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Merge pull request #1600 from AllenNeuralDynamics/release-v2.1.0
Release v2.1.0
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‎.github/copilot-instructions.md‎

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Always use the .venv
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Always use unittest
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Never add comments
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Never run linting

‎docs/source/acquisition.md‎

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@@ -71,24 +71,24 @@ The acquisition metadata is split into two parallel pieces: the DataStream and t
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At any given moment in time the active DataStream(s) represents all modalities of data being acquired,
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while the StimulusEpoch represents all stimuli being presented.
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| Field | Type | Description |
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| Field | Type | Title (Description) |
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|-------|------|-------------|
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| `subject_id` | `str` | Unique identifier for the subject |
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| `specimen_id` | `Optional[str]` | Specimen ID is required for in vitro imaging modalities |
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| `acquisition_start_time` | `datetime (timezone-aware)` | |
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| `acquisition_end_time` | `datetime (timezone-aware)` | |
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| `experimenters` | `List[str]` | |
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| `protocol_id` | `Optional[List[str]]` | DOI for protocols.io |
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| `ethics_review_id` | `Optional[List[str]]` | |
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| `instrument_id` | `str` | Should match the Instrument.instrument_id |
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| `acquisition_type` | `str` | Descriptive string detailing the type of acquisition, should be consistent across similar acquisitions for the same experiment. |
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| `notes` | `Optional[str]` | |
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| `coordinate_system` | Optional[[CoordinateSystem](components/coordinates.md#coordinatesystem)] | Origin and axis definitions for determining the configured position of devices during acquisition. Required when coordinates are provided within the Acquisition |
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| `calibrations` | List[[Calibration](components/measurements.md#calibration) or [VolumeCalibration](components/measurements.md#volumecalibration) or [PowerCalibration](components/measurements.md#powercalibration)] | List of calibration measurements taken prior to acquisition. |
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| `maintenance` | List[[Maintenance](components/measurements.md#maintenance)] | List of maintenance on instrument prior to acquisition. |
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| `data_streams` | List[[DataStream](acquisition.md#datastream)] | A data stream is a collection of devices that are acquiring data simultaneously. Each acquisition can include multiple streams. Streams should be split when configurations are changed. |
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| `stimulus_epochs` | List[[StimulusEpoch](acquisition.md#stimulusepoch)] | A stimulus epoch captures all stimuli being presented during an acquisition. Epochs should be split when the purpose of the stimulus changes. |
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| `subject_details` | Optional[[AcquisitionSubjectDetails](acquisition.md#acquisitionsubjectdetails)] | |
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| `subject_id` | `str` | Subject ID (Unique identifier for the subject) |
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| `specimen_id` | `Optional[str]` | Specimen ID (Specimen ID is required for in vitro imaging modalities) |
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| `acquisition_start_time` | `datetime (timezone-aware)` | Acquisition start time |
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| `acquisition_end_time` | `datetime (timezone-aware)` | Acquisition end time |
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| `experimenters` | `List[str]` | experimenter(s) |
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| `protocol_id` | `Optional[List[str]]` | Protocol ID (DOI for protocols.io) |
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| `ethics_review_id` | `Optional[List[str]]` | Ethics review ID |
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| `instrument_id` | `str` | Instrument ID (Should match the Instrument.instrument_id) |
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| `acquisition_type` | `str` | Acquisition type (Descriptive string detailing the type of acquisition, should be consistent across similar acquisitions for the same experiment.) |
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| `notes` | `Optional[str]` | Notes |
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| `coordinate_system` | Optional[[CoordinateSystem](components/coordinates.md#coordinatesystem)] | Coordinate system (Origin and axis definitions for determining the configured position of devices during acquisition. Required when coordinates are provided within the Acquisition) |
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| `calibrations` | List[[Calibration](components/measurements.md#calibration) or [VolumeCalibration](components/measurements.md#volumecalibration) or [PowerCalibration](components/measurements.md#powercalibration)] | Calibrations (List of calibration measurements taken prior to acquisition.) |
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| `maintenance` | List[[Maintenance](components/measurements.md#maintenance)] | Maintenance (List of maintenance on instrument prior to acquisition.) |
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| `data_streams` | List[[DataStream](acquisition.md#datastream)] | Data streams (A data stream is a collection of devices that are acquiring data simultaneously. Each acquisition can include multiple streams. Streams should be split when configurations are changed.) |
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| `stimulus_epochs` | List[[StimulusEpoch](acquisition.md#stimulusepoch)] | Stimulus (A stimulus epoch captures all stimuli being presented during an acquisition. Epochs should be split when the purpose of the stimulus changes.) |
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| `subject_details` | Optional[[AcquisitionSubjectDetails](acquisition.md#acquisitionsubjectdetails)] | Subject details |
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## Model definitions
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Details about the subject during an acquisition
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| Field | Type | Description |
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| Field | Type | Title (Description) |
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|-------|------|-------------|
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| `animal_weight_prior` | `Optional[decimal.Decimal]` | Animal weight before procedure |
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| `animal_weight_post` | `Optional[decimal.Decimal]` | Animal weight after procedure |
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| `weight_unit` | [MassUnit](aind_data_schema_models/units.md#massunit) | |
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| `anaesthesia` | Optional[[Anaesthetic](components/surgery_procedures.md#anaesthetic)] | |
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| `mouse_platform_name` | `str` | |
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| `reward_consumed_total` | `Optional[decimal.Decimal]` | |
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| `reward_consumed_unit` | Optional[[VolumeUnit](aind_data_schema_models/units.md#volumeunit)] | |
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| `animal_weight_prior` | `Optional[decimal.Decimal]` | Animal weight (g) (Animal weight before procedure) |
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| `animal_weight_post` | `Optional[decimal.Decimal]` | Animal weight (g) (Animal weight after procedure) |
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| `weight_unit` | [MassUnit](aind_data_schema_models/units.md#massunit) | Weight unit |
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| `anaesthesia` | Optional[[Anaesthetic](components/surgery_procedures.md#anaesthetic)] | Anaesthesia |
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| `mouse_platform_name` | `str` | Mouse platform |
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| `reward_consumed_total` | `Optional[decimal.Decimal]` | Total reward consumed (mL) |
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| `reward_consumed_unit` | Optional[[VolumeUnit](aind_data_schema_models/units.md#volumeunit)] | Reward consumed unit |
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### DataStream
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A set of devices that are acquiring data and their configurations starting and stopping at approximately the
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same time.
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| Field | Type | Description |
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| Field | Type | Title (Description) |
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|-------|------|-------------|
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| `stream_start_time` | `datetime (timezone-aware)` | |
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| `stream_end_time` | `datetime (timezone-aware)` | |
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| `modalities` | List[[Modality](aind_data_schema_models/modalities.md#modality)] | Modalities that are acquired in this stream |
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| `code` | Optional[List[[Code](components/identifiers.md#code)]] | |
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| `notes` | `Optional[str]` | |
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| `active_devices` | `List[str]` | Device names must match devices in the Instrument |
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| `configurations` | List[[LightEmittingDiodeConfig](components/configs.md#lightemittingdiodeconfig) or [LaserConfig](components/configs.md#laserconfig) or [ManipulatorConfig](components/configs.md#manipulatorconfig) or [DetectorConfig](components/configs.md#detectorconfig) or [PatchCordConfig](components/configs.md#patchcordconfig) or [FiberAssemblyConfig](components/configs.md#fiberassemblyconfig) or [MRIScan](components/configs.md#mriscan) or [LickSpoutConfig](components/configs.md#lickspoutconfig) or [AirPuffConfig](components/configs.md#airpuffconfig) or [ImagingConfig](components/configs.md#imagingconfig) or [SlapPlane](components/configs.md#slapplane) or [SampleChamberConfig](components/configs.md#samplechamberconfig) or [ProbeConfig](components/configs.md#probeconfig) or [EphysAssemblyConfig](components/configs.md#ephysassemblyconfig)] | Configurations are parameters controlling active devices during this stream |
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| `connections` | List[[Connection](components/connections.md#connection)] | Connections are links between devices that are specific to this acquisition (i.e. not already defined in the Instrument) |
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| `stream_start_time` | `datetime (timezone-aware)` | Stream start time |
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| `stream_end_time` | `datetime (timezone-aware)` | Stream stop time |
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| `modalities` | List[[Modality](aind_data_schema_models/modalities.md#modality)] | Modalities (Modalities that are acquired in this stream) |
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| `code` | Optional[List[[Code](components/identifiers.md#code)]] | Acquisition code |
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| `notes` | `Optional[str]` | Notes |
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| `active_devices` | `List[str]` | Active devices (Device names must match devices in the Instrument) |
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| `configurations` | List[[LightEmittingDiodeConfig](components/configs.md#lightemittingdiodeconfig) or [LaserConfig](components/configs.md#laserconfig) or [ManipulatorConfig](components/configs.md#manipulatorconfig) or [DetectorConfig](components/configs.md#detectorconfig) or [PatchCordConfig](components/configs.md#patchcordconfig) or [FiberAssemblyConfig](components/configs.md#fiberassemblyconfig) or [MRIScan](components/configs.md#mriscan) or [LickSpoutConfig](components/configs.md#lickspoutconfig) or [AirPuffConfig](components/configs.md#airpuffconfig) or [ImagingConfig](components/configs.md#imagingconfig) or [SlapPlane](components/configs.md#slapplane) or [SampleChamberConfig](components/configs.md#samplechamberconfig) or [ProbeConfig](components/configs.md#probeconfig) or [EphysAssemblyConfig](components/configs.md#ephysassemblyconfig) or [CatheterConfig](components/configs.md#catheterconfig)] | Device configurations (Configurations are parameters controlling active devices during this stream) |
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| `connections` | List[[Connection](components/connections.md#connection)] | Connections (Connections are links between devices that are specific to this acquisition (i.e. not already defined in the Instrument)) |
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### PerformanceMetrics
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Summary of a StimulusEpoch
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| Field | Type | Description |
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| Field | Type | Title (Description) |
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|-------|------|-------------|
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| `output_parameters` | `dict` | |
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| `reward_consumed_during_epoch` | `Optional[decimal.Decimal]` | |
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| `reward_consumed_unit` | Optional[[VolumeUnit](aind_data_schema_models/units.md#volumeunit)] | |
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| `trials_total` | `Optional[int]` | |
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| `trials_finished` | `Optional[int]` | |
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| `trials_rewarded` | `Optional[int]` | |
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| `output_parameters` | `dict` | Additional metrics |
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| `reward_consumed_during_epoch` | `Optional[decimal.Decimal]` | Reward consumed during training (uL) |
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| `reward_consumed_unit` | Optional[[VolumeUnit](aind_data_schema_models/units.md#volumeunit)] | Reward consumed unit |
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| `trials_total` | `Optional[int]` | Total trials |
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| `trials_finished` | `Optional[int]` | Finished trials |
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| `trials_rewarded` | `Optional[int]` | Rewarded trials |
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### StimulusEpoch
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All stimuli being presented to the subject. starting and stopping at approximately the
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| Field | Type | Description |
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| Field | Type | Title (Description) |
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|-------|------|-------------|
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| `stimulus_start_time` | `datetime (timezone-aware)` | When a specific stimulus begins. This might be the same as the acquisition start time. |
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| `stimulus_end_time` | `datetime (timezone-aware)` | When a specific stimulus ends. This might be the same as the acquisition end time. |
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| `stimulus_name` | `str` | |
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| `code` | Optional[[Code](components/identifiers.md#code)] | Custom code/script used to control the behavior/stimulus. Use the Code.parameters field to store stimulus properties |
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| `stimulus_modalities` | List[[StimulusModality](aind_data_schema_models/stimulus_modality.md#stimulusmodality)] | |
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| `performance_metrics` | Optional[[PerformanceMetrics](acquisition.md#performancemetrics)] | |
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| `notes` | `Optional[str]` | |
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| `active_devices` | `List[str]` | Device names must match devices in the Instrument |
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| `configurations` | List[[SpeakerConfig](components/configs.md#speakerconfig) or [LightEmittingDiodeConfig](components/configs.md#lightemittingdiodeconfig) or [LaserConfig](components/configs.md#laserconfig) or [MousePlatformConfig](components/configs.md#mouseplatformconfig)] | |
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| `training_protocol_name` | `Optional[str]` | Name of the training protocol used during the acquisition, must match a protocol in the Procedures |
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| `curriculum_status` | `Optional[str]` | Status within the training protocol curriculum |
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| `stimulus_start_time` | `datetime (timezone-aware)` | Stimulus start time (When a specific stimulus begins. This might be the same as the acquisition start time.) |
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| `stimulus_end_time` | `datetime (timezone-aware)` | Stimulus end time (When a specific stimulus ends. This might be the same as the acquisition end time.) |
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| `stimulus_name` | `str` | Stimulus name |
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| `code` | Optional[[Code](components/identifiers.md#code)] | Code or script (Custom code/script used to control the behavior/stimulus. Use the Code.parameters field to store stimulus properties) |
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| `stimulus_modalities` | List[[StimulusModality](aind_data_schema_models/stimulus_modality.md#stimulusmodality)] | Stimulus modalities |
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| `performance_metrics` | Optional[[PerformanceMetrics](acquisition.md#performancemetrics)] | Performance metrics |
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| `notes` | `Optional[str]` | Notes |
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| `active_devices` | `List[str]` | Active devices (Device names must match devices in the Instrument) |
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| `configurations` | List[[SpeakerConfig](components/configs.md#speakerconfig) or [LightEmittingDiodeConfig](components/configs.md#lightemittingdiodeconfig) or [LaserConfig](components/configs.md#laserconfig) or [MousePlatformConfig](components/configs.md#mouseplatformconfig) or [OlfactometerConfig](components/configs.md#olfactometerconfig)] | Device configurations |
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| `training_protocol_name` | `Optional[str]` | Training protocol name (Name of the training protocol used during the acquisition, must match a protocol in the Procedures) |
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| `curriculum_status` | `Optional[str]` | Curriculum status (Status within the training protocol curriculum) |

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