Add ophys devices from ndx-ophys-devices

README.md

@@ -36,8 +36,8 @@ classDiagram
         links
         --------------------------------------
         microscope : Microscope
-        light_source : MicroscopyLightSource
-        optical_channel : MicroscopyOpticalChannel
+        excitation_light_path : ExcitationLightPath
+        emission_light_path : EmissionLightPath
     }
 
     class PlanarMicroscopySeries {
@@ -86,6 +86,32 @@ classDiagram
         imaging_space : VolumetricImageSpace
     }
 
+    class MultiChannelMicroscopyVolume {
+        <<NWBDataInterface>>
+
+        --------------------------------------
+        attributes
+        --------------------------------------
+        description : text, optional
+        unit : text, optional
+        conversion : numeric, optional
+        offset : numeric, optional
+
+        --------------------------------------
+        datasets
+        --------------------------------------
+        data : numeric, frame x height x width x depth x emission_light_paths
+        --> unit : text
+        excitation_light_paths : ExcitationLightPath, excitation_light_paths
+        emission_light_paths : EmissionLightPath, emission_light_paths
+
+        --------------------------------------
+        links
+        --------------------------------------
+        imaging_space : VolumetricImageSpace
+        microscope : Microscope
+    }
+
     class ImagingSpace{
         <<NWBContainer>>
 
@@ -132,36 +158,34 @@ classDiagram
         reference_frame : text, optional
     }
 
-    class MicroscopyOpticalChannel{
+    class ExcitationLightPath{
         <<NWBContainer>>
 
         --------------------------------------
-        datasets
+        links
         --------------------------------------
-        description : text
+        excitation_source : ExcitationSource, optional
+        excitation_filter : OpticalFilter, optional
 
         --------------------------------------
         attributes
         --------------------------------------
-        indicator : text
-        filter_description : text, optional
-        emission_wavelength_in_nm : numeric, optional
+        excitation_wavelength_in_nm : numeric
     }
 
-    class MicroscopyLightSource{
-        <<Device>>
+    class EmissionLightPath{
+        <<NWBContainer>>
+
+        --------------------------------------
+        links
+        --------------------------------------
+        photodetector : Photodetector, optional
+        emission_filter : OpticalFilter, optional
 
         --------------------------------------
         attributes
         --------------------------------------
-        model : text, optional
-        filter_description : text, optional
-        excitation_wavelength_in_nm : numeric, optional
-        peak_power_in_W : numeric, optional
-        peak_pulse_energy_in_J : numeric, optional
-        intensity_in_W_per_m2 : numeric, optional
-        exposure_time_in_s : numeric, optional
-        pulse_rate_in_Hz : numeric, optional
+        emission_wavelength_in_nm : numeric
     }
 
     class Microscope{
@@ -182,8 +206,8 @@ classDiagram
     PlanarImagingSpace *-- ImagingSpace : extends
     VolumetricImagingSpace *-- ImagingSpace : extends
     MicroscopySeries ..> Microscope : links
-    MicroscopySeries ..> MicroscopyLightSource : links
-    MicroscopySeries ..> MicroscopyOpticalChannel : links
+    MicroscopySeries ..> ExcitationLightPath : links
+    MicroscopySeries ..> EmissionLightPath : links
 ```
 
 ---

requirements-min.txt

@@ -1 +1,3 @@
 pynwb
+git+https://github.com/catalystneuro/ndx-ophys-devices.git@main#egg=ndx-ophys-devices
+

spec/ndx-microscopy.extensions.yaml

@@ -6,67 +6,45 @@ groups:
     attributes:
       - name: model
         dtype: text
-        doc: Model identifier of the light source device.
+        doc: Model identifier of the microscope.
         required: false
 
-  - neurodata_type_def: MicroscopyLightSource
-    neurodata_type_inc: Device
-    doc: Light source used to illuminate an imaging space.
+  - neurodata_type_def: ExcitationLightPath
+    neurodata_type_inc: NWBContainer
+    doc: Excitation light path that illuminates an imaging space.
     attributes:
-      - name: model
-        dtype: text
-        doc: Model identifier of the light source device.
-        required: false
-      - name: filter_description
-        dtype: text
-        doc: Filter used to obtain the excitation wavelength of light, e.g. 'Short pass at 1040 nm'.
-        required: false
       - name: excitation_wavelength_in_nm
         dtype: numeric
         doc: Excitation wavelength of light, in nanometers.
+    links:
+      - name: excitation_source
+        target_type: ExcitationSource
+        doc: Link to ExcitationSource object which contains metadata about the excitation source device. If it is a pulsed excitation source link a PulsedExcitationSource object.
         required: false
-      - name: peak_power_in_W
-        dtype: numeric
-        doc: Incident power of stimulation device (in Watts).
-        required: false
-      - name: peak_pulse_energy_in_J
-        dtype: numeric
-        doc: If device is pulsed light source, pulse energy (in Joules).
-        required: false
-      - name: intensity_in_W_per_m2
-        dtype: numeric
-        doc: Intensity of the excitation in W/m^2, if known.
+      - name: excitation_filter
+        target_type: OpticalFilter
+        doc: Link to OpticalFilter object which contains metadata about the optical filter in this excitation light path. It can be either a BandOpticalFilter (e.g., 'Bandpass', 'Bandstop', 'Longpass', 'Shortpass') or a EdgeOpticalFilter (Longpass or Shortpass).
         required: false
-      - name: exposure_time_in_s
+
+  - neurodata_type_def: EmissionLightPath
+    neurodata_type_inc: NWBContainer
+    doc: Emission light path from an imaging space.
+    attributes:
+      - name: emission_wavelength_in_nm
         dtype: numeric
-        doc: Exposure time of the sample (in sec).
+        doc: Emission wavelength of light, in nanometers.
+    links:
+      - name: photodetector
+        target_type: Photodetector
+        doc: Link to Photodetector object which contains metadata about the photodetector device.
         required: false
-      - name: pulse_rate_in_Hz
-        dtype: numeric
-        doc: If device is pulsed light source, pulse rate (in Hz) used for stimulation.
+      - name: emission_filter
+        target_type: OpticalFilter
+        doc: Link to OpticalFilter object which contains metadata about the optical filter in this emission light path. It can be either a BandOpticalFilter (e.g., 'Bandpass', 'Bandstop', 'Longpass', 'Shortpass') or a EdgeOpticalFilter (Longpass or Shortpass).
         required: false
-
-  # Microscopy is added on to this only to differentiate from the OpticalChannel in the core namespace
-  # It would be removed when this structure is merged to core
-  - neurodata_type_def: MicroscopyOpticalChannel
-    neurodata_type_inc: LabMetaData  # Would prefer basic NWBContainer
-    doc: An optical channel used to filter light emission from an imaging space.
-    datasets:
-    - name: description
-      doc: Description or other notes about the channel.
-      dtype: text
-    attributes:
-    - name: indicator
-      doc: Identifier for the indicator pertaining to this optical channel.
-      dtype: text
-    - name: filter_description
-      doc: Metadata information about the filter used by this optical channel.
-      dtype: text
-      required: false
-    - name: emission_wavelength_in_nm
-      doc: Emission wavelength for this optical channel, in nanometers.
-      dtype: numeric
-      required: false
+      - name: indicator
+        target_type: Indicator
+        doc: Link to Indicator object which contains metadata about the indicator used in this light path.
 
   - neurodata_type_def: ImagingSpace
     neurodata_type_inc: LabMetaData  # Would prefer basic NWBContainer
@@ -97,10 +75,6 @@ groups:
         Use standard atlas names for anatomical regions when possible.
         Specify 'whole brain' if the entire brain is strictly contained within the space.
       required: false
-    links:
-    - name: microscope
-      target_type: Microscope
-      doc: Link to Microscope object which contains metadata about the device which imaged this space.
 
   - neurodata_type_def: PlanarImagingSpace
     neurodata_type_inc: ImagingSpace
@@ -273,13 +247,13 @@ groups:
     - name: microscope
       doc: Link to a Microscope object containing metadata about the device used to acquire this imaging data.
       target_type: Microscope
-    - name: light_source
-      doc: Link to a MicroscopyLightSource object containing metadata about the device used to illuminate the imaging space.
-      target_type: MicroscopyLightSource
-    - name: optical_channel
-      doc: Link to a MicroscopyOpticalChannel object containing metadata about the indicator and filters used to collect
+    - name: excitation_light_path
+      doc: Link to a ExcitationLightPath object containing metadata about the device used to illuminate the imaging space.
+      target_type: ExcitationLightPath
+    - name: emission_light_path
+      doc: Link to a EmissionLightPath object containing metadata about the indicator and filters used to collect
         this data.
-      target_type: MicroscopyOpticalChannel
+      target_type: EmissionLightPath
 
   - neurodata_type_def: PlanarMicroscopySeries
     neurodata_type_inc: MicroscopySeries
@@ -386,30 +360,30 @@ groups:
       - height
       - width
       - depths
-      - optical_channels
+      - emission_light_paths
       shape:
       - null
       - null
       - null
       - null
-    - name: light_sources
-      doc: An ordered list of references to MicroscopyLightSource objects containing metadata about the excitation methods.
+    - name: excitation_light_paths
+      doc: An ordered list of references to ExcitationLightPath objects containing metadata about the excitation methods.
       neurodata_type_inc: VectorData
       dtype:
         reftype: object
-        target_type: MicroscopyLightSource
+        target_type: ExcitationLightPath
       dims:
-        - light_sources
+        - excitation_light_paths
       shape:
         - null
-    - name: optical_channels
-      doc: An ordered list of references to MicroscopyOpticalChannel objects containing metadata about the indicator and filters used to collect this data. This maps to the last dimension of `data`, i.e., the i-th MicroscopyOpticalChannel contains metadata about the indicator and filters used to collect the volume at `data[:,:,:,i]`.
+    - name: emission_light_paths
+      doc: An ordered list of references to EmissionLightPath objects containing metadata about the indicator and filters used to collect this data. This maps to the last dimension of `data`, i.e., the i-th MicroscopyOpticalChannel contains metadata about the indicator and filters used to collect the volume at `data[:,:,:,i]`.
       neurodata_type_inc: VectorData
       dtype:
         reftype: object
-        target_type: MicroscopyOpticalChannel
+        target_type: EmissionLightPath
       dims:
-        - optical_channels
+        - emission_light_paths
       shape:
         - null
     links:
@@ -478,24 +452,24 @@ groups:
       - depths
       shape:
       - null
-    - name: light_sources
-      doc: An ordered list of references to MicroscopyLightSource objects containing metadata about the excitation methods.
+    - name: excitation_light_paths
+      doc: An ordered list of references to ExcitationLightPath objects containing metadata about the excitation methods.
       neurodata_type_inc: VectorData
       dtype:
         reftype: object
-        target_type: MicroscopyLightSource
+        target_type: ExcitationLightPath
       dims:
-        - light_sources
+        - excitation_light_paths
       shape:
         - null
-    - name: optical_channels
-      doc: An ordered list of references to MicroscopyOpticalChannel objects containing metadata about the indicator and filters used to collect this data. This maps to the last dimension of `data`, i.e., the i-th MicroscopyOpticalChannel contains metadata about the indicator and filters used to collect the volume at `data[:,:,:,i]`.
+    - name: emission_light_paths
+      doc: An ordered list of references to EmissionLightPath objects containing metadata about the indicator and filters used to collect this data. This maps to the last dimension of `data`, i.e., the i-th MicroscopyOpticalChannel contains metadata about the indicator and filters used to collect the volume at `data[:,:,:,i]`.
       neurodata_type_inc: VectorData
       dtype:
         reftype: object
-        target_type: MicroscopyOpticalChannel
+        target_type: EmissionLightPath
       dims:
-        - optical_channels
+        - emission_light_paths
       shape:
         - null
     links:

spec/ndx-microscopy.namespace.yaml

@@ -9,5 +9,6 @@ namespaces:
   - [email protected]
   schema:
   - namespace: core
+  - namespace: ndx-ophys-devices
   - source: ndx-microscopy.extensions.yaml
   version: 0.1.0

src/pynwb/ndx_microscopy/__init__.py

@@ -1,7 +1,7 @@
 import os
 
 from pynwb import get_class, load_namespaces
-
+from pynwb.spec import NWBNamespaceBuilder
 try:
     from importlib.resources import files
 except ImportError:
@@ -19,10 +19,11 @@
     __spec_path = __location_of_this_file.parent.parent.parent / "spec" / f"{extension_name}.namespace.yaml"
 
 load_namespaces(str(__spec_path))
+from ndx_ophys_devices import ExcitationSource, Indicator, OpticalFilter, Photodetector
 
 Microscope = get_class("Microscope", extension_name)
-MicroscopyLightSource = get_class("MicroscopyLightSource", extension_name)
-MicroscopyOpticalChannel = get_class("MicroscopyOpticalChannel", extension_name)
+ExcitationLightPath = get_class("ExcitationLightPath", extension_name)
+EmissionLightPath = get_class("EmissionLightPath", extension_name)
 ImagingSpace = get_class("ImagingSpace", extension_name)
 PlanarImagingSpace = get_class("PlanarImagingSpace", extension_name)
 VolumetricImagingSpace = get_class("VolumetricImagingSpace", extension_name)
@@ -40,9 +41,11 @@
 
 
 __all__ = [
+    "OpticalFilter",
+    "ExcitationSource",
+    "Indicator",
+    "Photodetector",
     "Microscope",
-    "MicroscopyLightSource",
-    "MicroscopyOpticalChannel",
     "ImagingSpace",
     "PlanarImagingSpace",
     "VolumetricImagingSpace",

src/pynwb/ndx_microscopy/testing/__init__.py

@@ -1,7 +1,7 @@
 from ._mock import (
+    mock_EmissionLightPath,
+    mock_ExcitationLightPath,
     mock_Microscope,
-    mock_MicroscopyLightSource,
-    mock_MicroscopyOpticalChannel,
     mock_MicroscopyPlaneSegmentation,
     mock_MicroscopyResponseSeries,
     mock_MicroscopyResponseSeriesContainer,
@@ -17,8 +17,8 @@
 
 __all__ = [
     "mock_Microscope",
-    "mock_MicroscopyLightSource",
-    "mock_MicroscopyOpticalChannel",
+    "mock_ExcitationLightPath",
+    "mock_EmissionLightPath",
     "mock_PlanarImagingSpace",
     "mock_VolumetricImagingSpace",
     "mock_MicroscopySegmentations",