# Configs ## Model definitions ### AirPuffConfig Air puff device configuration | Field | Type | Title (Description) | |-------|------|-------------| | `valence` | [Valence](#valence) | Valence | | `relative_position` | List[[AnatomicalRelative](../aind_data_schema_models/coordinates.md#anatomicalrelative)] | Initial relative position | | `coordinate_system` | Optional[[CoordinateSystem](coordinates.md#coordinatesystem)] | Device coordinate system | | `transform` | Optional[List[[Translation](coordinates.md#translation) or [Rotation](coordinates.md#rotation) or [Scale](coordinates.md#scale) or [Affine](coordinates.md#affine)]] | Device to acquisition transform | | `pressure` | `Optional[float]` | Pressure | | `pressure_unit` | Optional[[PressureUnit](../aind_data_schema_models/units.md#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](../aind_data_schema_models/external.md#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](#detectorconfig) | Detector configuration | | `additional_device_names` | Optional[List[[DeviceConfig](#deviceconfig)]] | Additional device names (Mirrors, dichroics, etc) | | `light_sources` | List[[LaserConfig](#laserconfig) or [LightEmittingDiodeConfig](#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](#deviceconfig)]] | Excitation filters | | `emission_filters` | Optional[List[[DeviceConfig](#deviceconfig)]] | Emission filters | | `emission_wavelength` | `Optional[int]` | Emission wavelength | | `emission_wavelength_unit` | Optional[[SizeUnit](../aind_data_schema_models/units.md#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](../aind_data_schema_models/units.md#sizeunit) | Depth unit | | `power` | `float` | Power | | `power_unit` | [PowerUnit](../aind_data_schema_models/units.md#powerunit) | Power unit | | `targeted_structure` | [BrainAtlas](../aind_data_schema_models/brain_atlas.md#ccfv3) | Targeted structure | ### DetectorConfig Configuration of detector settings | Field | Type | Title (Description) | |-------|------|-------------| | `exposure_time` | `Optional[float]` | Exposure time | | `exposure_time_unit` | [TimeUnit](../aind_data_schema_models/units.md#timeunit) | Exposure time unit | | `trigger_type` | [TriggerType](#triggertype) | Trigger type | | `compression` | Optional[[Code](identifiers.md#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](../aind_data_schema_models/units.md#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](#manipulatorconfig) | Manipulator configuration | | `probes` | List[[ProbeConfig](#probeconfig)] | Probe configurations | | `modules` | Optional[List[[MISModuleConfig](#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](#manipulatorconfig) | Manipulator configuration | | `probes` | List[[ProbeConfig](#probeconfig)] | Probe configurations | | `patch_cords` | List[[PatchCordConfig](#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](../aind_data_schema_models/units.md#sizeunit) | Dimensions unit | | `image_to_acquisition_transform` | List[[Translation](coordinates.md#translation) or [Rotation](coordinates.md#rotation) or [Scale](coordinates.md#scale) or [Affine](coordinates.md#affine)] | Image to acquisition transform (Position, rotation, and scale of the image. Note that depth should be in the planes.) | | `dimensions` | Optional[[Scale](coordinates.md#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](../aind_data_schema_models/units.md#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](../aind_data_schema_models/units.md#sizeunit) | Dimensions unit | | `image_to_acquisition_transform` | List[[Translation](coordinates.md#translation) or [Rotation](coordinates.md#rotation) or [Scale](coordinates.md#scale) or [Affine](coordinates.md#affine)] | Image to acquisition transform (Position, rotation, and scale of the image. Note that depth should be in the planes.) | | `dimensions` | Optional[[Scale](coordinates.md#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](coordinates.md#coordinatesystem)] | Coordinate system (Required for ImageSPIM objects and when the imaging coordinate system differs from the Acquisition.coordinate_system) | | `images` | List[[PlanarImage](#planarimage) or [PlanarImageStack](#planarimagestack) or [ImageSPIM](#imagespim)] | Images | | `sampling_strategy` | Optional[[SamplingStrategy](#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](../aind_data_schema_models/devices.md#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](../aind_data_schema_models/units.md#frequencyunit) | Frame rate unit | ### LaserConfig Configuration of laser settings in an acquisition | Field | Type | Title (Description) | |-------|------|-------------| | `wavelength` | `int` | Wavelength (nm) | | `wavelength_unit` | [SizeUnit](../aind_data_schema_models/units.md#sizeunit) | Wavelength unit | | `power` | `Optional[float]` | Excitation power | | `power_unit` | Optional[[PowerUnit](../aind_data_schema_models/units.md#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](#liquid) | Solution | | `solution_valence` | [Valence](#valence) | Valence | | `volume` | `float` | Volume | | `volume_unit` | [VolumeUnit](../aind_data_schema_models/units.md#volumeunit) | Volume unit | | `relative_position` | List[[AnatomicalRelative](../aind_data_schema_models/coordinates.md#anatomicalrelative)] | Initial relative position | | `coordinate_system` | Optional[[CoordinateSystem](coordinates.md#coordinatesystem)] | Device coordinate system | | `transform` | Optional[List[[Translation](coordinates.md#translation) or [Rotation](coordinates.md#rotation) or [Scale](coordinates.md#scale) or [Affine](coordinates.md#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](../aind_data_schema_models/units.md#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](#detectorconfig) | Detector configuration | | `module` | [MISModuleConfig](#mismoduleconfig) | Module | | `device_name` | `str` | Device name (Must match a device defined in the instrument.json) | | `relative_position` | List[[AnatomicalRelative](../aind_data_schema_models/coordinates.md#anatomicalrelative)] | Relative position | | `coordinate_system` | Optional[[CoordinateSystem](coordinates.md#coordinatesystem)] | Device coordinate system | | `transform` | Optional[List[[Translation](coordinates.md#translation) or [Rotation](coordinates.md#rotation) or [Scale](coordinates.md#scale) or [Affine](coordinates.md#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](../aind_data_schema_models/units.md#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](#pulsesequencetype) | Scan sequence (BIDS PulseSequenceType) | | `mr_acquisition_type` | [MRAcquisitionType](#mracquisitiontype) | MR acquisition type (BIDS MRAcquisitionType / DICOM Tag 0018,0023) | | `resolution` | Optional[[Scale](coordinates.md#scale)] | Voxel resolution | | `resolution_unit` | Optional[[SizeUnit](../aind_data_schema_models/units.md#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](../aind_data_schema_models/units.md#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](../aind_data_schema_models/units.md#timeunit) | Repetition time unit | | `scanner_coordinate_system` | Optional[[CoordinateSystem](coordinates.md#coordinatesystem)] | Scanner coordinate system | | `affine_transform` | Optional[List[[Translation](coordinates.md#translation) or [Rotation](coordinates.md#rotation) or [Scale](coordinates.md#scale) or [Affine](coordinates.md#affine)]] | MRI Scan affine transform (NIFTI sform/qform, Bruker vc_transform, etc) | | `subject_position` | [SubjectPosition](#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](coordinates.md#coordinatesystem) | Device coordinate system | | `local_axis_positions` | [Translation](coordinates.md#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](../aind_data_schema_models/units.md#concentrationunit) | Dilution unit | ### OlfactometerConfig Configuration of olfactometer | Field | Type | Title (Description) | |-------|------|-------------| | `channel_configs` | List[[OlfactometerChannelInfo](#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](#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](#plane) or [CoupledPlane](#coupledplane) or [Slap2Plane](#slap2plane)] | Imaging planes | | `channel_name` | `str` | Channel name | | `dimensions_unit` | [SizeUnit](../aind_data_schema_models/units.md#sizeunit) | Dimensions unit | | `image_to_acquisition_transform` | List[[Translation](coordinates.md#translation) or [Rotation](coordinates.md#rotation) or [Scale](coordinates.md#scale) or [Affine](coordinates.md#affine)] | Image to acquisition transform (Position, rotation, and scale of the image. Note that depth should be in the planes.) | | `dimensions` | Optional[[Scale](coordinates.md#scale)] | Dimensions | ### PlanarImageStack Description of a stack of images acquired in a specific imaging plane | Field | Type | Title (Description) | |-------|------|-------------| | `power_function` | [PowerFunction](#powerfunction) | Power function | | `depth_start` | `float` | Starting depth | | `depth_end` | `float` | Ending depth | | `depth_step` | `float` | Step size | | `depth_unit` | [SizeUnit](../aind_data_schema_models/units.md#sizeunit) | Depth unit | | `planes` | List[[Plane](#plane) or [CoupledPlane](#coupledplane) or [Slap2Plane](#slap2plane)] | Imaging planes | | `channel_name` | `str` | Channel name | | `dimensions_unit` | [SizeUnit](../aind_data_schema_models/units.md#sizeunit) | Dimensions unit | | `image_to_acquisition_transform` | List[[Translation](coordinates.md#translation) or [Rotation](coordinates.md#rotation) or [Scale](coordinates.md#scale) or [Affine](coordinates.md#affine)] | Image to acquisition transform (Position, rotation, and scale of the image. Note that depth should be in the planes.) | | `dimensions` | Optional[[Scale](coordinates.md#scale)] | Dimensions | ### Plane Configuration of an imaging plane | Field | Type | Title (Description) | |-------|------|-------------| | `depth` | `float` | Depth | | `depth_unit` | [SizeUnit](../aind_data_schema_models/units.md#sizeunit) | Depth unit | | `power` | `float` | Power | | `power_unit` | [PowerUnit](../aind_data_schema_models/units.md#powerunit) | Power unit | | `targeted_structure` | [BrainAtlas](../aind_data_schema_models/brain_atlas.md#ccfv3) | 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](../aind_data_schema_models/brain_atlas.md#ccfv3) | Targeted structure | | `other_targeted_structure` | Optional[List[[BrainAtlas](../aind_data_schema_models/brain_atlas.md#ccfv3)]] | Other targeted structure | | `atlas_coordinate` | Optional[[AtlasCoordinate](coordinates.md#atlascoordinate)] | Target coordinate in Acquisition.atlas | | `coordinate_system` | [CoordinateSystem](coordinates.md#coordinatesystem) | Device coordinate system (Device coordinate system, defines un-rotated probe's orientation relative to the Acquisition.coordinate_system) | | `transform` | List[[Translation](coordinates.md#translation) or [Rotation](coordinates.md#rotation) or [Scale](coordinates.md#scale) or [Affine](coordinates.md#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](#immersion) | Acquisition chamber immersion data | | `sample_immersion` | Optional[[Immersion](#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](../aind_data_schema_models/units.md#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: _###) | | `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](#neuronstructure)]] | Structure type | | `y_dilations` | `List[int]` | Unique Y dilations | | `y_dilations_unit` | [SizeUnit](../aind_data_schema_models/units.md#sizeunit) | Dilation unit | | `frame_rates` | `List[float]` | Unique frame rates | | `frame_rates_unit` | [FrequencyUnit](../aind_data_schema_models/units.md#frequencyunit) | Frame rate unit | | `depth` | `float` | Depth | | `depth_unit` | [SizeUnit](../aind_data_schema_models/units.md#sizeunit) | Depth unit | | `power` | `float` | Power | | `power_unit` | [PowerUnit](../aind_data_schema_models/units.md#powerunit) | Power unit | | `targeted_structure` | [BrainAtlas](../aind_data_schema_models/brain_atlas.md#ccfv3) | Targeted structure | ### SpeakerConfig Configuration of auditory speaker configuration | Field | Type | Title (Description) | |-------|------|-------------| | `volume` | `Optional[float]` | Volume (dB) | | `volume_unit` | Optional[[SoundIntensityUnit](../aind_data_schema_models/units.md#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](../aind_data_schema_models/units.md#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` |