schemas/neurosciencegraph/optophysiology/fluorescencetrace/v0.1.0.json

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+{
+    "@context": [
+      "{{base}}/contexts/neurosciencegraph/core/schema/v0.1.0",
+      {
+        "this": "{{base}}/schemas/neurosciencegraph/optophysiology/fluorescencetrace/v1.0.0/shapes/"
+      }
+    ],
+    "@type": "nxv:Schema",
+    "imports": [
+      "{{base}}/schemas/neurosciencegraph/commons/entity/v0.1.0",
+      "{{base}}/schemas/neurosciencegraph/commons/quantitativevalue/v0.1.2"
+    ],
+    "shapes": [
+      {
+        "@id": "this:FluorescenceTraceShape",
+        "@type": "sh:NodeShape",
+        "label": "Fluorescence trace shape definition.",
+        "targetClass": "nsg:FluorescenceTrace",
+        "nodeKind": "sh:BlankNodeOrIRI",
+        "and": [
+          {
+            "node": "{{base}}/schemas/neurosciencegraph/commons/entity/v0.1.0/shapes/EntityShape"
+          },
+          {
+            "property": [
+              {
+                "path": "nsg:timeStep",
+                "name": "Time step",
+                "description": "Time step (inverted sampling frequency) of data",
+                "node": "{{base}}/schemas/neurosciencegraph/commons/quantitativevalue/v0.1.2/shapes/QuantitativeValueShape",
+                "maxCount": 1
+              }
+            ]
+          }
+        ]
+      }
+    ]
+  }

modules/optophysiology/src/main/resources/schemas/neurosciencegraph/optophysiology/imagesequence/v0.1.0.json

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+{
+    "@context": [
+      "{{base}}/contexts/neurosciencegraph/core/schema/v0.1.0",
+      {
+        "this": "{{base}}/schemas/neurosciencegraph/optophysiology/imagesequence/v0.1.0/shapes/"
+      }
+    ],
+    "@type": "nxv:Schema",
+    "imports": [
+      "{{base}}/schemas/neurosciencegraph/commons/entity/v0.1.0",
+      "{{base}}/schemas/neurosciencegraph/commons/quantitativevalue/v0.1.0"
+    ],
+    "shapes": [
+      {
+        "@id": "this:ImageSequenceShape",
+        "@type": "sh:NodeShape",
+        "label": "Optophysiology image sequence definition.",
+        "targetClass": "nsg:ImageSequence",
+        "nodeKind": "sh:BlankNodeOrIRI",
+        "and": [
+          {
+            "node": "{{base}}/schemas/neurosciencegraph/commons/entity/v0.1.0/shapes/EntityShape"
+          },
+          {
+            "property": [
+              {
+                "path": "nsg:imageSize",
+                "name": "Image size",
+                "description": "Image size in pixels (assumed square)",
+                "datatype": "xsd:integer",
+                "minCount": 1,
+                "maxCount": 1
+              },
+              {
+                "path": "nsg:imageCount",
+                "name": "Image count",
+                "description": "Number of images in the series",
+                "datatype": "xsd:integer",
+                "minCount": 1,
+                "maxCount": 1
+              },
+              {
+                "path": "nsg:frameRate",
+                "name": "Frame rate",
+                "description": "Frame rate of data",
+                "node": "{{base}}/schemas/neurosciencegraph/commons/quantitativevalue/v0.1.0/shapes/QuantitativeValueShape",
+                "maxCount": 1
+              },
+              {
+                "path": "prov:wasGeneratedBy",
+                "name": "Was generated by",
+                "description": "Optophysiology experiment that generated trace",
+                "class": "nsg:TwoPhotonImaging",
+                "minCount": 1,
+                "maxCount": 1
+              }
+            ]
+          }
+        ]
+      }
+    ]
+  }

modules/optophysiology/src/main/resources/schemas/neurosciencegraph/optophysiology/motioncorrection/v0.1.0.json

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+{
+    "@context": [
+      "{{base}}/contexts/neurosciencegraph/core/schema/v0.1.0",
+      {
+        "this": "{{base}}/schemas/neurosciencegraph/optophysiology/motioncorrection/v0.1.0/shapes/"
+      }
+    ],
+    "imports": [
+      "{{base}}/schemas/neurosciencegraph/commons/activity/v0.1.4"
+    ],
+    "@type": "nxv:Schema",
+    "shapes": [
+      {
+        "@id": "this:MotionCorrectionShape",
+        "@type": "sh:NodeShape",
+        "label": "Motion correction shape definition",
+        "description": "Correction for x-y movement in image frames.",
+        "nodeKind": "sh:BlankNodeOrIRI",
+        "targetClass": "nsg:MotionCorrection",
+        "and": [
+          {
+            "node": "{{base}}/schemas/neurosciencegraph/commons/activity/v0.1.4/shapes/ActivityShape"
+          },
+          {
+            "property": [
+              {
+                "path": "prov:used",
+                "name": "Before",
+                "description": "The image sequence used",
+                "class": "nsg:ImageSequence",
+                "minCount": 1
+              },
+              {
+                "path": "prov:generated",
+                "name": "After",
+                "description": "The corrected image sequence generated",
+                "class": "nsg:ImageSequence",
+                "minCount": 1
+              }
+            ]
+          }
+        ]
+      }
+    ]
+  }