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Devices

Model definitions

AdditionalImagingDevice

Description of additional devices

Field Type Title (Description)
imaging_device_type ImagingDeviceType Device type
name str Device name
serial_number Optional[str] Serial number
manufacturer Optional[Organization] Manufacturer
model Optional[str] Model
additional_settings Optional[dict] Additional parameters
notes Optional[str] Notes

AirPuffDevice

Description of an air puff device

Field Type Title (Description)
diameter float Spout diameter
diameter_unit SizeUnit Size unit
name str Device name
serial_number Optional[str] Serial number
manufacturer Optional[Organization] Manufacturer
model Optional[str] Model
additional_settings Optional[dict] Additional parameters
notes Optional[str] Notes

Arena

Description of a rectangular arena

Field Type Title (Description)
size Scale 3D Size
size_unit SizeUnit Size unit
objects_in_arena List[Device] Objects in arena
name str Device name
serial_number Optional[str] Serial number
manufacturer Optional[Organization] Manufacturer
model Optional[str] Model
additional_settings Optional[dict] Additional parameters
notes Optional[str] Notes

Camera

Camera Detector

Field Type Title (Description)
detector_type DetectorType
manufacturer Organization
data_interface DataInterface Data interface
cooling Cooling Cooling
frame_rate Optional[decimal.Decimal] Frame rate (Hz) (Frame rate being used)
frame_rate_unit Optional[FrequencyUnit] Frame rate unit
immersion Optional[ImmersionMedium] Immersion
chroma Optional[CameraChroma] Camera chroma
sensor_width Optional[int] Width of the sensor (pixels)
sensor_height Optional[int] Height of the sensor (pixels)
size_unit SizeUnit Size unit
sensor_format Optional[str] Sensor format
sensor_format_unit Optional[str] Sensor format unit
bit_depth Optional[int] Bit depth
bin_mode BinMode Detector binning mode
bin_width Optional[int] Bin width
bin_height Optional[int] Bin height
bin_unit SizeUnit Bin size unit
gain Optional[decimal.Decimal] Gain
crop_offset_x Optional[int] Crop offset x
crop_offset_y Optional[int] Crop offset y
crop_width Optional[int] Crop width
crop_height Optional[int] Crop width
crop_unit SizeUnit Crop size unit
recording_software Optional[Software] Recording software
driver Optional[DeviceDriver] Driver
driver_version Optional[str] Driver version
name str Device name
serial_number Optional[str] Serial number
model Optional[str] Model
additional_settings Optional[dict] Additional parameters
notes Optional[str] Notes

CameraAssembly

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

Field Type Title (Description)
name str Camera assembly name
target CameraTarget Camera target
camera Camera Camera
lens Lens Lens
filter Optional[Filter] Filter
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)

Catheter

Description of a catheter device

Field Type Title (Description)
catheter_material CatheterMaterial Catheter material
catheter_design CatheterDesign Catheter design
catheter_port CatheterPort Catheter port
name str Device name
serial_number Optional[str] Serial number
manufacturer Optional[Organization] Manufacturer
model Optional[str] Model
additional_settings Optional[dict] Additional parameters
notes Optional[str] Notes

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 Title (Description)
operating_system Optional[str] Operating system
name str Device name
serial_number Optional[str] Serial number
manufacturer Optional[Organization] Manufacturer
model Optional[str] Model
additional_settings Optional[dict] Additional parameters
notes Optional[str] Notes

DAQChannel

Named input or output channel on a DAQ device

Field Type Title (Description)
channel_name str DAQ channel name
channel_type DaqChannelType DAQ channel type
port Optional[int] DAQ port
channel_index Optional[int] [DEPRECATED] Use DAQChannel.port instead. DAQ channel index
sample_rate Optional[decimal.Decimal] DAQ channel sample rate (Hz)
sample_rate_unit Optional[FrequencyUnit] Sample rate unit
event_based_sampling Optional[bool] Set to true if DAQ channel is sampled at irregular intervals

DAQDevice

Data acquisition device containing multiple I/O channels

Field Type Title (Description)
data_interface DataInterface Type of connection to PC
manufacturer Organization
channels List[DAQChannel] DAQ channels
firmware_version Optional[str] Firmware version
hardware_version Optional[str] Hardware version
name str Device name
serial_number Optional[str] Serial number
model Optional[str] Model
additional_settings Optional[dict] Additional parameters
notes Optional[str] Notes

Detector

Description of a generic detector

Field Type Title (Description)
detector_type DetectorType Detector Type
manufacturer Organization
data_interface DataInterface Data interface
cooling Cooling Cooling
frame_rate Optional[decimal.Decimal] Frame rate (Hz) (Frame rate being used)
frame_rate_unit Optional[FrequencyUnit] Frame rate unit
immersion Optional[ImmersionMedium] Immersion
chroma Optional[CameraChroma] Camera chroma
sensor_width Optional[int] Width of the sensor (pixels)
sensor_height Optional[int] Height of the sensor (pixels)
size_unit SizeUnit Size unit
sensor_format Optional[str] Sensor format
sensor_format_unit Optional[str] Sensor format unit
bit_depth Optional[int] Bit depth
bin_mode BinMode Detector binning mode
bin_width Optional[int] Bin width
bin_height Optional[int] Bin height
bin_unit SizeUnit Bin size unit
gain Optional[decimal.Decimal] Gain
crop_offset_x Optional[int] Crop offset x
crop_offset_y Optional[int] Crop offset y
crop_width Optional[int] Crop width
crop_height Optional[int] Crop width
crop_unit SizeUnit Crop size unit
recording_software Optional[Software] Recording software
driver Optional[DeviceDriver] Driver
driver_version Optional[str] Driver version
name str Device name
serial_number Optional[str] Serial number
model Optional[str] Model
additional_settings Optional[dict] Additional parameters
notes Optional[str] Notes

Device

Generic device

Field Type Title (Description)
name str Device name
serial_number Optional[str] Serial number
manufacturer Optional[Organization] Manufacturer
model Optional[str] Model
additional_settings Optional[dict] Additional parameters
notes Optional[str] Notes

DevicePosition

Position class for devices

Field Type Title (Description)
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)

DigitalMicromirrorDevice

Description of a Digital Micromirror Device (DMD)

Field Type Title (Description)
max_dmd_patterns int Max DMD patterns
invert_pixel_values bool Invert pixel values
motion_padding_x int Motion padding X (pixels)
motion_padding_y int Motion padding Y (pixels)
padding_unit SizeUnit Padding unit
pixel_size float DMD Pixel size (fraction of line scan period)
start_phase float DMD Start phase (fraction of line scan period)
dmd_curtain List[float] DMD Curtain (fraction of DMD scan period)
line_shear_anchors List[float] Line shear anchors at top and bottom of field of view (pixels)
line_shear_anchors_unit SizeUnit Line shear anchors unit
name str Device name
serial_number Optional[str] Serial number
manufacturer Optional[Organization] Manufacturer
model Optional[str] Model
additional_settings Optional[dict] Additional parameters
notes Optional[str] Notes

Disc

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

Field Type Title (Description)
radius decimal.Decimal Radius (cm)
radius_unit SizeUnit radius unit
output Optional[DaqChannelType] (analog or digital electronics)
encoder Optional[str] Encoder (Encoder hardware type)
decoder Optional[str] Decoder (Decoder chip type)
encoder_firmware Optional[Software] Encoder firmware (Firmware to read from decoder chip counts)
surface_material Optional[str] Surface material
name str Device name
serial_number Optional[str] Serial number
manufacturer Optional[Organization] Manufacturer
model Optional[str] Model
additional_settings Optional[dict] Additional parameters
notes Optional[str] Notes

Enclosure

Description of an enclosure

Field Type Title (Description)
size Scale Size
size_unit SizeUnit Size unit
internal_material Optional[str] Internal material
external_material str External material
grounded bool Grounded
laser_interlock bool Laser interlock
air_filtration bool Air filtration
name str Device name
serial_number Optional[str] Serial number
manufacturer Optional[Organization] Manufacturer
model Optional[str] Model
additional_settings Optional[dict] Additional parameters
notes Optional[str] Notes

EphysAssembly

Named assembly for combining a manipulator and extracellular ephys probes

Field Type Title (Description)
name str Ephys assembly name
manipulator Manipulator Manipulator
probes List[EphysProbe] Probes that are held by this module

EphysProbe

Probe used in an extracellular ephys experiment

Field Type Title (Description)
probe_model ProbeModel Probe model
headstage Optional[Device] Headstage for this probe
name str Device name
serial_number Optional[str] Serial number
manufacturer Optional[Organization] Manufacturer
model Optional[str] Model
additional_settings Optional[dict] Additional parameters
notes Optional[str] Notes

FiberAssembly

Module for inserted fiber photometry recording

Field Type Title (Description)
name str Fiber assembly name
manipulator Manipulator Manipulator
fibers List[FiberProbe] Probes that are held by this module

FiberPatchCord

Description of a patch cord

Field Type Title (Description)
core_diameter decimal.Decimal Core diameter (um)
numerical_aperture decimal.Decimal Numerical aperture
photobleaching_date Optional[datetime.date] Photobleaching date
name str Device name
serial_number Optional[str] Serial number
manufacturer Optional[Organization] Manufacturer
model Optional[str] Model
additional_settings Optional[dict] Additional parameters
notes Optional[str] Notes

FiberProbe

Description of a fiber optic probe

Field Type Title (Description)
core_diameter decimal.Decimal Core diameter (um)
core_diameter_unit SizeUnit Core diameter unit
numerical_aperture decimal.Decimal Numerical aperture
ferrule_material Optional[FerruleMaterial] Ferrule material
active_length Optional[decimal.Decimal] Active length (mm) (Length of taper)
total_length decimal.Decimal Total length (mm)
length_unit SizeUnit Length unit
name str Device name
serial_number Optional[str] Serial number
manufacturer Optional[Organization] Manufacturer
model Optional[str] Model
additional_settings Optional[dict] Additional parameters
notes Optional[str] Notes

Filter

Filter used in a light path

Field Type Title (Description)
filter_type FilterType Type of filter
manufacturer Organization
cut_off_wavelength Optional[int] Cut-off wavelength (nm)
cut_on_wavelength Optional[int] Cut-on wavelength (nm)
center_wavelength int or List[int] or NoneType Center wavelength (nm) (Single wavelength or list of wavelengths for MULTIBAND or MULTI_NOTCH filters)
wavelength_unit SizeUnit Wavelength unit
name str Device name
serial_number Optional[str] Serial number
model Optional[str] Model
additional_settings Optional[dict] Additional parameters
notes Optional[str] Notes

HarpDevice

DAQ that uses the Harp protocol for synchronization and data transmission

Field Type Title (Description)
manufacturer Organization
harp_device_type HarpDeviceType Type of Harp device
core_version Optional[str] Core version
tag_version Optional[str] Tag version
data_interface DataInterface Data interface
is_clock_generator bool Is Clock Generator
channels List[DAQChannel] DAQ channels
firmware_version Optional[str] Firmware version
hardware_version Optional[str] Hardware version
name str Device name
serial_number Optional[str] Serial number
model Optional[str] Model
additional_settings Optional[dict] Additional parameters
notes Optional[str] Notes

Lamp

Description of a Lamp lightsource

Field Type Title (Description)
wavelength_min Optional[int] Wavelength minimum (nm)
wavelength_max Optional[int] Wavelength maximum (nm)
wavelength_unit SizeUnit Wavelength unit
temperature Optional[int] Temperature (K)
temperature_unit Optional[TemperatureUnit] Temperature unit
name str Device name
serial_number Optional[str] Serial number
manufacturer Optional[Organization] Manufacturer
model Optional[str] Model
additional_settings Optional[dict] Additional parameters
notes Optional[str] Notes

Laser

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

Field Type Title (Description)
manufacturer Organization
wavelength int Wavelength (nm)
wavelength_unit SizeUnit Wavelength unit
coupling Optional[Coupling] Coupling
coupling_efficiency Optional[decimal.Decimal] Coupling efficiency (percent)
coupling_efficiency_unit "percent" Coupling efficiency unit
name str Device name
serial_number Optional[str] Serial number
model Optional[str] Model
additional_settings Optional[dict] Additional parameters
notes Optional[str] Notes

LaserAssembly

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

Field Type Title (Description)
name str Laser assembly name
manipulator Manipulator Manipulator
lasers List[Laser] Lasers connected to this module
collimator Device Collimator
fiber FiberPatchCord Fiber patch

Lens

Lens

Field Type Title (Description)
manufacturer Organization
name str Device name
serial_number Optional[str] Serial number
model Optional[str] Model
additional_settings Optional[dict] Additional parameters
notes Optional[str] Notes

LickSpout

Description of a lick spout

Field Type Title (Description)
spout_diameter decimal.Decimal Spout diameter (mm)
spout_diameter_unit SizeUnit Spout diameter unit
solenoid_valve Device Solenoid valve
lick_sensor Device or HarpDevice Lick sensor
lick_sensor_type Optional[LickSensorType] Lick sensor type
name str Device name
serial_number Optional[str] Serial number
manufacturer Optional[Organization] Manufacturer
model Optional[str] Model
additional_settings Optional[dict] Additional parameters
notes Optional[str] Notes

LickSpoutAssembly

Description of multiple lick spouts, possibly mounted on a stage

Field Type Title (Description)
name str Lick spout assembly name
lick_spouts List[LickSpout] Water spouts
motorized_stage Optional[MotorizedStage] Motorized stage

LightAssembly

Named assembly of a light source and lens

Field Type Title (Description)
name str Light assembly name
light Laser or LightEmittingDiode or Lamp
lens Lens Lens
filter Optional[Filter] Filter

LightEmittingDiode

Description of a Light Emitting Diode (LED) device

Field Type Title (Description)
manufacturer Organization
wavelength int Wavelength (nm)
wavelength_unit SizeUnit Wavelength unit
bandwidth Optional[int] Bandwidth (FWHM)
bandwidth_unit Optional[SizeUnit] Bandwidth unit
name str Device name
serial_number Optional[str] Serial number
model Optional[str] Model
additional_settings Optional[dict] Additional parameters
notes Optional[str] Notes

Manipulator

Manipulator used on a dome module

Field Type Title (Description)
manufacturer Organization
name str Device name
serial_number Optional[str] Serial number
model Optional[str] Model
additional_settings Optional[dict] Additional parameters
notes Optional[str] Notes

Microscope

Description of a microscope

Field Type Title (Description)
name str Device name
serial_number Optional[str] Serial number
manufacturer Optional[Organization] Manufacturer
model Optional[str] Model
additional_settings Optional[dict] Additional parameters
notes Optional[str] Notes

Monitor

Description of visual display for visual stimuli

Field Type Title (Description)
manufacturer Organization
refresh_rate int Refresh rate (Hz)
width int Width (pixels)
height int Height (pixels)
size_unit SizeUnit Size unit
viewing_distance decimal.Decimal Viewing distance (cm)
viewing_distance_unit SizeUnit Viewing distance unit
contrast Optional[int] Contrast (Monitor's contrast setting)
contrast_unit Optional[UnitlessUnit] Contrast unit
brightness Optional[int] Brightness (Monitor's brightness setting)
brightness_unit Optional[UnitlessUnit] Brightness unit
name str Device name
serial_number Optional[str] Serial number
model Optional[str] Model
additional_settings Optional[dict] Additional parameters
notes Optional[str] Notes
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)

MotorizedStage

Description of motorized stage

Field Type Title (Description)
travel decimal.Decimal Travel of device (mm)
travel_unit SizeUnit Travel unit
firmware Optional[Software] Firmware
name str Device name
serial_number Optional[str] Serial number
manufacturer Optional[Organization] Manufacturer
model Optional[str] Model
additional_settings Optional[dict] Additional parameters
notes Optional[str] Notes

MyomatrixArray

Description of a Myomatrix array

Field Type Title (Description)
array_type MyomatrixArrayType Array type
threads List[MyomatrixThread] Array threads
name str Device name
serial_number Optional[str] Serial number
manufacturer Optional[Organization] Manufacturer
model Optional[str] Model
additional_settings Optional[dict] Additional parameters
notes Optional[str] Notes

MyomatrixContact

Description of a contact on a myomatrix thread

Field Type Title (Description)
body_part MouseAnatomyModel Body part of contact insertion (Use MouseBodyParts)
relative_position AnatomicalRelative Relative position (Position relative to procedures coordinate system)
muscle MouseAnatomyModel Muscle of contact insertion (Use MouseEmgMuscles)
in_muscle bool In muscle

MyomatrixThread

Description of a thread of a myomatrix array

Field Type Title (Description)
ground_electrode_location MouseAnatomyModel Location of ground electrode (Use GroundWireLocations)
contacts List[MyomatrixContact] Contacts

NeuropixelsBasestation

PXI-based Neuropixels DAQ

Field Type Title (Description)
basestation_firmware_version str Basestation firmware version
bsc_firmware_version str Basestation connect board firmware
slot int Slot number for this basestation
ports List[ProbePort] Basestation ports
data_interface DataInterface
manufacturer Organization
channels List[DAQChannel] DAQ channels
firmware_version Optional[str] Firmware version
hardware_version Optional[str] Hardware version
name str Device name
serial_number Optional[str] Serial number
model Optional[str] Model
additional_settings Optional[dict] Additional parameters
notes Optional[str] Notes

Objective

Description of an objective device

Field Type Title (Description)
numerical_aperture decimal.Decimal Numerical aperture (in air)
magnification decimal.Decimal Magnification
immersion ImmersionMedium Immersion
objective_type Optional[ObjectiveType] Objective type
name str Device name
serial_number Optional[str] Serial number
manufacturer Optional[Organization] Manufacturer
model Optional[str] Model
additional_settings Optional[dict] Additional parameters
notes Optional[str] Notes

Olfactometer

Description of an olfactometer for odor stimuli

Field Type Title (Description)
manufacturer Organization
harp_device_type HarpDeviceType Type of Harp device
channels List[OlfactometerChannel]
core_version Optional[str] Core version
tag_version Optional[str] Tag version
data_interface DataInterface Data interface
is_clock_generator bool Is Clock Generator
firmware_version Optional[str] Firmware version
hardware_version Optional[str] Hardware version
name str Device name
serial_number Optional[str] Serial number
model Optional[str] Model
additional_settings Optional[dict] Additional parameters
notes Optional[str] Notes

OlfactometerChannel

description of a Olfactometer channel

Field Type Title (Description)
channel_index int Channel index
channel_type OlfactometerChannelType Channel type
flow_capacity int Flow capacity
flow_unit str Flow unit

OlfactometerChannelType

Olfactometer channel types

Name Value
ODOR Odor
CARRIER Carrier

OpenEphysAcquisitionBoard

Multichannel electrophysiology DAQ

Field Type Title (Description)
ports List[ProbePort] Acquisition board ports
data_interface "USB"
manufacturer Organization
channels List[DAQChannel] DAQ channels
firmware_version Optional[str] Firmware version
hardware_version Optional[str] Hardware version
name str Device name
serial_number Optional[str] Serial number
model Optional[str] Model
additional_settings Optional[dict] Additional parameters
notes Optional[str] Notes

PatchClampEphysAssembly

Assembly combining a manipulator and headstage used for Patch clamp ephys

Field Type Title (Description)
name str Patch clamp Assembly Name
manipulator Manipulator Manipulator
headstage Device Headstage

PockelsCell

Description of a Pockels Cell

Field Type Title (Description)
polygonal_scanner Optional[str] Polygonal scanner (Must match name of Polygonal scanner)
on_time Optional[decimal.Decimal] On time (fraction of cycle)
off_time Optional[decimal.Decimal] Off time (fraction of cycle)
time_setting_unit UnitlessUnit Time setting unit
beam_modulation Optional[decimal.Decimal] Beam modulation (V)
beam_modulation_unit Optional[VoltageUnit] Beam modulation unit
name str Device name
serial_number Optional[str] Serial number
manufacturer Optional[Organization] Manufacturer
model Optional[str] Model
additional_settings Optional[dict] Additional parameters
notes Optional[str] Notes

PolygonalScanner

Description of a Polygonal scanner

Field Type Title (Description)
speed int Speed (rpm)
speed_unit SpeedUnit Speed unit
number_faces int Number of faces
name str Device name
serial_number Optional[str] Serial number
manufacturer Optional[Organization] Manufacturer
model Optional[str] Model
additional_settings Optional[dict] Additional parameters
notes Optional[str] Notes

ProbePort

Port for a probe connection

Field Type Title (Description)
index int One-based port index
probes List[str] Names of probes connected to this port

Scanner

Description of a MRI Scanner

Field Type Title (Description)
magnetic_strength float Magnetic strength (T)
magnetic_strength_unit MagneticFieldUnit Magnetic strength unit
name str Device name
serial_number Optional[str] Serial number
manufacturer Optional[Organization] Manufacturer
model Optional[str] Model
additional_settings Optional[dict] Additional parameters
notes Optional[str] Notes

ScanningStage

Description of a scanning motorized stages

Field Type Title (Description)
stage_axis_direction StageAxisDirection Direction of stage axis
stage_axis_name AxisName Name of stage axis
travel decimal.Decimal Travel of device (mm)
travel_unit SizeUnit Travel unit
firmware Optional[Software] Firmware
name str Device name
serial_number Optional[str] Serial number
manufacturer Optional[Organization] Manufacturer
model Optional[str] Model
additional_settings Optional[dict] Additional parameters
notes Optional[str] Notes

Speaker

Description of a speaker for auditory stimuli

Field Type Title (Description)
manufacturer Organization
name str Device name
serial_number Optional[str] Serial number
model Optional[str] Model
additional_settings Optional[dict] Additional parameters
notes Optional[str] Notes
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)

Treadmill

Description of treadmill platform

Field Type Title (Description)
treadmill_width decimal.Decimal Width of treadmill (mm)
width_unit SizeUnit Width unit
encoder Optional[Device] Encoder
pulse_per_revolution Optional[int] Pulse per revolution
name str Device name
serial_number Optional[str] Serial number
manufacturer Optional[Organization] Manufacturer
model Optional[str] Model
additional_settings Optional[dict] Additional parameters
notes Optional[str] Notes

Tube

Description of a tube platform

Field Type Title (Description)
diameter decimal.Decimal Diameter
diameter_unit SizeUnit Diameter unit
name str Device name
serial_number Optional[str] Serial number
manufacturer Optional[Organization] Manufacturer
model Optional[str] Model
additional_settings Optional[dict] Additional parameters
notes Optional[str] Notes

Wheel

Description of a running wheel

Field Type Title (Description)
radius decimal.Decimal Radius (mm)
width decimal.Decimal Width (mm)
size_unit SizeUnit Size unit
encoder Device Encoder
pulse_per_revolution int Pulse per revolution
magnetic_brake Device Magnetic brake
torque_sensor Device Torque sensor
name str Device name
serial_number Optional[str] Serial number
manufacturer Optional[Organization] Manufacturer
model Optional[str] Model
additional_settings Optional[dict] Additional parameters
notes Optional[str] Notes