Configs¶

Model definitions¶

AirPuffConfig¶

Air puff device configuration

Field	Type	Title (Description)
`valence`	Valence	Valence
`relative_position`	List[AnatomicalRelative]	Initial relative position
`coordinate_system`	Optional[CoordinateSystem]	Device coordinate system
`transform`	Optional[List[Translation or Rotation or Scale or Affine]]	Device to acquisition transform
`pressure`	`Optional[float]`	Pressure
`pressure_unit`	Optional[PressureUnit]	Pressure unit
`duration`	`Optional[float]`	Duration
`device_name`	`str`	Device name (Must match a device defined in the instrument.json)

CatheterConfig¶

Configuration of a catheter

Field	Type	Title (Description)
`targeted_structure`	MouseAnatomyModel	Targeted blood vessel (Use options from MouseBloodVessels)
`device_name`	`str`	Device name (Must match a device defined in the instrument.json)

Channel¶

Configuration of a channel

Field	Type	Title (Description)
`channel_name`	`str`	Channel
`intended_measurement`	`Optional[str]`	Intended measurement (What signal is this channel measuring)
`detector`	DetectorConfig	Detector configuration
`additional_device_names`	Optional[List[DeviceConfig]]	Additional device names (Mirrors, dichroics, etc)
`light_sources`	List[LaserConfig or LightEmittingDiodeConfig]	Light source configurations
`variable_power`	`Optional[bool]`	Variable power (Set to true when the power varies across Planes – put the power in the Plane.power field)
`excitation_filters`	Optional[List[DeviceConfig]]	Excitation filters
`emission_filters`	Optional[List[DeviceConfig]]	Emission filters
`emission_wavelength`	`Optional[int]`	Emission wavelength
`emission_wavelength_unit`	Optional[SizeUnit]	Emission wavelength unit

CoupledPlane¶

Configuration of a pair of coupled imaging plane

Field	Type	Title (Description)
`plane_index`	`int`	Plane index
`coupled_plane_index`	`int`	Coupled plane index (Plane index of the coupled plane)
`power_ratio`	`float`	Power ratio
`depth`	`float`	Depth
`depth_unit`	SizeUnit	Depth unit
`power`	`float`	Power
`power_unit`	PowerUnit	Power unit
`targeted_structure`	BrainAtlas	Targeted structure

DetectorConfig¶

Configuration of detector settings

Field	Type	Title (Description)
`exposure_time`	`Optional[float]`	Exposure time
`exposure_time_unit`	TimeUnit	Exposure time unit
`trigger_type`	TriggerType	Trigger type
`compression`	Optional[Code]	Compression (Compression algorithm used during acquisition)
`crop_offset_x`	`Optional[int]`	Crop offset x (Overrides any value set in the Instrument metadata)
`crop_offset_y`	`Optional[int]`	Crop offset y (Overrides any value set in the Instrument metadata)
`crop_width`	`Optional[int]`	Crop width (Overrides any value set in the Instrument metadata)
`crop_height`	`Optional[int]`	Crop height (Overrides any value set in the Instrument metadata)
`crop_unit`	Optional[SizeUnit]	Crop size unit
`device_name`	`str`	Device name (Must match a device defined in the instrument.json)

DeviceConfig¶

Parent class for all configurations

Field	Type	Title (Description)
`device_name`	`str`	Device name (Must match a device defined in the instrument.json)

EphysAssemblyConfig¶

Group of configurations for an ephys assembly

Field	Type	Title (Description)
`manipulator`	ManipulatorConfig	Manipulator configuration
`probes`	List[ProbeConfig]	Probe configurations
`modules`	Optional[List[MISModuleConfig]]	Modules (Configurations for conveniently tracking manipulator modules, e.g. on the New Scale dome.)
`device_name`	`str`	Device name (Must match a device defined in the instrument.json)

FiberAssemblyConfig¶

Inserted fiber photometry probe recorded in a stream

Field	Type	Title (Description)
`manipulator`	ManipulatorConfig	Manipulator configuration
`probes`	List[ProbeConfig]	Probe configurations
`patch_cords`	List[PatchCordConfig]	Fiber photometry devices
`device_name`	`str`	Device name (Must match a device defined in the instrument.json)

Image¶

Description of an N-D image

Field	Type	Title (Description)
`channel_name`	`str`	Channel name
`dimensions_unit`	SizeUnit	Dimensions unit
`image_to_acquisition_transform`	List[Translation or Rotation or Scale or Affine]	Image to acquisition transform (Position, rotation, and scale of the image. Note that depth should be in the planes.)
`dimensions`	Optional[Scale]	Dimensions

ImageSPIM¶

Description of an N-D image acquired with SPIM

Field	Type	Title (Description)
`file_name`	`AssetPath`	File name
`imaging_angle`	`int`	Imaging angle (Angle of the detector relative to the image plane relative to perpendicular)
`imaging_angle_unit`	AngleUnit	Imaging angle unit
`image_start_time`	`Optional[datetime (timezone-aware)]`	Image acquisition start time
`image_end_time`	`Optional[datetime (timezone-aware)]`	Image acquisition end time
`channel_name`	`str`	Channel name
`dimensions_unit`	SizeUnit	Dimensions unit
`image_to_acquisition_transform`	List[Translation or Rotation or Scale or Affine]	Image to acquisition transform (Position, rotation, and scale of the image. Note that depth should be in the planes.)
`dimensions`	Optional[Scale]	Dimensions

ImagingConfig¶

Configuration of an imaging instrument

Field	Type	Title (Description)
`channels`	`List[typing.Annotated[aind_data_schema.components.configs.Channel, FieldInfo(annotation=NoneType, required=True, discriminator='object_type')]]`
`coordinate_system`	Optional[CoordinateSystem]	Coordinate system (Required for ImageSPIM objects and when the imaging coordinate system differs from the Acquisition.coordinate_system)
`images`	List[PlanarImage or PlanarImageStack or ImageSPIM]	Images
`sampling_strategy`	Optional[SamplingStrategy]	Sampling strategy
`device_name`	`str`	Device name (Must match a device defined in the instrument.json)

Immersion¶

Configuration of immersion medium

Field	Type	Title (Description)
`medium`	ImmersionMedium	Immersion medium
`refractive_index`	`float`	Index of refraction

InterleavedStrategy¶

Description of an interleaved image sampling strategy

Field	Type	Title (Description)
`image_index_sequence`	`List[int]`	Interleaving sequence
`frame_rate`	`float`	Frame rate
`frame_rate_unit`	FrequencyUnit	Frame rate unit

LaserConfig¶

Configuration of laser settings in an acquisition

Field	Type	Title (Description)
`wavelength`	`int`	Wavelength (nm)
`wavelength_unit`	SizeUnit	Wavelength unit
`power`	`Optional[float]`	Excitation power
`power_unit`	Optional[PowerUnit]	Excitation power unit
`power_measured_at`	`Optional[str]`	Power measurement location (For example: objective, patch cable, etc)
`device_name`	`str`	Device name (Must match a device defined in the instrument.json)

LickSpoutConfig¶

Lick spout acquisition information

Field	Type	Title (Description)
`solution`	Liquid	Solution
`solution_valence`	Valence	Valence
`volume`	`float`	Volume
`volume_unit`	VolumeUnit	Volume unit
`relative_position`	List[AnatomicalRelative]	Initial relative position
`coordinate_system`	Optional[CoordinateSystem]	Device coordinate system
`transform`	Optional[List[Translation or Rotation or Scale or Affine]]	Device to acquisition transform (Entry coordinate, depth, and rotation in the Acquisition.coordinate_system)
`notes`	`Optional[str]`	Notes
`device_name`	`str`	Device name (Must match a device defined in the instrument.json)

LightEmittingDiodeConfig¶

Configuration of LED settings

Field	Type	Title (Description)
`power`	`Optional[float]`	Excitation power
`power_unit`	Optional[PowerUnit]	Excitation power unit
`power_measured_at`	`Optional[str]`	Power measurement location (For example: objective, patch cable, etc)
`device_name`	`str`	Device name (Must match a device defined in the instrument.json)

Liquid¶

Solution names

Name	Value
`WATER`	`Water`
`SUCROSE`	`Sucrose`
`QUININE`	`Quinine`
`CITRIC_ACID`	`Citric acid`
`OTHER`	`Other`

MISCameraConfig¶

Configuration for a camera used in a New Scale modular insertion system

Field	Type	Title (Description)
`detector_config`	DetectorConfig	Detector configuration
`module`	MISModuleConfig	Module
`device_name`	`str`	Device name (Must match a device defined in the instrument.json)
`relative_position`	List[AnatomicalRelative]	Relative position
`coordinate_system`	Optional[CoordinateSystem]	Device coordinate system
`transform`	Optional[List[Translation or Rotation or Scale or Affine]]	Device to instrument transform (Position and orientation of the device in the instrument coordinate system)

MISModuleConfig¶

Modular insertion system module configuration

Field	Type	Title (Description)
`arc_angle`	`float`	Arc Angle (deg)
`module_angle`	`float`	Module Angle (deg)
`rotation_angle`	`Optional[float]`	Rotation Angle (deg)
`angle_unit`	AngleUnit	Angle unit
`notes`	`Optional[str]`	Notes

MRAcquisitionType¶

MRI acquisition type

Name	Value
`SCAN_2D`	`2D`
`SCAN_3D`	`3D`

MRIScan¶

Configuration of a 3D scan

Field	Type	Title (Description)
`index`	`int`	Index (Index of the scan in the session, starting at 1)
`setup`	`bool`	Setup (Positioning, shim, and other pre-scan adjustments)
`pulse_sequence_type`	PulseSequenceType	Scan sequence (BIDS PulseSequenceType)
`mr_acquisition_type`	MRAcquisitionType	MR acquisition type (BIDS MRAcquisitionType / DICOM Tag 0018,0023)
`resolution`	Optional[Scale]	Voxel resolution
`resolution_unit`	Optional[SizeUnit]	Voxel resolution unit
`additional_scan_parameters`	`Optional[dict]`	Parameters
`rare_factor`	`Optional[int]`	RARE factor
`echo_time`	`decimal.Decimal`	Echo time (s) (BIDS EchoTime / DICOM Tag 0018,0081)
`echo_time_unit`	TimeUnit	Echo time unit
`effective_echo_time`	`Optional[decimal.Decimal]`	Effective echo time
`repetition_time`	`decimal.Decimal`	Repetition time (s) (BIDS RepetitionTime / DICOM Tag 0018,0080)
`repetition_time_unit`	TimeUnit	Repetition time unit
`scanner_coordinate_system`	Optional[CoordinateSystem]	Scanner coordinate system
`affine_transform`	Optional[List[Translation or Rotation or Scale or Affine]]	MRI Scan affine transform (NIFTI sform/qform, Bruker vc_transform, etc)
`subject_position`	SubjectPosition	Subject position
`notes`	`Optional[str]`	Notes
`device_name`	`str`	Device name (Must match a device defined in the instrument.json)

ManipulatorConfig¶

Configuration of a manipulator

Field	Type	Title (Description)
`coordinate_system`	CoordinateSystem	Device coordinate system
`local_axis_positions`	Translation	Local axis positions
`device_name`	`str`	Device name (Must match a device defined in the instrument.json)

MousePlatformConfig¶

Configuration for mouse platforms

Field	Type	Title (Description)
`objects_in_arena`	`Optional[List[str]]`	Objects in area
`active_control`	`bool`	Active control (True when movement of the mouse platform is dynamically controlled by the experimenter)
`device_name`	`str`	Device name (Must match a device defined in the instrument.json)

NeuronStructure¶

Neuronal structures captured in imaging planes

Name	Value
`SOMA`	`Soma`
`DENDRITE`	`Dendrite`
`AXON`	`Axon`
`OTHER`	`Other`

OlfactometerChannelInfo¶

Configuration of a channel in an olfactometer

Field	Type	Title (Description)
`channel_index`	`int`	Channel index
`odorant`	`str`	Odorant
`dilution`	`decimal.Decimal`	Odorant dilution
`dilution_unit`	ConcentrationUnit	Dilution unit

OlfactometerConfig¶

Configuration of olfactometer

Field	Type	Title (Description)
`channel_configs`	List[OlfactometerChannelInfo]	Channel configurations (List of channels with their odorant and concentration)
`device_name`	`str`	Device name (Must match a device defined in the instrument.json)

PatchCordConfig¶

Configuration of a patch cord and its output power to another device

Field	Type	Title (Description)
`channels`	List[Channel]	Channels
`device_name`	`str`	Device name (Must match a device defined in the instrument.json)

PlanarImage¶

Description of an N-D image acquired in a specific imaging plane

Field	Type	Title (Description)
`planes`	List[Plane or CoupledPlane or Slap2Plane]	Imaging planes
`channel_name`	`str`	Channel name
`dimensions_unit`	SizeUnit	Dimensions unit
`image_to_acquisition_transform`	List[Translation or Rotation or Scale or Affine]	Image to acquisition transform (Position, rotation, and scale of the image. Note that depth should be in the planes.)
`dimensions`	Optional[Scale]	Dimensions

PlanarImageStack¶

Description of a stack of images acquired in a specific imaging plane

Field	Type	Title (Description)
`power_function`	PowerFunction	Power function
`depth_start`	`float`	Starting depth
`depth_end`	`float`	Ending depth
`depth_step`	`float`	Step size
`depth_unit`	SizeUnit	Depth unit
`planes`	List[Plane or CoupledPlane or Slap2Plane]	Imaging planes
`channel_name`	`str`	Channel name
`dimensions_unit`	SizeUnit	Dimensions unit
`image_to_acquisition_transform`	List[Translation or Rotation or Scale or Affine]	Image to acquisition transform (Position, rotation, and scale of the image. Note that depth should be in the planes.)
`dimensions`	Optional[Scale]	Dimensions

Plane¶

Configuration of an imaging plane

Field	Type	Title (Description)
`depth`	`float`	Depth
`depth_unit`	SizeUnit	Depth unit
`power`	`float`	Power
`power_unit`	PowerUnit	Power unit
`targeted_structure`	BrainAtlas	Targeted structure

PowerFunction¶

Power functions

Name	Value
`CONSTANT`	`Constant`
`LINEAR`	`Linear`
`EXPONENTIAL`	`Exponential`
`OTHER`	`Other`

ProbeConfig¶

Configuration for a device inserted into a brain

Field	Type	Title (Description)
`primary_targeted_structure`	BrainAtlas	Targeted structure
`other_targeted_structure`	Optional[List[BrainAtlas]]	Other targeted structure
`atlas_coordinate`	Optional[AtlasCoordinate]	Target coordinate in Acquisition.atlas
`coordinate_system`	CoordinateSystem	Device coordinate system (Device coordinate system, defines un-rotated probe’s orientation relative to the Acquisition.coordinate_system)
`transform`	List[Translation or Rotation or Scale or Affine]	Device to acquisition transform (Entry coordinate, depth, and rotation in the Acquisition.coordinate_system)
`dye`	`Optional[str]`	Dye
`notes`	`Optional[str]`	Notes
`device_name`	`str`	Device name (Must match a device defined in the instrument.json)

PulseSequenceType¶

MRI pulse sequence type

Name	Value
`RARE`	`RARE`
`FLASH`	`FLASH`
`MSME`	`MSME`
`OTHER`	`Other`

SampleChamberConfig¶

Configuration of a sample chamber

Field	Type	Title (Description)
`chamber_immersion`	Immersion	Acquisition chamber immersion data
`sample_immersion`	Optional[Immersion]	Acquisition sample immersion data
`device_name`	`str`	Device name (Must match a device defined in the instrument.json)

SamplingStrategy¶

Description of an image sampling strategy

Field	Type	Title (Description)
`frame_rate`	`float`	Frame rate
`frame_rate_unit`	FrequencyUnit	Frame rate unit

Slap2Plane¶

Configuration of a SLAP2 imaging plane (all imaging ROIs of a specific acquisition type at a particular depth)

Field	Type	Title (Description)
`slap2_acquisition_type`	{Slap2AcquisitionType}	SLAP2 ROI acquisition type
`specimen_id`	`Optional[str]`	Specimen ID (Unique index identifying the cell being imaged: <subject_id>_###)
`fov_index`	`Optional[int]`	Field of view index (For FOVs that are imaged multiple times, assign a shared index to each instance of the FOV)
`structure_types`	Optional[List[NeuronStructure]]	Structure type
`y_dilations`	`List[int]`	Unique Y dilations
`y_dilations_unit`	SizeUnit	Dilation unit
`frame_rates`	`List[float]`	Unique frame rates
`frame_rates_unit`	FrequencyUnit	Frame rate unit
`depth`	`float`	Depth
`depth_unit`	SizeUnit	Depth unit
`power`	`float`	Power
`power_unit`	PowerUnit	Power unit
`targeted_structure`	BrainAtlas	Targeted structure

SpeakerConfig¶

Configuration of auditory speaker configuration

Field	Type	Title (Description)
`volume`	`Optional[float]`	Volume (dB)
`volume_unit`	Optional[SoundIntensityUnit]	Volume unit
`device_name`	`str`	Device name (Must match a device defined in the instrument.json)

StackStrategy¶

Description of a stack image sampling strategy

Field	Type	Title (Description)
`image_repeats`	`int`	Number of image repeats
`stack_repeats`	`int`	Number of stack repeats
`frame_rate`	`float`	Frame rate
`frame_rate_unit`	FrequencyUnit	Frame rate unit

SubjectPosition¶

Subject position

Name	Value
`PRONE`	`Prone`
`SUPINE`	`Supine`

TriggerType¶

Types of detector triggers

Name	Value
`INTERNAL`	`Internal`
`EXTERNAL`	`External`
`ANALOG`	`Analog`

Valence¶

Valence of a stimulus

Name	Value
`POSITIVE`	`Positive`
`NEGATIVE`	`Negative`
`NEUTRAL`	`Neutral`
`UNKNOWN`	`Unknown`