Devices¶

Model definitions¶

AdditionalImagingDevice¶

Description of additional devices

Field	Type	Description
`imaging_device_type`	ImagingDeviceType
`name`	`str`
`serial_number`	`Optional[str]`
`manufacturer`	Optional[Organization]
`model`	`Optional[str]`
`additional_settings`	`Optional[dict]`
`notes`	`Optional[str]`

AirPuffDevice¶

Description of an air puff device

Field	Type	Description
`diameter`	`float`
`diameter_unit`	SizeUnit
`name`	`str`
`serial_number`	`Optional[str]`
`manufacturer`	Optional[Organization]
`model`	`Optional[str]`
`additional_settings`	`Optional[dict]`
`notes`	`Optional[str]`

Arena¶

Description of a rectangular arena

Field	Type	Description
`size`	Scale
`size_unit`	SizeUnit
`objects_in_arena`	List[Device]
`name`	`str`
`serial_number`	`Optional[str]`
`manufacturer`	Optional[Organization]
`model`	`Optional[str]`
`additional_settings`	`Optional[dict]`
`notes`	`Optional[str]`

Camera¶

Camera Detector

Field	Type	Description
`detector_type`	DetectorType
`manufacturer`	Organization
`data_interface`	DataInterface
`cooling`	Cooling
`frame_rate`	`Optional[decimal.Decimal]`	Frame rate being used
`frame_rate_unit`	Optional[FrequencyUnit]
`immersion`	Optional[ImmersionMedium]
`chroma`	Optional[CameraChroma]
`sensor_width`	`Optional[int]`
`sensor_height`	`Optional[int]`
`size_unit`	SizeUnit
`sensor_format`	`Optional[str]`
`sensor_format_unit`	`Optional[str]`
`bit_depth`	`Optional[int]`
`bin_mode`	BinMode
`bin_width`	`Optional[int]`
`bin_height`	`Optional[int]`
`bin_unit`	SizeUnit
`gain`	`Optional[decimal.Decimal]`
`crop_offset_x`	`Optional[int]`
`crop_offset_y`	`Optional[int]`
`crop_width`	`Optional[int]`
`crop_height`	`Optional[int]`
`crop_unit`	SizeUnit
`recording_software`	Optional[Software]
`driver`	Optional[DeviceDriver]
`driver_version`	`Optional[str]`
`name`	`str`
`serial_number`	`Optional[str]`
`model`	`Optional[str]`
`additional_settings`	`Optional[dict]`
`notes`	`Optional[str]`

CameraAssembly¶

Named assembly of a camera and lens (and optionally a filter)

Field	Type	Description
`name`	`str`
`target`	CameraTarget
`camera`	Camera
`lens`	Lens
`filter`	Optional[Filter]
`relative_position`	List[AnatomicalRelative]
`coordinate_system`	Optional[CoordinateSystem]
`transform`	Optional[List[Translation or Rotation or Scale or Affine]]	Position and orientation of the device in the instrument coordinate system

Catheter¶

Description of a catheter device

Field	Type	Description
`catheter_material`	CatheterMaterial
`catheter_design`	CatheterDesign
`catheter_port`	CatheterPort
`name`	`str`
`serial_number`	`Optional[str]`
`manufacturer`	Optional[Organization]
`model`	`Optional[str]`
`additional_settings`	`Optional[dict]`
`notes`	`Optional[str]`

CatheterDesign¶

Type of catheter design

Name	Value
`MAGNETIC`	`Magnetic`
`NONMAGNETIC`	`Non-magnetic`
`NA`	`N/A`

CatheterMaterial¶

Type of catheter material

Name	Value
`NAKED`	`Naked`
`SILICONE`	`VAB silicone`
`MESH`	`VAB mesh`

CatheterPort¶

Type of catheter port

Name	Value
`SINGLE`	`Single`
`DOUBLE`	`Double`

Computer¶

Description of a computer

Field	Type	Description
`operating_system`	`Optional[str]`
`name`	`str`
`serial_number`	`Optional[str]`
`manufacturer`	Optional[Organization]
`model`	`Optional[str]`
`additional_settings`	`Optional[dict]`
`notes`	`Optional[str]`

DAQChannel¶

Named input or output channel on a DAQ device

Field	Type	Description
`channel_name`	`str`
`channel_type`	DaqChannelType
`port`	`Optional[int]`
`channel_index`	`Optional[int]`
`sample_rate`	`Optional[decimal.Decimal]`
`sample_rate_unit`	Optional[FrequencyUnit]
`event_based_sampling`	`Optional[bool]`

DAQDevice¶

Data acquisition device containing multiple I/O channels

Field	Type	Description
`data_interface`	DataInterface
`manufacturer`	Organization
`channels`	List[DAQChannel]
`firmware_version`	`Optional[str]`
`hardware_version`	`Optional[str]`
`name`	`str`
`serial_number`	`Optional[str]`
`model`	`Optional[str]`
`additional_settings`	`Optional[dict]`
`notes`	`Optional[str]`

Detector¶

Description of a generic detector

Field	Type	Description
`detector_type`	DetectorType
`manufacturer`	Organization
`data_interface`	DataInterface
`cooling`	Cooling
`frame_rate`	`Optional[decimal.Decimal]`	Frame rate being used
`frame_rate_unit`	Optional[FrequencyUnit]
`immersion`	Optional[ImmersionMedium]
`chroma`	Optional[CameraChroma]
`sensor_width`	`Optional[int]`
`sensor_height`	`Optional[int]`
`size_unit`	SizeUnit
`sensor_format`	`Optional[str]`
`sensor_format_unit`	`Optional[str]`
`bit_depth`	`Optional[int]`
`bin_mode`	BinMode
`bin_width`	`Optional[int]`
`bin_height`	`Optional[int]`
`bin_unit`	SizeUnit
`gain`	`Optional[decimal.Decimal]`
`crop_offset_x`	`Optional[int]`
`crop_offset_y`	`Optional[int]`
`crop_width`	`Optional[int]`
`crop_height`	`Optional[int]`
`crop_unit`	SizeUnit
`recording_software`	Optional[Software]
`driver`	Optional[DeviceDriver]
`driver_version`	`Optional[str]`
`name`	`str`
`serial_number`	`Optional[str]`
`model`	`Optional[str]`
`additional_settings`	`Optional[dict]`
`notes`	`Optional[str]`

Device¶

Generic device

Field	Type	Description
`name`	`str`
`serial_number`	`Optional[str]`
`manufacturer`	Optional[Organization]
`model`	`Optional[str]`
`additional_settings`	`Optional[dict]`
`notes`	`Optional[str]`

DevicePosition¶

Position class for devices

Field	Type	Description
`relative_position`	List[AnatomicalRelative]
`coordinate_system`	Optional[CoordinateSystem]
`transform`	Optional[List[Translation or Rotation or Scale or Affine]]	Position and orientation of the device in the instrument coordinate system

DigitalMicromirrorDevice¶

Description of a Digital Micromirror Device (DMD)

Field	Type	Description
`max_dmd_patterns`	`int`
`double_bounce_design`	`bool`
`invert_pixel_values`	`bool`
`motion_padding_x`	`int`
`motion_padding_y`	`int`
`padding_unit`	SizeUnit
`pixel_size`	`decimal.Decimal`
`pixel_size_unit`	SizeUnit
`start_phase`	`decimal.Decimal`
`dmd_flip`	`bool`
`dmd_curtain`	`List[decimal.Decimal]`
`dmd_curtain_unit`	SizeUnit
`line_shear`	`List[int]`
`line_shear_unit`	SizeUnit
`name`	`str`
`serial_number`	`Optional[str]`
`manufacturer`	Optional[Organization]
`model`	`Optional[str]`
`additional_settings`	`Optional[dict]`
`notes`	`Optional[str]`

Disc¶

Description of a running disc (i.e. MindScope Disc)

Field	Type	Description
`radius`	`decimal.Decimal`
`radius_unit`	SizeUnit
`output`	Optional[DaqChannelType]	analog or digital electronics
`encoder`	`Optional[str]`	Encoder hardware type
`decoder`	`Optional[str]`	Decoder chip type
`encoder_firmware`	Optional[Software]	Firmware to read from decoder chip counts
`surface_material`	`Optional[str]`
`name`	`str`
`serial_number`	`Optional[str]`
`manufacturer`	Optional[Organization]
`model`	`Optional[str]`
`additional_settings`	`Optional[dict]`
`notes`	`Optional[str]`

Enclosure¶

Description of an enclosure

Field	Type	Description
`size`	Scale
`size_unit`	SizeUnit
`internal_material`	`Optional[str]`
`external_material`	`str`
`grounded`	`bool`
`laser_interlock`	`bool`
`air_filtration`	`bool`
`name`	`str`
`serial_number`	`Optional[str]`
`manufacturer`	Optional[Organization]
`model`	`Optional[str]`
`additional_settings`	`Optional[dict]`
`notes`	`Optional[str]`

EphysAssembly¶

Named assembly for combining a manipulator and ephys probes

Field	Type	Description
`name`	`str`
`manipulator`	Manipulator
`probes`	List[EphysProbe]

EphysProbe¶

Probe used in an ephys experiment

Field	Type	Description
`probe_model`	ProbeModel
`headstage`	Optional[Device]
`name`	`str`
`serial_number`	`Optional[str]`
`manufacturer`	Optional[Organization]
`model`	`Optional[str]`
`additional_settings`	`Optional[dict]`
`notes`	`Optional[str]`

FiberAssembly¶

Module for inserted fiber photometry recording

Field	Type	Description
`name`	`str`
`manipulator`	Manipulator
`fibers`	List[FiberProbe]

FiberPatchCord¶

Description of a patch cord

Field	Type	Description
`core_diameter`	`decimal.Decimal`
`numerical_aperture`	`decimal.Decimal`
`photobleaching_date`	`Optional[datetime.date]`
`name`	`str`
`serial_number`	`Optional[str]`
`manufacturer`	Optional[Organization]
`model`	`Optional[str]`
`additional_settings`	`Optional[dict]`
`notes`	`Optional[str]`

FiberProbe¶

Description of a fiber optic probe

Field	Type	Description
`core_diameter`	`decimal.Decimal`
`core_diameter_unit`	SizeUnit
`numerical_aperture`	`decimal.Decimal`
`ferrule_material`	Optional[FerruleMaterial]
`active_length`	`Optional[decimal.Decimal]`	Length of taper
`total_length`	`decimal.Decimal`
`length_unit`	SizeUnit
`name`	`str`
`serial_number`	`Optional[str]`
`manufacturer`	Optional[Organization]
`model`	`Optional[str]`
`additional_settings`	`Optional[dict]`
`notes`	`Optional[str]`

Filter¶

Filter used in a light path

Field	Type	Description
`filter_type`	FilterType
`manufacturer`	Organization
`cut_off_wavelength`	`Optional[int]`
`cut_on_wavelength`	`Optional[int]`
`center_wavelength`	`int or List[int] or NoneType`	Single wavelength or list of wavelengths for MULTIBAND or MULTI_NOTCH filters
`wavelength_unit`	SizeUnit
`name`	`str`
`serial_number`	`Optional[str]`
`model`	`Optional[str]`
`additional_settings`	`Optional[dict]`
`notes`	`Optional[str]`

HarpDevice¶

DAQ that uses the Harp protocol for synchronization and data transmission

Field	Type	Description
`manufacturer`	Organization
`harp_device_type`	HarpDeviceType
`core_version`	`Optional[str]`
`tag_version`	`Optional[str]`
`data_interface`	DataInterface
`is_clock_generator`	`bool`
`channels`	List[DAQChannel]
`firmware_version`	`Optional[str]`
`hardware_version`	`Optional[str]`
`name`	`str`
`serial_number`	`Optional[str]`
`model`	`Optional[str]`
`additional_settings`	`Optional[dict]`
`notes`	`Optional[str]`

Lamp¶

Description of a Lamp lightsource

Field	Type	Description
`wavelength_min`	`Optional[int]`
`wavelength_max`	`Optional[int]`
`wavelength_unit`	SizeUnit
`temperature`	`Optional[int]`
`temperature_unit`	Optional[TemperatureUnit]
`name`	`str`
`serial_number`	`Optional[str]`
`manufacturer`	Optional[Organization]
`model`	`Optional[str]`
`additional_settings`	`Optional[dict]`
`notes`	`Optional[str]`

Laser¶

Laser module with a specific wavelength (may be a sub-component of a larger assembly)

Field	Type	Description
`manufacturer`	Organization
`wavelength`	`int`
`wavelength_unit`	SizeUnit
`coupling`	Optional[Coupling]
`coupling_efficiency`	`Optional[decimal.Decimal]`
`coupling_efficiency_unit`	`"percent"`
`name`	`str`
`serial_number`	`Optional[str]`
`model`	`Optional[str]`
`additional_settings`	`Optional[dict]`
`notes`	`Optional[str]`

LaserAssembly¶

Named assembly combining a manipulator, lasers, collimator, and fibers

Field	Type	Description
`name`	`str`
`manipulator`	Manipulator
`lasers`	List[Laser]
`collimator`	Device
`fiber`	FiberPatchCord

Lens¶

Lens

Field	Type	Description
`manufacturer`	Organization
`name`	`str`
`serial_number`	`Optional[str]`
`model`	`Optional[str]`
`additional_settings`	`Optional[dict]`
`notes`	`Optional[str]`

LickSpout¶

Description of a lick spout

Field	Type	Description
`spout_diameter`	`decimal.Decimal`
`spout_diameter_unit`	SizeUnit
`solenoid_valve`	Device
`lick_sensor`	Device
`lick_sensor_type`	Optional[LickSensorType]
`name`	`str`
`serial_number`	`Optional[str]`
`manufacturer`	Optional[Organization]
`model`	`Optional[str]`
`additional_settings`	`Optional[dict]`
`notes`	`Optional[str]`

LickSpoutAssembly¶

Description of multiple lick spouts, possibly mounted on a stage

Field	Type	Description
`name`	`str`
`lick_spouts`	List[LickSpout]
`motorized_stage`	Optional[MotorizedStage]

LightAssembly¶

Named assembly of a light source and lens

Field	Type	Description
`name`	`str`
`light`	Laser or LightEmittingDiode or Lamp
`lens`	Lens
`filter`	Optional[Filter]

LightEmittingDiode¶

Description of a Light Emitting Diode (LED) device

Field	Type	Description
`manufacturer`	Organization
`wavelength`	`int`
`wavelength_unit`	SizeUnit
`bandwidth`	`Optional[int]`
`bandwidth_unit`	Optional[SizeUnit]
`name`	`str`
`serial_number`	`Optional[str]`
`model`	`Optional[str]`
`additional_settings`	`Optional[dict]`
`notes`	`Optional[str]`

Manipulator¶

Manipulator used on a dome module

Field	Type	Description
`manufacturer`	Organization
`name`	`str`
`serial_number`	`Optional[str]`
`model`	`Optional[str]`
`additional_settings`	`Optional[dict]`
`notes`	`Optional[str]`

Microscope¶

Description of a microscope

Field	Type	Description
`name`	`str`
`serial_number`	`Optional[str]`
`manufacturer`	Optional[Organization]
`model`	`Optional[str]`
`additional_settings`	`Optional[dict]`
`notes`	`Optional[str]`

Monitor¶

Description of visual display for visual stimuli

Field	Type	Description
`manufacturer`	Organization
`refresh_rate`	`int`
`width`	`int`
`height`	`int`
`size_unit`	SizeUnit
`viewing_distance`	`decimal.Decimal`
`viewing_distance_unit`	SizeUnit
`contrast`	`Optional[int]`	Monitor’s contrast setting
`brightness`	`Optional[int]`	Monitor’s brightness setting
`name`	`str`
`serial_number`	`Optional[str]`
`model`	`Optional[str]`
`additional_settings`	`Optional[dict]`
`notes`	`Optional[str]`
`relative_position`	List[AnatomicalRelative]
`coordinate_system`	Optional[CoordinateSystem]
`transform`	Optional[List[Translation or Rotation or Scale or Affine]]	Position and orientation of the device in the instrument coordinate system

MotorizedStage¶

Description of motorized stage

Field	Type	Description
`travel`	`decimal.Decimal`
`travel_unit`	SizeUnit
`firmware`	Optional[Software]
`name`	`str`
`serial_number`	`Optional[str]`
`manufacturer`	Optional[Organization]
`model`	`Optional[str]`
`additional_settings`	`Optional[dict]`
`notes`	`Optional[str]`

MyomatrixArray¶

Description of a Myomatrix array

Field	Type	Description
`array_type`	MyomatrixArrayType
`threads`	List[MyomatrixThread]
`name`	`str`
`serial_number`	`Optional[str]`
`manufacturer`	Optional[Organization]
`model`	`Optional[str]`
`additional_settings`	`Optional[dict]`
`notes`	`Optional[str]`

MyomatrixContact¶

Description of a contact on a myomatrix thread

Field	Type	Description
`body_part`	MouseAnatomyModel	Use MouseBodyParts
`relative_position`	AnatomicalRelative	Position relative to procedures coordinate system
`muscle`	MouseAnatomyModel	Use MouseEmgMuscles
`in_muscle`	`bool`

MyomatrixThread¶

Description of a thread of a myomatrix array

Field	Type	Description
`ground_electrode_location`	MouseAnatomyModel	Use GroundWireLocations
`contacts`	List[MyomatrixContact]

NeuropixelsBasestation¶

PXI-based Neuropixels DAQ

Field	Type	Description
`basestation_firmware_version`	`str`
`bsc_firmware_version`	`str`
`slot`	`int`
`ports`	List[ProbePort]
`data_interface`	DataInterface
`manufacturer`	Organization
`channels`	List[DAQChannel]
`firmware_version`	`Optional[str]`
`hardware_version`	`Optional[str]`
`name`	`str`
`serial_number`	`Optional[str]`
`model`	`Optional[str]`
`additional_settings`	`Optional[dict]`
`notes`	`Optional[str]`

Objective¶

Description of an objective device

Field	Type	Description
`numerical_aperture`	`decimal.Decimal`
`magnification`	`decimal.Decimal`
`immersion`	ImmersionMedium
`objective_type`	Optional[ObjectiveType]
`name`	`str`
`serial_number`	`Optional[str]`
`manufacturer`	Optional[Organization]
`model`	`Optional[str]`
`additional_settings`	`Optional[dict]`
`notes`	`Optional[str]`

Olfactometer¶

Description of an olfactometer for odor stimuli

Field	Type	Description
`manufacturer`	Organization
`harp_device_type`	HarpDeviceType
`channels`	List[OlfactometerChannel]
`core_version`	`Optional[str]`
`tag_version`	`Optional[str]`
`data_interface`	DataInterface
`is_clock_generator`	`bool`
`firmware_version`	`Optional[str]`
`hardware_version`	`Optional[str]`
`name`	`str`
`serial_number`	`Optional[str]`
`model`	`Optional[str]`
`additional_settings`	`Optional[dict]`
`notes`	`Optional[str]`

OlfactometerChannel¶

description of a Olfactometer channel

Field	Type	Description
`channel_index`	`int`
`channel_type`	OlfactometerChannelType
`flow_capacity`	`100 or 1000`
`flow_unit`	`str`

OlfactometerChannelType¶

Olfactometer channel types

Name	Value
`ODOR`	`Odor`
`CARRIER`	`Carrier`

OpenEphysAcquisitionBoard¶

Multichannel electrophysiology DAQ

Field	Type	Description
`ports`	List[ProbePort]
`data_interface`	`"DataInterface.USB"`
`manufacturer`	Organization
`channels`	List[DAQChannel]
`firmware_version`	`Optional[str]`
`hardware_version`	`Optional[str]`
`name`	`str`
`serial_number`	`Optional[str]`
`model`	`Optional[str]`
`additional_settings`	`Optional[dict]`
`notes`	`Optional[str]`

PockelsCell¶

Description of a Pockels Cell

Field	Type	Description
`polygonal_scanner`	`Optional[str]`	Must match name of Polygonal scanner
`on_time`	`Optional[decimal.Decimal]`
`off_time`	`Optional[decimal.Decimal]`
`time_setting_unit`	UnitlessUnit
`beam_modulation`	`Optional[decimal.Decimal]`
`beam_modulation_unit`	Optional[VoltageUnit]
`name`	`str`
`serial_number`	`Optional[str]`
`manufacturer`	Optional[Organization]
`model`	`Optional[str]`
`additional_settings`	`Optional[dict]`
`notes`	`Optional[str]`

PolygonalScanner¶

Description of a Polygonal scanner

Field	Type	Description
`speed`	`int`
`speed_unit`	SpeedUnit
`number_faces`	`int`
`name`	`str`
`serial_number`	`Optional[str]`
`manufacturer`	Optional[Organization]
`model`	`Optional[str]`
`additional_settings`	`Optional[dict]`
`notes`	`Optional[str]`

ProbePort¶

Port for a probe connection

Field	Type	Description
`index`	`int`
`probes`	`List[str]`

Scanner¶

Description of a MRI Scanner

Field	Type	Description
`magnetic_strength`	`float`
`magnetic_strength_unit`	MagneticFieldUnit
`name`	`str`
`serial_number`	`Optional[str]`
`manufacturer`	Optional[Organization]
`model`	`Optional[str]`
`additional_settings`	`Optional[dict]`
`notes`	`Optional[str]`

ScanningStage¶

Description of a scanning motorized stages

Field	Type	Description
`stage_axis_direction`	StageAxisDirection
`stage_axis_name`	AxisName
`travel`	`decimal.Decimal`
`travel_unit`	SizeUnit
`firmware`	Optional[Software]
`name`	`str`
`serial_number`	`Optional[str]`
`manufacturer`	Optional[Organization]
`model`	`Optional[str]`
`additional_settings`	`Optional[dict]`
`notes`	`Optional[str]`

Speaker¶

Description of a speaker for auditory stimuli

Field	Type	Description
`manufacturer`	Organization
`name`	`str`
`serial_number`	`Optional[str]`
`model`	`Optional[str]`
`additional_settings`	`Optional[dict]`
`notes`	`Optional[str]`
`relative_position`	List[AnatomicalRelative]
`coordinate_system`	Optional[CoordinateSystem]
`transform`	Optional[List[Translation or Rotation or Scale or Affine]]	Position and orientation of the device in the instrument coordinate system

Treadmill¶

Description of treadmill platform

Field	Type	Description
`treadmill_width`	`decimal.Decimal`
`width_unit`	SizeUnit
`encoder`	Optional[Device]
`pulse_per_revolution`	`Optional[int]`
`name`	`str`
`serial_number`	`Optional[str]`
`manufacturer`	Optional[Organization]
`model`	`Optional[str]`
`additional_settings`	`Optional[dict]`
`notes`	`Optional[str]`

Tube¶

Description of a tube platform

Field	Type	Description
`diameter`	`decimal.Decimal`
`diameter_unit`	SizeUnit
`name`	`str`
`serial_number`	`Optional[str]`
`manufacturer`	Optional[Organization]
`model`	`Optional[str]`
`additional_settings`	`Optional[dict]`
`notes`	`Optional[str]`

Wheel¶

Description of a running wheel

Field	Type	Description
`radius`	`decimal.Decimal`
`width`	`decimal.Decimal`
`size_unit`	SizeUnit
`encoder`	Device
`pulse_per_revolution`	`int`
`magnetic_brake`	Device
`torque_sensor`	Device
`name`	`str`
`serial_number`	`Optional[str]`
`manufacturer`	Optional[Organization]
`model`	`Optional[str]`
`additional_settings`	`Optional[dict]`
`notes`	`Optional[str]`