create extension spec

spec/ndx-fiber-photometry.extensions.yaml

@@ -1,8 +1,176 @@
 groups:
-- neurodata_type_def: TetrodeSeries
-  neurodata_type_inc: ElectricalSeries
-  doc: An extension of ElectricalSeries to include the tetrode ID for each time series.
+- neurodata_type_def: OpticalFiber
+  neurodata_type_inc: Device
+  name: fiber
+  doc: Extends Device to hold metadata on the Optica Fiber.
   attributes:
-  - name: trode_id
-    dtype: int32
-    doc: The tetrode ID.
+  - name: model
+    dtype: text
+    doc: Model of optical fiber.
+    required: false
+  - name: numerical_aperture
+    dtype: float
+    doc: Numerical aperture, e.g., 0.39 NA.
+    required: false
+- neurodata_type_def: ExcitationSource
+  neurodata_type_inc: Device
+  name: excitation_source
+  doc: Extends Device to hold metadata on the Excitation Source.
+  attributes:
+  - name: model
+    dtype: text
+    doc: Model of excitation source device.
+    required: false
+  - name: illumination_type
+    dtype: text
+    doc: Illumination type, e.g., laser ot LED.
+  - name: excitation_wavelength_in_nm
+    dtype: float
+    doc: Excitation wavelength of the stimulation light (nanometers).
+- neurodata_type_def: Photodetector
+  neurodata_type_inc: Device
+  name: excitation_source
+  doc: Extends Device to hold metadata on the Excitation Source.
+  attributes:
+  - name: model
+    dtype: text
+    doc: Model of excitation source device.
+    required: false
+  - name: detector_type
+    dtype: text
+    doc: Technology used to detect the light, e.g., PMT or photodiode.
+  - name: detected_wavelength_in_nm
+    dtype: float
+    doc: Wavelength detected by photodetector.
+  - name: gain
+    dtype: float
+    doc: Gain on the photodetector.
+- neurodata_type_def: DichroicMirror
+  neurodata_type_inc: Device
+  doc: Extends Device to hold a Dichroic Mirror.
+  attributes:
+  - name: cut_on_wavelength_in_nm
+    dtype: float
+    doc: Wavelength at which the mirror starts to transmit light more than reflect.
+  - name: cut_off_wavelength_in_nm
+    dtype: float
+    doc: Wavelength at which transmission shifts back to reflection, for mirrors with
+      complex transmission spectra.
+    required: false
+  - name: reflection_bandwidth_in_nm
+    dtype: float
+    shape:
+    - 2
+    doc: The range of wavelengths that are primarily reflected. The start and end
+      wavelengths needs to be specified.
+    required: false
+  - name: transmission_bandwidth_in_nm
+    dtype: float
+    shape:
+    - 2
+    doc: The range of wavelengths that are primarily transmitted. The start and end
+      wavelengths needs to be specified.
+    required: false
+  - name: angle_of_incidence_in_degrees
+    dtype: float
+    doc: Intended angle at which light strikes the mirror.
+    required: false
+  - name: model
+    dtype: text
+    doc: Model of the dichroic mirror.
+    required: false
+- neurodata_type_def: OpticalFilter
+  neurodata_type_inc: Device
+  doc: Extends Device to hold a Optical Filter.
+  attributes:
+  - name: peak_wavelength_in_nm
+    dtype: float
+    doc: Wavelength that the filter is designed to pass or reflect.
+  - name: bandwidth_in_nm
+    dtype: float
+    doc: Width of the wavelength range that the filter allows to pass through or blocks.
+  - name: filter_type
+    dtype: text
+    doc: Type of filter (e.g., 'Excitation', 'Emission', 'Bandpass', 'Longpass', 'Shortpass').
+  - name: model
+    dtype: text
+    doc: Model of the optical filter.
+    required: false
+- neurodata_type_def: FiberPhotometryTable
+  neurodata_type_inc: DynamicTable
+  name: fiber_photometry_table
+  doc: Extends DynamicTable to hold metadata on the Fiber Photometry system.
+  datasets:
+  - name: location
+    neurodata_type_inc: VectorData
+    dtype: text
+    shape:
+    - null
+    doc: Location of fiber.
+  - name: coordinates
+    neurodata_type_inc: VectorData
+    dtype: float
+    shape:
+    - null
+    - 3
+    doc: Fiber placement in stereotactic coordinates (AP, ML, DV) mm relative to Bregma.
+    quantity: '?'
+  - name: indicator
+    neurodata_type_inc: VectorData
+    dtype: text
+    shape:
+    - null
+    doc: Indicator notation.
+  - name: notes
+    neurodata_type_inc: VectorData
+    dtype: text
+    shape:
+    - null
+    doc: Description of system.
+    quantity: '?'
+  - name: fiber
+    neurodata_type_inc: VectorData
+    dtype:
+      target_type: Device
+      reftype: object
+    shape:
+    - null
+    doc: Link to the fiber device.
+  - name: excitation_source
+    neurodata_type_inc: VectorData
+    dtype:
+      target_type: Device
+      reftype: object
+    shape:
+    - null
+    doc: Link to the excitation source device.
+  - name: photodetector
+    neurodata_type_inc: VectorData
+    dtype:
+      target_type: Device
+      reftype: object
+    shape:
+    - null
+    doc: Link to the photodetector device.
+  - name: dichroic_mirror
+    neurodata_type_inc: VectorData
+    dtype:
+      target_type: Device
+      reftype: object
+    shape:
+    - null
+    doc: Link to the dichroic mirror device.
+- neurodata_type_def: FiberPhotometryResponseSeries
+  neurodata_type_inc: TimeSeries
+  doc: Extends TimeSeries to hold Fiber Photometry data.
+  datasets:
+  - name: data
+    shape:
+    - null
+    - null
+    doc: The data values. May be 1D or 2D. The first dimension must be time. The optional
+      second dimension referes to the fiber that record the series.
+  - name: fiber_photometry_table
+    neurodata_type_inc: DynamicTableRegion
+    doc: References row(s) of FiberPhotometryTable.
+    quantity: '?'

spec/ndx-fiber-photometry.namespace.yaml

@@ -5,11 +5,22 @@ namespaces:
   - Paul Adkisson
   - Szonja Weigl
   contact:
-  - [email protected]
+  - [email protected]
+  - [email protected]
+  - [email protected]
+  - [email protected]
   doc: This is an NWB extension for storing fiber photometry recordings and associated
     metadata.
   name: ndx-fiber-photometry
   schema:
   - namespace: core
+    neurodata_types:
+    - TimeSeries
+    - Device
+  - namespace: hdmf-common
+    neurodata_types:
+    - DynamicTable
+    - DynamicTableRegion
+    - VectorData
   - source: ndx-fiber-photometry.extensions.yaml
   version: 0.1.0