Configs¶

Model definitions¶

AirPuffConfig¶

Air puff device configuration

Field	Type	Description
`valence`	Valence
`relative_position`	List[AnatomicalRelative]
`coordinate_system`	Optional[CoordinateSystem]
`transform`	Optional[List[Translation or Rotation or Scale or Affine]]
`pressure`	`Optional[float]`
`pressure_unit`	Optional[PressureUnit]
`duration`	`Optional[float]`
`device_name`	`str`	Must match a device defined in the instrument.json

CatheterConfig¶

Configuration of a catheter

Field	Type	Description
`targeted_structure`	MouseAnatomyModel	Use options from MouseBloodVessels
`device_name`	`str`	Must match a device defined in the instrument.json

Channel¶

Configuration of a channel

Field	Type	Description
`channel_name`	`str`
`intended_measurement`	`Optional[str]`	What signal is this channel measuring
`detector`	DetectorConfig
`additional_device_names`	Optional[List[DeviceConfig]]	Mirrors, dichroics, etc
`light_sources`	List[LaserConfig or LightEmittingDiodeConfig]
`variable_power`	`Optional[bool]`	Set to true when the power varies across Planes – put the power in the Plane.power field
`excitation_filters`	Optional[List[DeviceConfig]]
`emission_filters`	Optional[List[DeviceConfig]]
`emission_wavelength`	`Optional[int]`
`emission_wavelength_unit`	Optional[SizeUnit]

CoupledPlane¶

Configuration of a pair of coupled imaging plane

Field	Type	Description
`plane_index`	`int`
`coupled_plane_index`	`int`	Plane index of the coupled plane
`power_ratio`	`float`
`depth`	`float`
`depth_unit`	SizeUnit
`power`	`float`
`power_unit`	PowerUnit
`targeted_structure`	BrainAtlas

DetectorConfig¶

Configuration of detector settings

Field	Type	Description
`exposure_time`	`float`
`exposure_time_unit`	TimeUnit
`trigger_type`	TriggerType
`compression`	Optional[Code]	Compression algorithm used during acquisition
`device_name`	`str`	Must match a device defined in the instrument.json

DeviceConfig¶

Parent class for all configurations

Field	Type	Description
`device_name`	`str`	Must match a device defined in the instrument.json

EphysAssemblyConfig¶

Group of configurations for an ephys assembly

Field	Type	Description
`manipulator`	ManipulatorConfig
`probes`	List[ProbeConfig]
`modules`	Optional[List[MISModuleConfig]]	Configurations for conveniently tracking manipulator modules, e.g. on the New Scale dome.
`device_name`	`str`	Must match a device defined in the instrument.json

FiberAssemblyConfig¶

Inserted fiber photometry probe recorded in a stream

Field	Type	Description
`manipulator`	ManipulatorConfig
`probes`	List[ProbeConfig]
`patch_cords`	List[PatchCordConfig]
`device_name`	`str`	Must match a device defined in the instrument.json

Image¶

Description of an N-D image

Field	Type	Description
`channel_name`	`str`
`dimensions_unit`	SizeUnit
`image_to_acquisition_transform`	List[Translation or Rotation or Scale or Affine]	Position, rotation, and scale of the image. Note that depth should be in the planes.
`dimensions`	Optional[Scale]

ImageSPIM¶

Description of an N-D image acquired with SPIM

Field	Type	Description
`file_name`	`AssetPath`
`imaging_angle`	`int`	Angle of the detector relative to the image plane relative to perpendicular
`imaging_angle_unit`	AngleUnit
`image_start_time`	`Optional[datetime (timezone-aware)]`
`image_end_time`	`Optional[datetime (timezone-aware)]`
`channel_name`	`str`
`dimensions_unit`	SizeUnit
`image_to_acquisition_transform`	List[Translation or Rotation or Scale or Affine]	Position, rotation, and scale of the image. Note that depth should be in the planes.
`dimensions`	Optional[Scale]

ImagingConfig¶

Configuration of an imaging instrument

Field	Type	Description
`channels`	List[Channel or SlapChannel]
`coordinate_system`	Optional[CoordinateSystem]	Required for ImageSPIM objects and when the imaging coordinate system differs from the Acquisition.coordinate_system
`images`	List[PlanarImage or PlanarImageStack or ImageSPIM]
`sampling_strategy`	Optional[SamplingStrategy]
`device_name`	`str`	Must match a device defined in the instrument.json

Immersion¶

Configuration of immersion medium

Field	Type	Description
`medium`	ImmersionMedium
`refractive_index`	`float`

InterleavedStrategy¶

Description of an interleaved image sampling strategy

Field	Type	Description
`image_index_sequence`	`List[int]`
`frame_rate`	`float`
`frame_rate_unit`	FrequencyUnit

LaserConfig¶

Configuration of laser settings in an acquisition

Field	Type	Description
`wavelength`	`int`
`wavelength_unit`	SizeUnit
`power`	`Optional[float]`
`power_unit`	Optional[PowerUnit]
`device_name`	`str`	Must match a device defined in the instrument.json

LickSpoutConfig¶

Lick spout acquisition information

Field	Type	Description
`solution`	Liquid
`solution_valence`	Valence
`volume`	`float`
`volume_unit`	VolumeUnit
`relative_position`	List[AnatomicalRelative]
`coordinate_system`	Optional[CoordinateSystem]
`transform`	Optional[List[Translation or Rotation or Scale or Affine]]	Entry coordinate, depth, and rotation in the Acquisition.coordinate_system
`notes`	`Optional[str]`
`device_name`	`str`	Must match a device defined in the instrument.json

LightEmittingDiodeConfig¶

Configuration of LED settings

Field	Type	Description
`power`	`Optional[float]`
`power_unit`	Optional[PowerUnit]
`device_name`	`str`	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`

MISModuleConfig¶

Modular insertion system module configuration

Field	Type	Description
`arc_angle`	`float`
`module_angle`	`float`
`rotation_angle`	`Optional[float]`
`angle_unit`	AngleUnit
`notes`	`Optional[str]`

MRIScan¶

Configuration of a 3D scan

Field	Type	Description
`scan_index`	`int`
`scan_type`	ScanType
`primary_scan`	`bool`	Indicates the primary scan used for downstream analysis
`scan_sequence_type`	MriScanSequence
`rare_factor`	`Optional[int]`
`echo_time`	`decimal.Decimal`
`echo_time_unit`	TimeUnit
`effective_echo_time`	`Optional[decimal.Decimal]`
`repetition_time`	`decimal.Decimal`
`repetition_time_unit`	TimeUnit
`scan_coordinate_system`	Optional[CoordinateSystem]
`scan_affine_transform`	Optional[List[Translation or Rotation or Scale or Affine]]	NIFTI sform/qform, Bruker vc_transform, etc
`subject_position`	SubjectPosition
`resolution`	Optional[Scale]
`resolution_unit`	Optional[SizeUnit]
`additional_scan_parameters`	`dict`
`notes`	`Optional[str]`
`device_name`	`str`	Must match a device defined in the instrument.json

ManipulatorConfig¶

Configuration of a manipulator

Field	Type	Description
`coordinate_system`	CoordinateSystem
`local_axis_positions`	Translation
`device_name`	`str`	Must match a device defined in the instrument.json

MousePlatformConfig¶

Configuration for mouse platforms

Field	Type	Description
`objects_in_arena`	`Optional[List[str]]`
`active_control`	`bool`	True when movement of the mouse platform is dynamically controlled by the experimenter
`device_name`	`str`	Must match a device defined in the instrument.json

MriScanSequence¶

MRI scan sequence

Name	Value
`RARE`	`RARE`
`OTHER`	`Other`

PatchCordConfig¶

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

Field	Type	Description
`channels`	List[Channel]
`device_name`	`str`	Must match a device defined in the instrument.json

PlanarImage¶

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

Field	Type	Description
`planes`	List[Plane or CoupledPlane or SlapPlane]
`channel_name`	`str`
`dimensions_unit`	SizeUnit
`image_to_acquisition_transform`	List[Translation or Rotation or Scale or Affine]	Position, rotation, and scale of the image. Note that depth should be in the planes.
`dimensions`	Optional[Scale]

PlanarImageStack¶

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

Field	Type	Description
`power_function`	PowerFunction
`depth_start`	`float`
`depth_end`	`float`
`depth_step`	`float`
`depth_unit`	SizeUnit
`planes`	List[Plane or CoupledPlane or SlapPlane]
`channel_name`	`str`
`dimensions_unit`	SizeUnit
`image_to_acquisition_transform`	List[Translation or Rotation or Scale or Affine]	Position, rotation, and scale of the image. Note that depth should be in the planes.
`dimensions`	Optional[Scale]

Plane¶

Configuration of an imaging plane

Field	Type	Description
`depth`	`float`
`depth_unit`	SizeUnit
`power`	`float`
`power_unit`	PowerUnit
`targeted_structure`	BrainAtlas

PowerFunction¶

Power functions

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

ProbeConfig¶

Configuration for a device inserted into a brain

Field	Type	Description
`primary_targeted_structure`	BrainAtlas
`other_targeted_structure`	Optional[List[BrainAtlas]]
`atlas_coordinate`	Optional[AtlasCoordinate]
`coordinate_system`	CoordinateSystem
`transform`	List[Translation or Rotation or Scale or Affine]	Entry coordinate, depth, and rotation in the Acquisition.coordinate_system
`dye`	`Optional[str]`
`notes`	`Optional[str]`
`device_name`	`str`	Must match a device defined in the instrument.json

SampleChamberConfig¶

Configuration of a sample chamber

Field	Type	Description
`chamber_immersion`	Immersion
`sample_immersion`	Optional[Immersion]
`device_name`	`str`	Must match a device defined in the instrument.json

SamplingStrategy¶

Description of an image sampling strategy

Field	Type	Description
`frame_rate`	`float`
`frame_rate_unit`	FrequencyUnit

ScanType¶

Type of scan

Name	Value
`SETUP`	`Set Up`
`SCAN_3D`	`3D Scan`

SlapAcquisitionType¶

Type of slap acquisition

Name	Value
`PARENT`	`Parent`
`BRANCH`	`Branch`

SlapChannel¶

Configuration of a channel for Slap

Field	Type	Description
`dilation`	`int`
`dilation_unit`	SizeUnit
`description`	`Optional[str]`
`channel_name`	`str`
`intended_measurement`	`Optional[str]`	What signal is this channel measuring
`detector`	DetectorConfig
`additional_device_names`	Optional[List[DeviceConfig]]	Mirrors, dichroics, etc
`light_sources`	List[LaserConfig or LightEmittingDiodeConfig]
`variable_power`	`Optional[bool]`	Set to true when the power varies across Planes – put the power in the Plane.power field
`excitation_filters`	Optional[List[DeviceConfig]]
`emission_filters`	Optional[List[DeviceConfig]]
`emission_wavelength`	`Optional[int]`
`emission_wavelength_unit`	Optional[SizeUnit]

SlapPlane¶

Configuration of an imagine plane on a Slap microscope

Field	Type	Description
`dmd_dilation_x`	`int`
`dmd_dilation_y`	`int`
`dilation_unit`	SizeUnit
`slap_acquisition_type`	SlapAcquisitionType
`target_neuron`	`Optional[str]`
`target_branch`	`Optional[str]`
`path_to_array_of_frame_rates`	`AssetPath`	Relative path from metadata json to file
`depth`	`float`
`depth_unit`	SizeUnit
`power`	`float`
`power_unit`	PowerUnit
`targeted_structure`	BrainAtlas

SpeakerConfig¶

Configuration of auditory speaker configuration

Field	Type	Description
`volume`	`Optional[float]`
`volume_unit`	Optional[SoundIntensityUnit]
`device_name`	`str`	Must match a device defined in the instrument.json

StackStrategy¶

Description of a stack image sampling strategy

Field	Type	Description
`image_repeats`	`int`
`stack_repeats`	`int`
`frame_rate`	`float`
`frame_rate_unit`	FrequencyUnit

SubjectPosition¶

Subject position

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

TriggerType¶

Types of detector triggers

Name	Value
`INTERNAL`	`Internal`
`EXTERNAL`	`External`

Valence¶

Valence of a stimulus

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