Create extension spec

notebooks/metadata_example.yaml

@@ -0,0 +1,74 @@
+NWBFile:
+  session_description: Description.
+  session_start_time: 2000-07-23T00:00:00-07:00
+  institution: My University
+  lab: My Lab
+  experimenter:
+    - Last, First Middle
+Subject:
+  subject_id: subid012345
+  genotype: not defined
+  description: not defined
+  species: Mus musculus
+  date_of_birth: 2023-03-17T00:00:00
+  sex: F
+Ophys:
+  FiberPhotometry:
+    FiberPhotometryTable:
+      location: Location of this fiber
+      coordinates: [0.0, 0.0, 0.0] # Fiber placement stereotactic coordinates in (AP, ML, DV) in mm relative to Bregma
+      notes: extra notes
+    OpticalFibers:
+      - name: fiber0
+        description: fiber0 description
+        manufacturer: fiber0 manufacturer
+        model: fiber0 model
+        numerical_aperture: 0.2
+    ExcitationSources:
+      - name: laser0
+        description: laser0 description
+        manufacturer: laser0 manufacturer
+        model: laser0 model
+        illumination_type: laser # LED or laser
+        excitation_wavelength_in_nm: 465.0
+    Photodetectors:
+      - name: photodetector0
+        description: photodetector0 description
+        manufacturer: photodetector0 manufacturer
+        model: photodetector0 model
+        detector_type: PMT # PMT or photodiode
+        detected_wavelength_in_nm: 500.0
+    OpticalFilters:
+      - name: filter0
+        description: filter0 description
+        manufacturer: filter0 manufacturer
+        model: filter0 model
+        peak_wavelength_in_nm: 465.0
+        bandwidth_in_nm: 20.0
+        filter_type: Excitation
+      - name: filter1
+        description: filter1 description
+        manufacturer: filter1 manufacturer
+        model: filter1 model
+        peak_wavelength_in_nm: 500.0
+        bandwidth_in_nm: 20.0
+        filter_type: Emission
+    DichroicMirrors:
+      - name: dichroic0
+        description: dichroic0 description
+        manufacturer: dichroic0 manufacturer
+        model: dichroic0 model
+        cut_on_wavelength_in_nm: 465.0
+        cut_off_wavelength_in_nm: 500.0
+    Indicator:
+      - name: indicator0
+        label: dlight
+        location: VTA
+        emission_peak_wavelength: 500.0
+        excitation_peak_wavelength: 465.0
+        coordinates: [0.0, 0.0, 0.0] # Fluorophore injection site in taxonomical coordinates in (AP, ML, Z) in mm relative to Bregma
+    FiberPhotometryResponseSeries:
+      - name: _405A
+        description: isosbestic signal
+        unit: F
+        fiber_photometry_table_region: [0]

spec/ndx-fiber-photometry.extensions.yaml

@@ -1,8 +1,249 @@
 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: Indicator
+  neurodata_type_inc: Device
+  doc: Extends Device to hold metadata on the Indicator.
   attributes:
-  - name: trode_id
-    dtype: int32
-    doc: The tetrode ID.
+  - name: label
+    dtype: text
+    doc: Indicator standard notation.
+  - name: injection_location
+    dtype: text
+    doc: Injection brain region name.
+    required: false
+  - name: injection_coordinates_in_mm
+    dtype: float
+    shape:
+    - 3
+    doc: Indicator injection location in stereotactic coordinates (AP, ML, DV) mm
+      relative to Bregma.
+    required: false
+- neurodata_type_def: OpticalFiber
+  neurodata_type_inc: Device
+  doc: Extends Device to hold metadata on the Optical Fiber.
+  attributes:
+  - 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
+  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 or LED.
+  - name: excitation_wavelength_in_nm
+    dtype: float
+    doc: Excitation wavelength of the stimulation light (nanometers).
+- neurodata_type_def: Photodetector
+  neurodata_type_inc: Device
+  doc: Extends Device to hold metadata on the Photodetector.
+  attributes:
+  - name: model
+    dtype: text
+    doc: Model of photodetector 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
+    shape:
+    - 2
+    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
+  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: '?'
+    attributes:
+    - name: unit
+      dtype: text
+      value: millimeters
+      doc: coordinates unit
+  - name: indicator
+    neurodata_type_inc: VectorData
+    dtype:
+      target_type: Device
+      reftype: object
+    shape:
+    - null
+    doc: Link to the indicator object.
+  - name: notes
+    neurodata_type_inc: VectorData
+    dtype: text
+    shape:
+    - null
+    doc: Description of system.
+    quantity: '?'
+  - name: optical_fiber
+    neurodata_type_inc: VectorData
+    dtype:
+      target_type: Device
+      reftype: object
+    shape:
+    - null
+    doc: Link to the optical 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: commanded_voltage_series
+    neurodata_type_inc: VectorData
+    dtype:
+      target_type: TimeSeries
+      reftype: object
+    shape:
+    - null
+    - null
+    doc: Link to the commanded voltage series.
+  - 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.
+  - name: emission_filter
+    neurodata_type_inc: VectorData
+    dtype:
+      target_type: Device
+      reftype: object
+    shape:
+    - null
+    doc: Link to the emission filter device.
+    quantity: '?'
+  - name: excitation_filter
+    neurodata_type_inc: VectorData
+    dtype:
+      target_type: Device
+      reftype: object
+    shape:
+    - null
+    doc: Link to the excitation filter device.
+    quantity: '?'
+- 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 refers to the fiber that record the series.
+  - name: fiber_photometry_table_region
+    neurodata_type_inc: DynamicTableRegion
+    doc: References row(s) of FiberPhotometryTable.
+    quantity: '?'
+- neurodata_type_def: CommandedVoltageSeries
+  neurodata_type_inc: TimeSeries
+  doc: Extends TimeSeries to hold a Commanded Voltage
+  datasets:
+  - name: data
+    dtype: float
+    shape:
+    - null
+    doc: Voltages (length number timesteps) in unit volts.
+    attributes:
+    - name: unit
+      dtype: text
+      value: volts
+      doc: data unit
+  - name: frequency
+    dtype: float
+    doc: Voltage frequency in unit hertz.
+    quantity: '?'
+    attributes:
+    - name: unit
+      dtype: text
+      value: hertz
+      doc: frequency unit

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

src/pynwb/ndx_fiber_photometry/__init__.py

@@ -22,7 +22,16 @@
 # Either have PyNWB generate a class from the spec using `get_class` as shown
 # below or write a custom class and register it using the class decorator
 # `@register_class("TetrodeSeries", "ndx-fiber-photometry")`
-TetrodeSeries = get_class("TetrodeSeries", "ndx-fiber-photometry")
+Indicator = get_class("Indicator", "ndx-fiber-photometry")
+OpticalFiber = get_class("OpticalFiber", "ndx-fiber-photometry")
+ExcitationSource = get_class("ExcitationSource", "ndx-fiber-photometry")
+Photodetector = get_class("Photodetector", "ndx-fiber-photometry")
+DichroicMirror = get_class("DichroicMirror", "ndx-fiber-photometry")
+OpticalFilter = get_class("OpticalFilter", "ndx-fiber-photometry")
+FiberPhotometryTable = get_class("FiberPhotometryTable", "ndx-fiber-photometry")
+FiberPhotometryResponseSeries = get_class("FiberPhotometryResponseSeries", "ndx-fiber-photometry")
+CommandedVoltageSeries = get_class("CommandedVoltageSeries", "ndx-fiber-photometry")
+
 
 # NOTE: `widgets/tetrode_series_widget.py` adds a "widget"
 # attribute to the TetrodeSeries class. This attribute is used by NWBWidgets.