1. ndx-ophys-devices

Version alpha Sep 19, 2025

1.1. Format Overview

1.1.1. ndx-ophys-devices

  • Description: This is an NWB extension for storing metadata of devices used in optical experimental setup (microscopy, fiber photometry, optogenetic stimulation etc.)

  • Name: ndx-ophys-devices

  • Version: 0.3.1

  • Authors:

    • Alessandra Trapani

  • Contacts:
  • Schema:

    • namespace: core

    • neurodata_types: [‘Device’, ‘DeviceModel’]

    • source: ndx-ophys-devices.extensions.yaml

1.1.2. Type Hierarchy

1.2. Type Specifications

1.2.1. ndx-ophys-devices.extensions.yaml

1.2.1.1. ExcitationSourceModel

Overview: Extends DeviceModel to hold metadata on the Excitation Source Model.

ExcitationSourceModel extends DeviceModel and includes all elements of DeviceModel with the following additions or changes.

  • Extends: DeviceModel

  • Primitive Type: Group

  • Inherits from: DeviceModel, NWBContainer, Container

  • Source filename: ndx-ophys-devices.extensions.yaml

  • Source Specification: see Section 1.3.2.1

ExcitationSourceModel
Table 1.1 Datasets, Links, and Attributes contained in <ExcitationSourceModel>

Id

Type

Description

<ExcitationSourceModel>

Group

Top level Group for <ExcitationSourceModel>

.source_type

Attribute

Type of source. Suggested values: LED, Gas Laser (e.g., Argon, Krypton), Solid-State Laser (e.g., Diode, DPSS).

  • Data Type: text

  • Name: source_type

.excitation_mode

Attribute

The type of excitation used in the light path (e.g., ‘one-photon’, ‘two-photon’, ‘three-photon’, ‘other’).

  • Data Type: text

  • Name: excitation_mode

.wavelength_range_in_nm

Attribute

The range of wavelengths that can be produced by the source.

  • Data Type: float

  • Shape: [2]

  • Required: False

  • Name: wavelength_range_in_nm

1.2.1.2. ExcitationSource

Overview: Extends Device to hold metadata on the Excitation Source instance.

ExcitationSource extends Device and includes all elements of Device with the following additions or changes.

ExcitationSource
Table 1.2 Datasets, Links, and Attributes contained in <ExcitationSource>

Id

Type

Description

<ExcitationSource>

Group

Top level Group for <ExcitationSource>

.power_in_W

Attribute

Incident power of stimulation device (in Watts).

  • Data Type: float

  • Required: False

  • Name: power_in_W

.intensity_in_W_per_m2

Attribute

Intensity of the excitation in W/m^2, if known.

  • Data Type: float

  • Required: False

  • Name: intensity_in_W_per_m2

.exposure_time_in_s

Attribute

Exposure time of the sample (in sec).

  • Data Type: float

  • Required: False

  • Name: exposure_time_in_s

1.2.1.3. PulsedExcitationSource

Overview: Extends ExcitationSource to hold metadata on the Pulsed Excitation Source instance.

PulsedExcitationSource extends ExcitationSource and includes all elements of ExcitationSource with the following additions or changes.

PulsedExcitationSource
Table 1.3 Datasets, Links, and Attributes contained in <PulsedExcitationSource>

Id

Type

Description

<PulsedExcitationSource>

Group

Top level Group for <PulsedExcitationSource>

.pulse_rate_in_Hz

Attribute

If device is pulsed light source, pulse rate (in Hz) used for stimulation.

  • Data Type: float

  • Name: pulse_rate_in_Hz

.peak_power_in_W

Attribute

Incident peak power of stimulation device (in Watts).

  • Data Type: float

  • Required: False

  • Name: peak_power_in_W

.peak_pulse_energy_in_J

Attribute

If device is pulsed light source, pulse energy (in Joules).

  • Data Type: float

  • Required: False

  • Name: peak_pulse_energy_in_J

1.2.1.4. PhotodetectorModel

Overview: Extends DeviceModel to hold metadata on the Photodetector Model.

PhotodetectorModel extends DeviceModel and includes all elements of DeviceModel with the following additions or changes.

  • Extends: DeviceModel

  • Primitive Type: Group

  • Inherits from: DeviceModel, NWBContainer, Container

  • Source filename: ndx-ophys-devices.extensions.yaml

  • Source Specification: see Section 1.3.2.4

PhotodetectorModel
Table 1.4 Datasets, Links, and Attributes contained in <PhotodetectorModel>

Id

Type

Description

<PhotodetectorModel>

Group

Top level Group for <PhotodetectorModel>

.detector_type

Attribute

Technology used to detect the light. Suggested values: CCD, Intensified CCD, PMT, Photodiode, CMOS, EBCCD, FTIR.

  • Data Type: text

  • Name: detector_type

.wavelength_range_in_nm

Attribute

The range of wavelengths that can be detected.

  • Data Type: float

  • Shape: [2]

  • Required: False

  • Name: wavelength_range_in_nm

.gain

Attribute

Gain on the photodetector.

  • Data Type: float

  • Required: False

  • Name: gain

.gain_unit

Attribute

Unit of the gain value.

  • Data Type: text

  • Required: False

  • Name: gain_unit

1.2.1.5. Photodetector

Overview: Extends Device to hold metadata on the Photodetector instance.

Photodetector extends Device and includes all elements of Device with the following additions or changes.

1.2.1.6. DichroicMirrorModel

Overview: Extends DeviceModel to hold metadata on the Dichroic Mirror Model.

DichroicMirrorModel extends DeviceModel and includes all elements of DeviceModel with the following additions or changes.

  • Extends: DeviceModel

  • Primitive Type: Group

  • Inherits from: DeviceModel, NWBContainer, Container

  • Source filename: ndx-ophys-devices.extensions.yaml

  • Source Specification: see Section 1.3.2.6

DichroicMirrorModel
Table 1.5 Datasets, Links, and Attributes contained in <DichroicMirrorModel>

Id

Type

Description

<DichroicMirrorModel>

Group

Top level Group for <DichroicMirrorModel>

.cut_on_wavelength_in_nm

Attribute

Wavelength at which the mirror starts to transmit light more than reflect.

  • Data Type: float

  • Required: False

  • Name: cut_on_wavelength_in_nm

.cut_off_wavelength_in_nm

Attribute

Wavelength at which transmission shifts back to reflection, for mirrors with complex transmission spectra.

  • Data Type: float

  • Required: False

  • Name: cut_off_wavelength_in_nm

.reflection_band_in_nm

Attribute

The range of wavelengths that are primarily reflected.The start and end wavelengths needs to be specified.

  • Data Type: float

  • Shape: [2]

  • Required: False

  • Name: reflection_band_in_nm

.transmission_band_in_nm

Attribute

The range of wavelengths that are primarily transmitted.The start and end wavelengths needs to be specified.

  • Data Type: float

  • Shape: [2]

  • Required: False

  • Name: transmission_band_in_nm

.angle_of_incidence_in_degrees

Attribute

Intended angle at which light strikes the mirror.

  • Data Type: float

  • Required: False

  • Name: angle_of_incidence_in_degrees

1.2.1.7. DichroicMirror

Overview: Extends Device to hold a Dichroic Mirror instance.

DichroicMirror extends Device and includes all elements of Device with the following additions or changes.

1.2.1.8. OpticalFilterModel

Overview: Extends DeviceModel to hold metadata on the Optical Filter Model.

OpticalFilterModel extends DeviceModel and includes all elements of DeviceModel with the following additions or changes.

Table 1.6 Datasets, Links, and Attributes contained in <OpticalFilterModel>

Id

Type

Description

<OpticalFilterModel>

Group

Top level Group for <OpticalFilterModel>

.filter_type

Attribute

Type of filter (e.g., ‘Bandpass’, ‘Bandstop’, ‘Longpass’, ‘Shortpass’).

  • Data Type: text

  • Name: filter_type

1.2.1.9. OpticalFilter

Overview: Extends Device to hold an Optical Filter instance.

OpticalFilter extends Device and includes all elements of Device with the following additions or changes.

1.2.1.10. BandOpticalFilterModel

Overview: Extends OpticalFilterModel to hold metadata on the Band Optical Filter Model (Bandpass or Bandstop).

BandOpticalFilterModel extends OpticalFilterModel and includes all elements of OpticalFilterModel with the following additions or changes.

BandOpticalFilterModel
Table 1.7 Datasets, Links, and Attributes contained in <BandOpticalFilterModel>

Id

Type

Description

<BandOpticalFilterModel>

Group

Top level Group for <BandOpticalFilterModel>

.center_wavelength_in_nm

Attribute

The midpoint of the band of wavelengths that the filter transmits or blocks.

  • Data Type: float

  • Name: center_wavelength_in_nm

.bandwidth_in_nm

Attribute

The width of the wavelength range that the filter transmits or blocks (full width at half maximum).

  • Data Type: float

  • Name: bandwidth_in_nm

1.2.1.11. BandOpticalFilter

Overview: Extends OpticalFilter to hold a Band Optical Filter instance (Bandpass or Bandstop).

BandOpticalFilter extends OpticalFilter and includes all elements of OpticalFilter with the following additions or changes.

1.2.1.12. EdgeOpticalFilterModel

Overview: Extends OpticalFilterModel to hold metadata on the Edge Optical Filter Model (Longpass or Shortpass).

EdgeOpticalFilterModel extends OpticalFilterModel and includes all elements of OpticalFilterModel with the following additions or changes.

EdgeOpticalFilterModel
Table 1.8 Datasets, Links, and Attributes contained in <EdgeOpticalFilterModel>

Id

Type

Description

<EdgeOpticalFilterModel>

Group

Top level Group for <EdgeOpticalFilterModel>

.cut_wavelength_in_nm

Attribute

The wavelength at which the filter transmits half as much as its peak transmission.

  • Data Type: float

  • Name: cut_wavelength_in_nm

.slope_in_percent_cut_wavelength

Attribute

The steepness of the transition from high blocking to high transmission (or vice versa). Specified as a percentage of the cut wavelength.

  • Data Type: float

  • Required: False

  • Name: slope_in_percent_cut_wavelength

.slope_starting_transmission_in_percent

Attribute

The percent transmission that defines the starting point for the slope (e.g. 10%).

  • Data Type: float

  • Required: False

  • Name: slope_starting_transmission_in_percent

.slope_ending_transmission_in_percent

Attribute

The percent transmission that defines the ending point for the slope (e.g. 80%).

  • Data Type: float

  • Required: False

  • Name: slope_ending_transmission_in_percent

1.2.1.13. EdgeOpticalFilter

Overview: Extends OpticalFilter to hold an Edge Optical Filter instance (Longpass or Shortpass).

EdgeOpticalFilter extends OpticalFilter and includes all elements of OpticalFilter with the following additions or changes.

1.2.1.14. OpticalFiberModel

Overview: Extends DeviceModel to hold metadata on the Optical Fiber Model.

OpticalFiberModel extends DeviceModel and includes all elements of DeviceModel with the following additions or changes.

  • Extends: DeviceModel

  • Primitive Type: Group

  • Inherits from: DeviceModel, NWBContainer, Container

  • Source filename: ndx-ophys-devices.extensions.yaml

  • Source Specification: see Section 1.3.2.14

OpticalFiberModel
Table 1.9 Datasets, Links, and Attributes contained in <OpticalFiberModel>

Id

Type

Description

<OpticalFiberModel>

Group

Top level Group for <OpticalFiberModel>

.numerical_aperture

Attribute

Numerical aperture, e.g., 0.39 NA.

  • Data Type: float

  • Name: numerical_aperture

.core_diameter_in_um

Attribute

Core diameter in micrometers.

  • Data Type: float

  • Required: False

  • Name: core_diameter_in_um

.active_length_in_mm

Attribute

Active length in mm for a tapered fiber, e.g., Optogenix Lambda fiber. See https://www.optogenix.com/lambda-fibers/ for details of one example.

  • Data Type: float

  • Required: False

  • Name: active_length_in_mm

.ferrule_name

Attribute

Product name of the ferrule.

  • Data Type: text

  • Required: False

  • Name: ferrule_name

.ferrule_model

Attribute

Model (or product ID) of the ferrule from the manufacturer.

  • Data Type: text

  • Required: False

  • Name: ferrule_model

.ferrule_diameter_in_mm

Attribute

Ferrule diameter in mm, e.g., 1.25 mm (LC) or 2.5 mm (FC).

  • Data Type: float

  • Required: False

  • Name: ferrule_diameter_in_mm

1.2.1.15. FiberInsertion

Overview: Metadata about the insertion of a fiber into the brain, which can be used to determine the location of the fiber in the brain.

FiberInsertion extends NWBContainer and includes all elements of NWBContainer with the following additions or changes.

FiberInsertion
Table 1.10 Datasets, Links, and Attributes contained in <FiberInsertion>

Id

Type

Description

<FiberInsertion>

Group

Top level Group for <FiberInsertion>

.insertion_position_ap_in_mm

Attribute

Anteroposterior (AP) stereotactic coordinate of where the fiber was inserted, in millimeters. + is anterior. Coordinate is relative to the zero-point described in position_reference.

  • Data Type: float

  • Required: False

  • Name: insertion_position_ap_in_mm

.insertion_position_ml_in_mm

Attribute

Mediolateral (ML) stereotactic coordinate of where the fiber was inserted, in millimeters. + is right. Coordinate is relative to the zero-point described in position_reference.

  • Data Type: float

  • Required: False

  • Name: insertion_position_ml_in_mm

.insertion_position_dv_in_mm

Attribute

Dorsoventral (DV) stereotactic coordinate of where the fiber was inserted, in millimeters. + is up. Coordinate is relative to the zero-point described in position_reference. The zero-point is typically the surface of the brain, so this value is typically 0.

  • Data Type: float

  • Required: False

  • Name: insertion_position_dv_in_mm

.depth_in_mm

Attribute

Depth that the fiber was driven along insertion_angle starting from insertion_position_{X}_in_mm, in millimeters.

  • Data Type: float

  • Required: False

  • Name: depth_in_mm

.position_reference

Attribute

Location of the origin (0, 0, 0) for insertion_position_{X}_in_mm coordinates, e.g., “(AP, ML, DV) = (0, 0, 0) corresponds to bregma at the cortical surface”.

  • Data Type: text

  • Required: False

  • Name: position_reference

.hemisphere

Attribute

The hemisphere (“left” or “right”) of the targeted location of the optogenetic stimulus site. Should be consistent with insertion_position_in_mm.ml coordinate (left = ml < 0, right = ml > 0).

  • Data Type: text

  • Required: False

  • Name: hemisphere

.insertion_angle_yaw_in_deg

Attribute

The yaw angle of the fiber at the time of insertion, in degrees. Yaw = rotation around dorsal-ventral axis, like shaking (+ is rotating the nose rightward). Zero is defined as the fiber being parallel to an sagittal slice of the brain. The order of rotations is yaw, pitch, roll.

  • Data Type: float

  • Required: False

  • Name: insertion_angle_yaw_in_deg

.insertion_angle_pitch_in_deg

Attribute

The pitch angle of the fiber at the time of insertion, in degrees. Pitch = rotation around left-right axis, like nodding (+ is rotating the nose upward). Zero is defined as the fiber being parallel to an axial slice of the brain. The order of rotations is yaw, pitch, roll.

  • Data Type: float

  • Required: False

  • Name: insertion_angle_pitch_in_deg

.insertion_angle_roll_in_deg

Attribute

The roll angle of the fiber at the time of insertion, in degrees. Roll = rotation around anterior-posterior axis, like tilting (+ is rotating the right side downward). Zero is defined as the fiber being parallel to a coronal slice of the brain. The order of rotations is yaw, pitch, roll.

  • Data Type: float

  • Required: False

  • Name: insertion_angle_roll_in_deg

1.2.1.16. OpticalFiber

Overview: Extends Device to hold metadata on the Optical Fiber instance.

OpticalFiber extends Device and includes all elements of Device with the following additions or changes.

Table 1.11 Groups contained in <OpticalFiber>

Id

Type

Description

<OpticalFiber>

Group

Top level Group for <OpticalFiber>

.fiber_insertion

Group

Information about the insertion of an optical fiber into the brain.
1.2.1.16.1. Groups: fiber_insertion

Information about the insertion of an optical fiber into the brain.

1.2.1.17. OpticalLensModel

Overview: Extends DeviceModel to hold metadata on the Optical Lens Model.

OpticalLensModel extends DeviceModel and includes all elements of DeviceModel with the following additions or changes.

  • Extends: DeviceModel

  • Primitive Type: Group

  • Inherits from: DeviceModel, NWBContainer, Container

  • Source filename: ndx-ophys-devices.extensions.yaml

  • Source Specification: see Section 1.3.2.17

OpticalLensModel
Table 1.12 Datasets, Links, and Attributes contained in <OpticalLensModel>

Id

Type

Description

<OpticalLensModel>

Group

Top level Group for <OpticalLensModel>

.numerical_aperture

Attribute

Numerical aperture, e.g., 0.39 NA.

  • Data Type: float

  • Name: numerical_aperture

.magnification

Attribute

The magnification of the lens as specified by the manufacturer, i.e. ‘60.0’ is a 60X lens.

  • Data Type: float

  • Required: False

  • Name: magnification

1.2.1.18. LensPositioning

Overview: Metadata about the positioning of a lens relative to the brain, which can describe both inserted lenses (e.g., GRIN lenses) and surface-positioned lenses (e.g., optical lenses above cranial windows).

LensPositioning extends NWBContainer and includes all elements of NWBContainer with the following additions or changes.

LensPositioning
Table 1.13 Datasets, Links, and Attributes contained in <LensPositioning>

Id

Type

Description

<LensPositioning>

Group

Top level Group for <LensPositioning>

.positioning_type

Attribute

Type of lens positioning. Suggested values are “inserted” (lens penetrates brain tissue), “surface” (lens positioned above brain surface or cranial window), “transcranial” (lens positioned above intact skull).

  • Data Type: text

  • Name: positioning_type

.target_position_ap_in_mm

Attribute

Anteroposterior (AP) stereotactic coordinate of the target location, in millimeters. + is anterior. Coordinate is relative to the zero-point described in position_reference.

  • Data Type: float

  • Required: False

  • Name: target_position_ap_in_mm

.target_position_ml_in_mm

Attribute

Mediolateral (ML) stereotactic coordinate of the target location, in millimeters. + is right. Coordinate is relative to the zero-point described in position_reference.

  • Data Type: float

  • Required: False

  • Name: target_position_ml_in_mm

.target_position_dv_in_mm

Attribute

Dorsoventral (DV) stereotactic coordinate of the target location, in millimeters. + is up. Coordinate is relative to the zero-point described in position_reference.

  • Data Type: float

  • Required: False

  • Name: target_position_dv_in_mm

.depth_in_mm

Attribute

Depth that the lens was inserted into the brain tissue, measured along the optical axis from the brain surface, in millimeters. 0 is the surface of the brain.

  • Data Type: float

  • Name: depth_in_mm

.working_distance_in_mm

Attribute

Distance between the lens front element and the brain surface or cranial window surface, in millimeters.

  • Data Type: float

  • Required: False

  • Name: working_distance_in_mm

.position_reference

Attribute

Location of the origin (0, 0, 0) for position coordinates, e.g., “(AP, ML, DV) = (0, 0, 0) corresponds to bregma at the cortical surface”.

  • Data Type: text

  • Required: False

  • Name: position_reference

.hemisphere

Attribute

The hemisphere (“left” or “right”) of the targeted location. Should be consistent with target_position_ml_in_mm coordinate (left = ml < 0, right = ml > 0).

  • Data Type: text

  • Required: False

  • Name: hemisphere

.optical_axis_angle_yaw_in_deg

Attribute

The yaw angle of the lens optical axis, in degrees. Yaw = rotation around dorsal-ventral axis (+ is rotating the nose rightward). Zero is parallel to a sagittal slice. Order: yaw, pitch, roll.

  • Data Type: float

  • Required: False

  • Name: optical_axis_angle_yaw_in_deg

.optical_axis_angle_pitch_in_deg

Attribute

The pitch angle of the lens optical axis, in degrees. Pitch = rotation around left-right axis (+ is rotating the nose upward). Zero is parallel to an axial slice. Order: yaw, pitch, roll.

  • Data Type: float

  • Required: False

  • Name: optical_axis_angle_pitch_in_deg

.optical_axis_angle_roll_in_deg

Attribute

The roll angle of the lens optical axis, in degrees. Roll = rotation around anterior-posterior axis (+ is rotating the right side downward). Zero is parallel to a coronal slice. Order: yaw, pitch, roll.

  • Data Type: float

  • Required: False

  • Name: optical_axis_angle_roll_in_deg

1.2.1.19. OpticalLens

Overview: Extends Device to hold metadata on the Optical Lens instance.

OpticalLens extends Device and includes all elements of Device with the following additions or changes.

Table 1.14 Groups contained in <OpticalLens>

Id

Type

Description

<OpticalLens>

Group

Top level Group for <OpticalLens>

.lens_positioning

Group

Information about the positioning of the optical lens relative to the brain.
1.2.1.19.1. Groups: lens_positioning

Information about the positioning of the optical lens relative to the brain.

1.2.1.20. ViralVector

Overview: Metadata about the viral vector used to deliver indicators or effectors for ophys experiments.

ViralVector extends NWBContainer and includes all elements of NWBContainer with the following additions or changes.

ViralVector
Table 1.15 Datasets, Links, and Attributes contained in <ViralVector>

Id

Type

Description

<ViralVector>

Group

Top level Group for <ViralVector>

.construct_name

Attribute

Name of the virus construct/vector, e.g., “AAV-EF1a-DIO-hChR2(H134R)-EYFP”.

  • Data Type: text

  • Name: construct_name

.description

Attribute

Description of the virus.

  • Data Type: text

  • Required: False

  • Name: description

.manufacturer

Attribute

Manufacturer of the virus.

  • Data Type: text

  • Name: manufacturer

.titer_in_vg_per_ml

Attribute

Titer of the virus, in vg/ml, e.g., 1x10^12 vg/ml.

  • Data Type: float

  • Name: titer_in_vg_per_ml

1.2.1.21. ViralVectorInjection

Overview: Information about the injection of a viral vector that delivers indicators or effectors for ophys experiments. Use two ViralVectorInjection objects for a bilateral injection, one per hemisphere.

ViralVectorInjection extends NWBContainer and includes all elements of NWBContainer with the following additions or changes.

ViralVectorInjection
Table 1.16 Datasets, Links, and Attributes contained in <ViralVectorInjection>

Id

Type

Description

<ViralVectorInjection>

Group

Top level Group for <ViralVectorInjection>

.description

Attribute

Description of the virus injection.

  • Data Type: text

  • Required: False

  • Name: description

.location

Attribute

Name of the targeted location of the virus injection.

  • Data Type: text

  • Name: location

.hemisphere

Attribute

The hemisphere (“left” or “right”) of the targeted location of the virus injection. Should be consistent with ml_in_mm coordinate.

  • Data Type: text

  • Name: hemisphere

.reference

Attribute

Reference point for ap_in_mm, ml_in_mm, and dv_in_mm coordinates, e.g., “Bregma at the cortical surface”.

  • Data Type: text

  • Name: reference

.ap_in_mm

Attribute

Anteroposterior coordinate in mm of the virus injection site (+ is anterior), with reference to reference.

  • Data Type: float

  • Name: ap_in_mm

.ml_in_mm

Attribute

Mediolateral coordinate in mm of the virus injection site (+ is right), with reference to reference.

  • Data Type: float

  • Name: ml_in_mm

.dv_in_mm

Attribute

Dorsoventral coordinate in mm of the virus injection site (+ is dorsal/above the brain), with reference to reference.

  • Data Type: float

  • Name: dv_in_mm

.pitch_in_deg

Attribute

Pitch angle in degrees of the virus injection (rotation around left-right axis, + is rotating the nose upward).

  • Data Type: float

  • Required: False

  • Name: pitch_in_deg

.yaw_in_deg

Attribute

Yaw angle in degrees of the virus injection (rotation around dorsal-ventral axis, + is rotating the nose rightward).

  • Data Type: float

  • Required: False

  • Name: yaw_in_deg

.roll_in_deg

Attribute

Roll angle in degrees of the virus injection (rotation around anterior-posterior axis, + is rotating the right side downward).

  • Data Type: float

  • Required: False

  • Name: roll_in_deg

.stereotactic_rotation_in_deg

Attribute

TODO

  • Data Type: float

  • Required: False

  • Name: stereotactic_rotation_in_deg

.stereotactic_tilt_in_deg

Attribute

TODO

  • Data Type: float

  • Required: False

  • Name: stereotactic_tilt_in_deg

.volume_in_uL

Attribute

Volume of injection, in uL., e.g., 0.45 uL (450 nL)

  • Data Type: float

  • Name: volume_in_uL

.injection_date

Attribute

Date of injection.

  • Data Type: text

  • Required: False

  • Name: injection_date

.viral_vector

Link

Link to ViralVector object with metadata about the name, manufacturer, and titer.
Table 1.17 Groups contained in <ViralVectorInjection>

Id

Type

Description

<ViralVectorInjection>

Group

Top level Group for <ViralVectorInjection>

.viral_vector

Link

Link to ViralVector object with metadata about the name, manufacturer, and titer.

1.2.1.22. Indicator

Overview: An NWBContainer to hold metadata on the Indicator.

Indicator extends NWBContainer and includes all elements of NWBContainer with the following additions or changes.

Indicator
Table 1.18 Datasets, Links, and Attributes contained in <Indicator>

Id

Type

Description

<Indicator>

Group

Top level Group for <Indicator>

.label

Attribute

Indicator standard notation.

  • Data Type: text

  • Name: label

.description

Attribute

Indicator description.

  • Data Type: text

  • Required: False

  • Name: description

.manufacturer

Attribute

Indicator manufacturer.

  • Data Type: text

  • Required: False

  • Name: manufacturer

.viral_vector_injection

Link

Link to ViralVectorInjection object with metadata about the injection of the indicator.
Table 1.19 Groups contained in <Indicator>

Id

Type

Description

<Indicator>

Group

Top level Group for <Indicator>

.viral_vector_injection

Link

Link to ViralVectorInjection object with metadata about the injection of the indicator.

1.2.1.23. Effector

Overview: An NWBContainer to hold metadata on the Effector or Opsin.

Effector extends NWBContainer and includes all elements of NWBContainer with the following additions or changes.

Effector
Table 1.20 Datasets, Links, and Attributes contained in <Effector>

Id

Type

Description

<Effector>

Group

Top level Group for <Effector>

.label

Attribute

Effector standard notation.

  • Data Type: text

  • Name: label

.description

Attribute

Effector description.

  • Data Type: text

  • Required: False

  • Name: description

.manufacturer

Attribute

Effector manufacturer.

  • Data Type: text

  • Required: False

  • Name: manufacturer

.viral_vector_injection

Link

Link to ViralVectorInjection object with metadata about the injection of the effector.
Table 1.21 Groups contained in <Effector>

Id

Type

Description

<Effector>

Group

Top level Group for <Effector>

.viral_vector_injection

Link

Link to ViralVectorInjection object with metadata about the injection of the effector.

1.3. Schema Sources

Source Specification: see Section 1.3.1

1.3.1. ndx-ophys-devices

Description: see Section 1.1.1

YAML Specification:

 1name: ndx-ophys-devices
 2doc: This is an NWB extension for storing metadata of devices used in optical
 3  experimental setup (microscopy, fiber photometry, optogenetic stimulation
 4  etc.)
 5schema:
 6- namespace: core
 7  neurodata_types:
 8  - Device
 9  - DeviceModel
10- source: ndx-ophys-devices.extensions.yaml
11version: 0.3.1
12author:
13- Alessandra Trapani
14contact:
15- alessandra.trapani@catalystneuro.com

1.3.2. ndx-ophys-devices.extensions.yaml

1.3.2.1. ExcitationSourceModel

Extends: DeviceModel

Description: see Section 1.2.1.1

YAML Specification:

 1neurodata_type_def: ExcitationSourceModel
 2neurodata_type_inc: DeviceModel
 3doc: Extends DeviceModel to hold metadata on the Excitation Source Model.
 4attributes:
 5- name: source_type
 6  dtype: text
 7  doc: 'Type of source. Suggested values: LED, Gas Laser (e.g., Argon, Krypton), Solid-State
 8    Laser (e.g., Diode, DPSS).'
 9- name: excitation_mode
10  dtype: text
11  doc: The type of excitation used in the light path (e.g., 'one-photon',
12    'two-photon', 'three-photon', 'other').
13- name: wavelength_range_in_nm
14  dtype: float
15  shape:
16  - 2
17  doc: The range of wavelengths that can be produced by the source.
18  required: false

1.3.2.2. ExcitationSource

Extends: Device

Description: see Section 1.2.1.2

YAML Specification:

 1neurodata_type_def: ExcitationSource
 2neurodata_type_inc: Device
 3doc: Extends Device to hold metadata on the Excitation Source instance.
 4attributes:
 5- name: power_in_W
 6  dtype: float
 7  doc: Incident power of stimulation device (in Watts).
 8  required: false
 9- name: intensity_in_W_per_m2
10  dtype: float
11  doc: Intensity of the excitation in W/m^2, if known.
12  required: false
13- name: exposure_time_in_s
14  dtype: float
15  doc: Exposure time of the sample (in sec).
16  required: false

1.3.2.3. PulsedExcitationSource

Extends: ExcitationSource

Description: see Section 1.2.1.3

YAML Specification:

 1neurodata_type_def: PulsedExcitationSource
 2neurodata_type_inc: ExcitationSource
 3doc: Extends ExcitationSource to hold metadata on the Pulsed Excitation Source
 4  instance.
 5attributes:
 6- name: pulse_rate_in_Hz
 7  dtype: float
 8  doc: If device is pulsed light source, pulse rate (in Hz) used for
 9    stimulation.
10- name: peak_power_in_W
11  dtype: float
12  doc: Incident peak power of stimulation device (in Watts).
13  required: false
14- name: peak_pulse_energy_in_J
15  dtype: float
16  doc: If device is pulsed light source, pulse energy (in Joules).
17  required: false

1.3.2.4. PhotodetectorModel

Extends: DeviceModel

Description: see Section 1.2.1.4

YAML Specification:

 1neurodata_type_def: PhotodetectorModel
 2neurodata_type_inc: DeviceModel
 3doc: Extends DeviceModel to hold metadata on the Photodetector Model.
 4attributes:
 5- name: detector_type
 6  dtype: text
 7  doc: 'Technology used to detect the light. Suggested values: CCD, Intensified CCD,
 8    PMT, Photodiode, CMOS, EBCCD, FTIR.'
 9- name: wavelength_range_in_nm
10  dtype: float
11  shape:
12  - 2
13  doc: The range of wavelengths that can be detected.
14  required: false
15- name: gain
16  dtype: float
17  doc: Gain on the photodetector.
18  required: false
19- name: gain_unit
20  dtype: text
21  doc: Unit of the gain value.
22  required: false

1.3.2.5. Photodetector

Extends: Device

Description: see Section 1.2.1.5

YAML Specification:

1neurodata_type_def: Photodetector
2neurodata_type_inc: Device
3doc: Extends Device to hold metadata on the Photodetector instance.

1.3.2.6. DichroicMirrorModel

Extends: DeviceModel

Description: see Section 1.2.1.6

YAML Specification:

 1neurodata_type_def: DichroicMirrorModel
 2neurodata_type_inc: DeviceModel
 3doc: Extends DeviceModel to hold metadata on the Dichroic Mirror Model.
 4attributes:
 5- name: cut_on_wavelength_in_nm
 6  dtype: float
 7  doc: Wavelength at which the mirror starts to transmit light more than
 8    reflect.
 9  required: false
10- name: cut_off_wavelength_in_nm
11  dtype: float
12  doc: Wavelength at which transmission shifts back to reflection, for mirrors
13    with complex transmission spectra.
14  required: false
15- name: reflection_band_in_nm
16  dtype: float
17  shape:
18  - 2
19  doc: The range of wavelengths that are primarily reflected.The start and end
20    wavelengths needs to be specified.
21  required: false
22- name: transmission_band_in_nm
23  dtype: float
24  shape:
25  - 2
26  doc: The range of wavelengths that are primarily transmitted.The start and end
27    wavelengths needs to be specified.
28  required: false
29- name: angle_of_incidence_in_degrees
30  dtype: float
31  doc: Intended angle at which light strikes the mirror.
32  required: false

1.3.2.7. DichroicMirror

Extends: Device

Description: see Section 1.2.1.7

YAML Specification:

1neurodata_type_def: DichroicMirror
2neurodata_type_inc: Device
3doc: Extends Device to hold a Dichroic Mirror instance.

1.3.2.8. OpticalFilterModel

Extends: DeviceModel

Description: see Section 1.2.1.8

YAML Specification:

1neurodata_type_def: OpticalFilterModel
2neurodata_type_inc: DeviceModel
3doc: Extends DeviceModel to hold metadata on the Optical Filter Model.
4attributes:
5- name: filter_type
6  dtype: text
7  doc: Type of filter (e.g., 'Bandpass', 'Bandstop', 'Longpass', 'Shortpass').

1.3.2.9. OpticalFilter

Extends: Device

Description: see Section 1.2.1.9

YAML Specification:

1neurodata_type_def: OpticalFilter
2neurodata_type_inc: Device
3doc: Extends Device to hold an Optical Filter instance.

1.3.2.10. BandOpticalFilterModel

Extends: OpticalFilterModel

Description: see Section 1.2.1.10

YAML Specification:

 1neurodata_type_def: BandOpticalFilterModel
 2neurodata_type_inc: OpticalFilterModel
 3doc: Extends OpticalFilterModel to hold metadata on the Band Optical Filter
 4  Model (Bandpass or Bandstop).
 5attributes:
 6- name: center_wavelength_in_nm
 7  dtype: float
 8  doc: The midpoint of the band of wavelengths that the filter transmits or
 9    blocks.
10- name: bandwidth_in_nm
11  dtype: float
12  doc: The width of the wavelength range that the filter transmits or blocks
13    (full width at half maximum).

1.3.2.11. BandOpticalFilter

Extends: OpticalFilter

Description: see Section 1.2.1.11

YAML Specification:

1neurodata_type_def: BandOpticalFilter
2neurodata_type_inc: OpticalFilter
3doc: Extends OpticalFilter to hold a Band Optical Filter instance (Bandpass or
4  Bandstop).

1.3.2.12. EdgeOpticalFilterModel

Extends: OpticalFilterModel

Description: see Section 1.2.1.12

YAML Specification:

 1neurodata_type_def: EdgeOpticalFilterModel
 2neurodata_type_inc: OpticalFilterModel
 3doc: Extends OpticalFilterModel to hold metadata on the Edge Optical Filter
 4  Model (Longpass or Shortpass).
 5attributes:
 6- name: cut_wavelength_in_nm
 7  dtype: float
 8  doc: The wavelength at which the filter transmits half as much as its peak
 9    transmission.
10- name: slope_in_percent_cut_wavelength
11  dtype: float
12  doc: The steepness of the transition from high blocking to high transmission
13    (or vice versa). Specified as a percentage of the cut wavelength.
14  required: false
15- name: slope_starting_transmission_in_percent
16  dtype: float
17  doc: The percent transmission that defines the starting point for the slope
18    (e.g. 10%).
19  required: false
20- name: slope_ending_transmission_in_percent
21  dtype: float
22  doc: The percent transmission that defines the ending point for the slope
23    (e.g. 80%).
24  required: false

1.3.2.13. EdgeOpticalFilter

Extends: OpticalFilter

Description: see Section 1.2.1.13

YAML Specification:

1neurodata_type_def: EdgeOpticalFilter
2neurodata_type_inc: OpticalFilter
3doc: Extends OpticalFilter to hold an Edge Optical Filter instance (Longpass or
4  Shortpass).

1.3.2.14. OpticalFiberModel

Extends: DeviceModel

Description: see Section 1.2.1.14

YAML Specification:

 1neurodata_type_def: OpticalFiberModel
 2neurodata_type_inc: DeviceModel
 3doc: Extends DeviceModel to hold metadata on the Optical Fiber Model.
 4attributes:
 5- name: numerical_aperture
 6  dtype: float
 7  doc: Numerical aperture, e.g., 0.39 NA.
 8- name: core_diameter_in_um
 9  dtype: float
10  doc: Core diameter in micrometers.
11  required: false
12- name: active_length_in_mm
13  dtype: float
14  doc: Active length in mm for a tapered fiber, e.g., Optogenix Lambda fiber.
15    See https://www.optogenix.com/lambda-fibers/ for details of one example.
16  required: false
17- name: ferrule_name
18  dtype: text
19  doc: Product name of the ferrule.
20  required: false
21- name: ferrule_model
22  dtype: text
23  doc: Model (or product ID) of the ferrule from the manufacturer.
24  required: false
25- name: ferrule_diameter_in_mm
26  dtype: float
27  doc: Ferrule diameter in mm, e.g., 1.25 mm (LC) or 2.5 mm (FC).
28  required: false

1.3.2.15. FiberInsertion

Extends: NWBContainer

Description: see Section 1.2.1.15

YAML Specification:

 1neurodata_type_def: FiberInsertion
 2neurodata_type_inc: NWBContainer
 3default_name: fiber_insertion
 4doc: Metadata about the insertion of a fiber into the brain, which can be used
 5  to determine the location of the fiber in the brain.
 6attributes:
 7- name: insertion_position_ap_in_mm
 8  dtype: float
 9  doc: Anteroposterior (AP) stereotactic coordinate of where the fiber was
10    inserted, in millimeters. + is anterior. Coordinate is relative to the
11    zero-point described in `position_reference`.
12  required: false
13- name: insertion_position_ml_in_mm
14  dtype: float
15  doc: Mediolateral (ML) stereotactic coordinate of where the fiber was
16    inserted, in millimeters. + is right. Coordinate is relative to the
17    zero-point described in `position_reference`.
18  required: false
19- name: insertion_position_dv_in_mm
20  dtype: float
21  doc: Dorsoventral (DV) stereotactic coordinate of where the fiber was
22    inserted, in millimeters. + is up. Coordinate is relative to the zero-point
23    described in `position_reference`. The zero-point is typically the surface
24    of the brain, so this value is typically 0.
25  required: false
26- name: depth_in_mm
27  dtype: float
28  doc: Depth that the fiber was driven along `insertion_angle` starting from
29    `insertion_position_{X}_in_mm`, in millimeters.
30  required: false
31- name: position_reference
32  dtype: text
33  doc: Location of the origin (0, 0, 0) for `insertion_position_{X}_in_mm`
34    coordinates, e.g., "(AP, ML, DV) = (0, 0, 0) corresponds to bregma at the
35    cortical surface".
36  required: false
37- name: hemisphere
38  dtype: text
39  doc: The hemisphere ("left" or "right") of the targeted location of the
40    optogenetic stimulus site. Should be consistent with
41    `insertion_position_in_mm.ml` coordinate (left = ml < 0, right = ml > 0).
42  required: false
43- name: insertion_angle_yaw_in_deg
44  dtype: float
45  doc: The yaw angle of the fiber at the time of insertion, in degrees. Yaw =
46    rotation around dorsal-ventral axis, like shaking (+ is rotating the nose
47    rightward). Zero is defined as the fiber being parallel to an sagittal slice
48    of the brain. The order of rotations is yaw, pitch, roll.
49  required: false
50- name: insertion_angle_pitch_in_deg
51  dtype: float
52  doc: The pitch angle of the fiber at the time of insertion, in degrees. Pitch
53    = rotation around left-right axis, like nodding (+ is rotating the nose
54    upward). Zero is defined as the fiber being parallel to an axial slice of
55    the brain. The order of rotations is yaw, pitch, roll.
56  required: false
57- name: insertion_angle_roll_in_deg
58  dtype: float
59  doc: The roll angle of the fiber at the time of insertion, in degrees. Roll =
60    rotation around anterior-posterior axis, like tilting (+ is rotating the
61    right side downward). Zero is defined as the fiber being parallel to a
62    coronal slice of the brain. The order of rotations is yaw, pitch, roll.
63  required: false

1.3.2.16. OpticalFiber

Extends: Device

Description: see Section 1.2.1.16

YAML Specification:

1neurodata_type_def: OpticalFiber
2neurodata_type_inc: Device
3doc: Extends Device to hold metadata on the Optical Fiber instance.
4groups:
5- name: fiber_insertion
6  neurodata_type_inc: FiberInsertion
7  doc: Information about the insertion of an optical fiber into the brain.

1.3.2.17. OpticalLensModel

Extends: DeviceModel

Description: see Section 1.2.1.17

YAML Specification:

 1neurodata_type_def: OpticalLensModel
 2neurodata_type_inc: DeviceModel
 3doc: Extends DeviceModel to hold metadata on the Optical Lens Model.
 4attributes:
 5- name: numerical_aperture
 6  dtype: float
 7  doc: Numerical aperture, e.g., 0.39 NA.
 8- name: magnification
 9  dtype: float
10  doc: The magnification of the lens as specified by the manufacturer, i.e.
11    '60.0' is a 60X lens.
12  required: false

1.3.2.18. LensPositioning

Extends: NWBContainer

Description: see Section 1.2.1.18

YAML Specification:

 1neurodata_type_def: LensPositioning
 2neurodata_type_inc: NWBContainer
 3default_name: lens_positioning
 4doc: Metadata about the positioning of a lens relative to the brain, which can
 5  describe both inserted lenses (e.g., GRIN lenses) and surface-positioned
 6  lenses (e.g., optical lenses above cranial windows).
 7attributes:
 8- name: positioning_type
 9  dtype: text
10  doc: Type of lens positioning. Suggested values are "inserted" (lens
11    penetrates brain tissue), "surface" (lens positioned above brain surface or
12    cranial window), "transcranial" (lens positioned above intact skull).
13- name: target_position_ap_in_mm
14  dtype: float
15  doc: "Anteroposterior (AP) stereotactic coordinate of the target location,\nin millimeters.
16    + is anterior. Coordinate is relative to the zero-point described\nin `position_reference`.\n"
17  required: false
18- name: target_position_ml_in_mm
19  dtype: float
20  doc: "Mediolateral (ML) stereotactic coordinate of the target location,\nin millimeters.
21    + is right. Coordinate is relative to the zero-point described\nin `position_reference`.\n"
22  required: false
23- name: target_position_dv_in_mm
24  dtype: float
25  doc: "Dorsoventral (DV) stereotactic coordinate of the target location,\nin millimeters.
26    + is up. Coordinate is relative to the zero-point described\nin `position_reference`.\n"
27  required: false
28- name: depth_in_mm
29  dtype: float
30  doc: "Depth that the lens was inserted into the brain tissue, measured\nalong the
31    optical axis from the brain surface, in millimeters. 0 is the surface of the brain.\n"
32- name: working_distance_in_mm
33  dtype: float
34  doc: "Distance between the lens front element and the brain surface or \ncranial
35    window surface, in millimeters.\n"
36  required: false
37- name: position_reference
38  dtype: text
39  doc: "Location of the origin (0, 0, 0) for position coordinates,\ne.g., \"(AP, ML,
40    DV) = (0, 0, 0) corresponds to bregma at the cortical surface\".\n"
41  required: false
42- name: hemisphere
43  dtype: text
44  doc: "The hemisphere (\"left\" or \"right\") of the targeted location.\nShould be
45    consistent with target_position_ml_in_mm coordinate\n(left = ml < 0, right = ml
46    > 0).\n"
47  required: false
48- name: optical_axis_angle_yaw_in_deg
49  dtype: float
50  doc: "The yaw angle of the lens optical axis, in degrees. Yaw = rotation\naround
51    dorsal-ventral axis (+ is rotating the nose rightward).\nZero is parallel to a
52    sagittal slice. Order: yaw, pitch, roll.\n"
53  required: false
54- name: optical_axis_angle_pitch_in_deg
55  dtype: float
56  doc: "The pitch angle of the lens optical axis, in degrees. Pitch = rotation\naround
57    left-right axis (+ is rotating the nose upward).\nZero is parallel to an axial
58    slice. Order: yaw, pitch, roll.\n"
59  required: false
60- name: optical_axis_angle_roll_in_deg
61  dtype: float
62  doc: "The roll angle of the lens optical axis, in degrees. Roll = rotation\naround
63    anterior-posterior axis (+ is rotating the right side downward).\nZero is parallel
64    to a coronal slice. Order: yaw, pitch, roll.\n"
65  required: false

1.3.2.19. OpticalLens

Extends: Device

Description: see Section 1.2.1.19

YAML Specification:

1neurodata_type_def: OpticalLens
2neurodata_type_inc: Device
3doc: Extends Device to hold metadata on the Optical Lens instance.
4groups:
5- name: lens_positioning
6  neurodata_type_inc: LensPositioning
7  doc: "Information about the positioning of the optical lens relative to the brain.\n"
8  quantity: '?'

1.3.2.20. ViralVector

Extends: NWBContainer

Description: see Section 1.2.1.20

YAML Specification:

 1neurodata_type_def: ViralVector
 2neurodata_type_inc: NWBContainer
 3doc: Metadata about the viral vector used to deliver indicators or effectors for
 4  ophys experiments.
 5attributes:
 6- name: construct_name
 7  dtype: text
 8  doc: Name of the virus construct/vector, e.g.,
 9    "AAV-EF1a-DIO-hChR2(H134R)-EYFP".
10- name: description
11  dtype: text
12  doc: Description of the virus.
13  required: false
14- name: manufacturer
15  dtype: text
16  doc: Manufacturer of the virus.
17- name: titer_in_vg_per_ml
18  dtype: float
19  doc: Titer of the virus, in vg/ml, e.g., 1x10^12 vg/ml.

1.3.2.21. ViralVectorInjection

Extends: NWBContainer

Description: see Section 1.2.1.21

YAML Specification:

 1neurodata_type_def: ViralVectorInjection
 2neurodata_type_inc: NWBContainer
 3doc: Information about the injection of a viral vector that delivers indicators
 4  or effectors for ophys experiments. Use two ViralVectorInjection objects for a
 5  bilateral injection, one per hemisphere.
 6attributes:
 7- name: description
 8  dtype: text
 9  doc: Description of the virus injection.
10  required: false
11- name: location
12  dtype: text
13  doc: Name of the targeted location of the virus injection.
14- name: hemisphere
15  dtype: text
16  doc: The hemisphere ("left" or "right") of the targeted location of the virus
17    injection. Should be consistent with `ml_in_mm` coordinate.
18- name: reference
19  dtype: text
20  doc: Reference point for `ap_in_mm`, `ml_in_mm`, and `dv_in_mm` coordinates,
21    e.g., "Bregma at the cortical surface".
22- name: ap_in_mm
23  dtype: float
24  doc: Anteroposterior coordinate in mm of the virus injection site (+ is
25    anterior), with reference to `reference`.
26- name: ml_in_mm
27  dtype: float
28  doc: Mediolateral coordinate in mm of the virus injection site (+ is right),
29    with reference to `reference`.
30- name: dv_in_mm
31  dtype: float
32  doc: Dorsoventral coordinate in mm of the virus injection site (+ is
33    dorsal/above the brain), with reference to `reference`.
34- name: pitch_in_deg
35  dtype: float
36  doc: Pitch angle in degrees of the virus injection (rotation around left-right
37    axis, + is rotating the nose upward).
38  required: false
39- name: yaw_in_deg
40  dtype: float
41  doc: Yaw angle in degrees of the virus injection (rotation around
42    dorsal-ventral axis, + is rotating the nose rightward).
43  required: false
44- name: roll_in_deg
45  dtype: float
46  doc: Roll angle in degrees of the virus injection (rotation around
47    anterior-posterior axis, + is rotating the right side downward).
48  required: false
49- name: stereotactic_rotation_in_deg
50  dtype: float
51  doc: TODO
52  required: false
53- name: stereotactic_tilt_in_deg
54  dtype: float
55  doc: TODO
56  required: false
57- name: volume_in_uL
58  dtype: float
59  doc: Volume of injection, in uL., e.g., 0.45 uL (450 nL)
60- name: injection_date
61  dtype: text
62  doc: Date of injection.
63  required: false
64links:
65- name: viral_vector
66  target_type: ViralVector
67  doc: Link to ViralVector object with metadata about the name, manufacturer,
68    and titer.

1.3.2.22. Indicator

Extends: NWBContainer

Description: see Section 1.2.1.22

YAML Specification:

 1neurodata_type_def: Indicator
 2neurodata_type_inc: NWBContainer
 3doc: An NWBContainer to hold metadata on the Indicator.
 4attributes:
 5- name: label
 6  dtype: text
 7  doc: Indicator standard notation.
 8- name: description
 9  dtype: text
10  doc: Indicator description.
11  required: false
12- name: manufacturer
13  dtype: text
14  doc: Indicator manufacturer.
15  required: false
16links:
17- name: viral_vector_injection
18  target_type: ViralVectorInjection
19  doc: Link to ViralVectorInjection object with metadata about the injection of
20    the indicator.
21  quantity: '?'

1.3.2.23. Effector

Extends: NWBContainer

Description: see Section 1.2.1.23

YAML Specification:

 1neurodata_type_def: Effector
 2neurodata_type_inc: NWBContainer
 3doc: An NWBContainer to hold metadata on the Effector or Opsin.
 4attributes:
 5- name: label
 6  dtype: text
 7  doc: Effector standard notation.
 8- name: description
 9  dtype: text
10  doc: Effector description.
11  required: false
12- name: manufacturer
13  dtype: text
14  doc: Effector manufacturer.
15  required: false
16links:
17- name: viral_vector_injection
18  target_type: ViralVectorInjection
19  doc: Link to ViralVectorInjection object with metadata about the injection of
20    the effector.
21  quantity: '?'