configs.md

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