V1 microscopy schemas

schemas/fluorescentIndicator.tpl.json → schemas/activity/fluorescentIndicator.tpl.json

@@ -25,7 +25,7 @@
         },
         "onKinetics": {
             "_instruction": "Add rise time (on-kinetics) of fluorescence after calcium binding, typically in milliseconds.",
-            "_linkedCategories": "core:QuantitativeValue", 
+            "_linkedCategories": "core:QuantitativeValue"
         },
         "offKinetics": {
             "_instruction": "Add decay time (off-kinetics) of fluorescence after calcium unbinding, typically in milliseconds.",

schemas/activity/ophysAcquisition.tpl.json

@@ -0,0 +1,64 @@
+{
+    "_type": "microscopy: ophysAcquisition",
+    "_extends": "/core/schemas/research/experimentalAcitivity.schema.tpl.json", 
+    "required": [
+        "imagingMode",
+        "setup",
+        "frameRate",
+        "fieldOfView", 
+        "pixelSize"
+    ],
+    "properties": {
+        "imagingMode": {
+            "type": "string",
+            "_instruction": "Enter optical imaging modality used during acquisition.", 
+            "_linkedCategories": "controlledTerms:?" 
+        }, 
+        "setup": {
+            "_instruction": "Add classification of the indicator.",
+            "_linkedCategories": [
+                "microscopy:OphysDevice", 
+                "microscopy:OphysDeviceUsage"
+            ]
+        },
+        "frameRate": {
+            "_instruction": "Add imaging frame rate corresponding to the number of frames acquired per second",
+            "_linkedCategories": "core:QuantitativeValue" 
+        },
+        "fieldOfView": {
+            "_instruction": "Add spatial extent of the umaged region in micrometers.",
+            "_linkedCategories": "sands:mathematicalShapes"
+        },
+        "pixelSize": {
+            "_instruction": "Add effective sampling size of each pixel along x, y, (and optional z) dimensions in micrometers.",
+            "_linkedCategories": [
+                "core:QuantitativeValueArray", 
+                "core: optional z ? "
+            ]
+        }, 
+        "scanPattern": {
+            "_instruction": "Add scanner pattern to traverse the sample.",
+            "_linkedCategories": "controlledTerms:?"
+        },
+        "scanningMode": {
+            "_instruction": "Add scanner mechanism or readout type.",
+            "_linkedCategories": "controlledTerms:?"
+        },
+        "zoomFactor": {
+            "type": "float",
+            "_instruction": "Add dimensionless zoom setting applied on the microscope optics (affects FOV and pixel size)."
+        },
+        "numberOfPlane": {
+            "type": "integer",
+            "_instruction": "Number of imaging planes or mulpiplane or volumetric imaging acquired in one session."
+        },
+        "planeSepraration": {
+            "_instruction": "Add distance between sucessive imaging planes in micrometer (µm).",
+            "_linkedCategories": "core:QuantitativeValue"
+        },
+        "filterWheelPositions": {
+            "_instruction": "Add filter or emission bands selected during the acquisition (e.g., 525/50 nm)",
+            "_linkedCategories": "array of strings ?"
+        }
+    }
+}

schemas/device/OphysSetup.tpl.json

@@ -0,0 +1,13 @@
+{
+    "_type": "microscopy: ophysSetup",
+    "_extends": "/core/schemas/research/device.schema.tpl.json", 
+    "required": [
+        "hasPart"
+    ],
+    "properties": {
+        "hasPart": {
+            "_instruction": "Add all components, including other setups, that are part of this optical setup.", 
+            "_linkedCategories": "opticalSetupComponents" 
+        }
+    }
+}

schemas/device/detector.tpl.json

@@ -0,0 +1,23 @@
+{
+    "_type": "microscopy: detector",
+    "_extends": "/core/schemas/research/device.schema.tpl.json", 
+    "required": [
+        "quantumEfficiency",
+        "bitDepth"
+   ],
+    "properties": {
+        "quantumEfficiency": {
+            "type": "float",
+            "_instruction": "Enter fraction of photons detected at peak wavelength (0-1 or %)"
+        }, 
+        "bitDepth": {
+            "type": "integer",
+            "_instruction": "Add bit depth of the detector's analog-to-digital conversion."
+        },
+        "readNoise": {
+            "type": "float",
+            "_instruction": "Add read-out noise of the detector, usually in electron microscope (rms)."
+        }
+
+    }
+}

schemas/device/detectorUsage.tpl.json

@@ -0,0 +1,11 @@
+{
+    "_type": "microscopy: detectorUsage",
+    "_extends": "/core/schemas/research/deviceUsage.schema.tpl.json", 
+    "required": [],
+    "properties": {
+        "detectorGains": {
+            "_instruction": "Add gain or sensitivity settings applied to the detector(s) during acquisition (e.g., PMT voltage in volts, sCMOS gain in arbitrary units). Values should be reported per channel if multiple detectors are used.",
+            "_linkedCategories": "core:QuantitativeValue" 
+        }  
+    }
+}

schemas/device/grinLens.tpl.json

@@ -0,0 +1,23 @@
+{
+    "_type": "microscopy: grinLens",
+    "_extends": "/core/schemas/research/device.schema.tpl.json", 
+    "required": "lensDiameter",
+    "properties": {
+        "lensDiameter": {
+            "_instruction": "Add rod diameter.",
+            "_linkedCategories": "core:QuantitativeValue" 
+        },
+        "lensLength": {
+            "_instruction": "Add length of lens.",
+            "_linkedCategories": "core:QuantitativeValue"
+        },
+        "FOVAtDepth": {
+            "_instruction": "Add field of view achievable at imaging depth.",
+            "_linkedCategories": "core:QuantitativeValue" 
+        },
+        "tipShape": {
+            "_instruction": "Add tipshape",
+            "_linkedCategories": "controlledterms:?" 
+        }
+    }
+}

schemas/device/grinLensUsage.tpl.json

@@ -0,0 +1,6 @@
+{
+    "_type": "microscopy: grinLensUsage",
+    "_extends": "/core/schemas/research/deviceUsage.schema.tpl.json", 
+    "required": "",
+    "properties": {}
+}

schemas/device/laser.tpl.json

@@ -0,0 +1,25 @@
+{
+    "_type": "microscopy: LaserUsage",
+    "_extends": "/core/schemas/research/device.schema.tpl.json", 
+    "required": [
+        "excitationPeak"
+    ],
+    "properties": {
+        "excitationPeak": {
+            "_instruction": "Add peak excitation wavelength in nanometers.",
+            "_linkedCategories": "core:QuantitativeValue" 
+        },
+        "tunable": {
+            "_instruction": "Indicates if the source is tunable across wavelengths.",
+            "_linkedCategories": "boolean" 
+        },
+        "pulseWidth": {
+            "_instruction": "Add pulse width (duration) of source if pulsed, in femtoseconds (fs).",
+            "_linkedCategories": "core:QuantitativeValue" 
+        },
+        "repRate": {
+            "_instruction": "Add repetition rate of the pulsed source in megahertz (MHz).",
+            "_linkedCategories": "core:QuantitativeValue" 
+        }
+    }
+}

schemas/device/laserUsage.tpl.json

@@ -0,0 +1,15 @@
+{
+    "_type": "microscopy: LaserUsage",
+    "_extends": "/core/schemas/research/deviceUsage.schema.tpl.json", 
+    "required": [],
+    "properties": {
+        "wavelengthExcitation": {
+            "_instruction": "Add excitation wavelength(s) actually used during the acquisition, expressed in nanometers.",
+            "_linkedCategories": "core:QuantitativeValue" 
+        },
+        "laserPowerAtSample": {
+            "_instruction": "Add optical power delivered to the sample at the excitation wavelength, typically reported as median or range, in milliwatts.",
+            "_linkedCategories": "core:QuantitativeValueArray" 
+        }  
+    }
+}

schemas/device/microprism.tpl.json

@@ -0,0 +1,39 @@
+{
+    "_type": "microscopy: microprism",
+    "_extends": "/core/schemas/research/device.schema.tpl.json", 
+    "required": [
+        "dimensions", 
+        "prismAngleDeg",
+        "orientation"
+    ],
+    "properties": {
+        "material": {
+            "_instruction": "Add microprism optical material.",
+            "_linkedCategories": "chemicals:chemicalMixture" 
+        },
+        "dimensions": {
+            "_instruction": "Add edge/face dimensions of the prism.",
+            "_linkedCategories": "?" 
+        },
+        "prismAngleDeg": {
+            "_instruction": "Add apex or right angle spec.",
+            "_linkedCategories": "core:QuantitativeValue" 
+        },
+        "orientation": {
+            "type": "string",
+            "_instruction": "Add orientation of reflective face vs cortical layers"
+        },
+        "distanceFromSurface": {
+            "_instruction": "Add distance between prism face and pial surface (move to device implantion)",
+            "_linkedCategories": "core:QuantitativeValue" 
+        },
+        "tissueReliefCuts": {
+            "_instruction": "Indicate the presence of relief cuts.",
+            "_linkedCategories": "boolean" 
+        },
+        "edgePolishQuality": {
+            "type": "string",
+            "_instruction": "Add quality spec of polished edges."
+        }
+    }
+}

schemas/device/microprismUsage.tpl.json

@@ -0,0 +1,11 @@
+{
+    "_type": "microscopy: microprismUsage",
+    "_extends": "/core/schemas/research/deivceUsage.schema.tpl.json", 
+    "required": [],
+    "properties": {
+        "opticalInterfaceMedium": {
+            "_instruction": "Add medium between prism face and tissue.",
+            "_linkedCategories": "chemicals:chemicalMixture" 
+        }
+    }
+}

schemas/device/objectiveLens.tpl.json

@@ -0,0 +1,24 @@
+{
+    "_type": "microscopy: objectiveLens",
+    "_extends": "/core/schemas/research/device.schema.tpl.json", 
+    "required": [
+        "magnification",
+        "numericalAperture"
+    ],
+    "properties": {
+        "magnification": {
+            "type": "string",
+            "_instruction": "Add nominal magnification of the objective (e.g., 16x, 20x)."
+        },
+        "numericalAperture": {
+            "type": "float",
+            "minItems": 0,
+            "maxItems": 2,
+            "_instruction": "Add numerical aperture indicating light-gathering ability (NA=n⋅sin(θ))."
+        },
+        "workingDistance": {
+            "_instruction": "Add working distance of the lens, typically in millimeters.",
+            "_linkedCategories": "core:QuantitativeValue" 
+        }
+    }
+}

schemas/device/objectiveLensUsage.tpl.json

@@ -0,0 +1,19 @@
+{
+    "_type": "microscopy: objectiveLensUsage",
+    "_extends": "/core/schemas/research/deviceUsage.schema.tpl.json", 
+    "required": [
+        "immersionMedium ?"
+    ],
+    "properties": {
+        "immersionMedium": {
+            "_instruction": "Add immersion medium between lens and sample (air, water, oil...).",
+            "_linkedCategories": "chemicals:chemicalMixture"
+
+        },
+        "correctionCollar": {
+            "_instruction": "Add setting of the objective lens correction collar, used to compensate for coverslip thickness or spherical aberrations. Typically given in millimeters.",
+            "_linkedCategories": "core:QuantitativeValue"
+
+        }
+    }
+}