aind_data_schema.ephys package

Submodules

aind_data_schema.ephys.ephys_rig module

ephys rig schemas

class aind_data_schema.ephys.ephys_rig.EphysAssembly(*, ephys_assembly_name: str, manipulator: aind_data_schema.ephys.ephys_rig.Manipulator, probes: List[aind_data_schema.ephys.ephys_rig.EphysProbe])

Bases: aind_data_schema.base.AindModel

Module for electrophysiological recording

ephys_assembly_name: str

manipulator: aind_data_schema.ephys.ephys_rig.Manipulator

probes: List[aind_data_schema.ephys.ephys_rig.EphysProbe]

class aind_data_schema.ephys.ephys_rig.EphysProbe(*, name: Optional[str] = None, serial_number: Optional[str] = None, manufacturer: Optional[aind_data_schema.device.Manufacturer] = None, model: Optional[str] = None, notes: Optional[str] = None, probe_model: aind_data_schema.ephys.ephys_rig.ProbeModel, lasers: Optional[List[aind_data_schema.device.Laser]] = None, headstage: Optional[aind_data_schema.ephys.ephys_rig.Headstage] = None)

Bases: aind_data_schema.device.Device

Named probe used in an ephys experiment

headstage: Optional[aind_data_schema.ephys.ephys_rig.Headstage]

lasers: Optional[List[aind_data_schema.device.Laser]]

probe_model: aind_data_schema.ephys.ephys_rig.ProbeModel

class aind_data_schema.ephys.ephys_rig.EphysRig(*, describedBy: str = 'https://raw.githubusercontent.com/AllenNeuralDynamics/aind-data-schema/main/src/aind_data_schema/ephys/ephys_rig.py', schema_version: str = '0.6.3', rig_id: str, ephys_assemblies: Optional[types.ConstrainedListValue[aind_data_schema.ephys.ephys_rig.EphysAssembly]] = None, stick_microscopes: Optional[List[aind_data_schema.ephys.ephys_rig.StickMicroscopeAssembly]] = None, laser_assemblies: Optional[types.ConstrainedListValue[aind_data_schema.ephys.ephys_rig.LaserAssembly]] = None, cameras: Optional[types.ConstrainedListValue[aind_data_schema.device.CameraAssembly]] = None, visual_monitors: Optional[types.ConstrainedListValue[aind_data_schema.device.Monitor]] = None, mouse_platform: Optional[Union[aind_data_schema.device.Tube, aind_data_schema.device.Treadmill, aind_data_schema.device.Disc]] = None, daqs: Optional[List[Union[aind_data_schema.device.HarpDevice, aind_data_schema.ephys.ephys_rig.NeuropixelsBasestation, aind_data_schema.ephys.ephys_rig.OpenEphysAcquisitionBoard, aind_data_schema.device.DAQDevice]]] = None, additional_devices: Optional[types.ConstrainedListValue[aind_data_schema.device.Device]] = None, notes: Optional[str] = None)

Bases: aind_data_schema.base.AindCoreModel

Description of an ephys rig

additional_devices: Optional[List[aind_data_schema.device.Device]]

cameras: Optional[List[aind_data_schema.device.CameraAssembly]]

daqs: Optional[List[Union[aind_data_schema.device.HarpDevice, aind_data_schema.ephys.ephys_rig.NeuropixelsBasestation, aind_data_schema.ephys.ephys_rig.OpenEphysAcquisitionBoard, aind_data_schema.device.DAQDevice]]]

describedBy: str

ephys_assemblies: Optional[List[aind_data_schema.ephys.ephys_rig.EphysAssembly]]

laser_assemblies: Optional[List[aind_data_schema.ephys.ephys_rig.LaserAssembly]]

mouse_platform: Optional[Union[aind_data_schema.device.Tube, aind_data_schema.device.Treadmill, aind_data_schema.device.Disc]]

notes: Optional[str]

rig_id: str

schema_version: str

stick_microscopes: Optional[List[aind_data_schema.ephys.ephys_rig.StickMicroscopeAssembly]]

classmethod validate_device_names(values)

validate that all DAQ channels are connected to devices that actually exist

classmethod validate_probe_names(values)

validate that all DAQ probe ports are connected to probes that actually exist

visual_monitors: Optional[List[aind_data_schema.device.Monitor]]

class aind_data_schema.ephys.ephys_rig.Headstage(*, name: Optional[str] = None, serial_number: Optional[str] = None, manufacturer: Optional[aind_data_schema.device.Manufacturer] = None, model: Optional[str] = None, notes: Optional[str] = None, headstage_model: Optional[aind_data_schema.ephys.ephys_rig.HeadstageModel] = None)

Bases: aind_data_schema.device.Device

Headstage used with an ephys probe

headstage_model: Optional[aind_data_schema.ephys.ephys_rig.HeadstageModel]

class aind_data_schema.ephys.ephys_rig.HeadstageModel(value)

Bases: enum.Enum

Headstage model name

RHD_16_CH = 'Intan RHD 16-channel'

RHD_32_CH = 'Intan RHD 32-channel'

RHD_64_CH = 'Intan RHD 64-channel'

class aind_data_schema.ephys.ephys_rig.LaserAssembly(*, laser_assembly_name: str, manipulator: aind_data_schema.ephys.ephys_rig.Manipulator, lasers: List[aind_data_schema.device.Laser])

Bases: aind_data_schema.base.AindModel

Assembly for optogenetic stimulation

laser_assembly_name: str

lasers: List[aind_data_schema.device.Laser]

manipulator: aind_data_schema.ephys.ephys_rig.Manipulator

class aind_data_schema.ephys.ephys_rig.Manipulator(*, name: Optional[str] = None, serial_number: Optional[str] = None, manufacturer: typing_extensions.Literal[New Scale Technologies], model: Optional[str] = None, notes: Optional[str] = None)

Bases: aind_data_schema.device.Device

Manipulator used on a dome module

manufacturer: typing_extensions.Literal[New Scale Technologies]

class aind_data_schema.ephys.ephys_rig.NeuropixelsBasestation(*, name: Optional[str] = None, serial_number: Optional[str] = None, manufacturer: aind_data_schema.device.Manufacturer = Manufacturer.IMEC, model: Optional[str] = None, notes: Optional[str] = None, data_interface: aind_data_schema.device.DataInterface = 'PXI', computer_name: str, channels: Optional[List[aind_data_schema.device.DAQChannel]] = None, basestation_firmware_version: str, bsc_firmware_version: str, slot: int, ports: List[aind_data_schema.ephys.ephys_rig.ProbePort])

Bases: aind_data_schema.device.DAQDevice

PXI-based Neuropixels DAQ

basestation_firmware_version: str

bsc_firmware_version: str

data_interface: DataInterface

manufacturer: Manufacturer

ports: List[ProbePort]

slot: int

class aind_data_schema.ephys.ephys_rig.OpenEphysAcquisitionBoard(*, name: Optional[str] = None, serial_number: Optional[str] = None, manufacturer: aind_data_schema.device.Manufacturer = Manufacturer.OEPS, model: Optional[str] = None, notes: Optional[str] = None, data_interface: aind_data_schema.device.DataInterface = 'USB', computer_name: str, channels: Optional[List[aind_data_schema.device.DAQChannel]] = None, ports: List[aind_data_schema.ephys.ephys_rig.ProbePort])

Bases: aind_data_schema.device.DAQDevice

Multichannel electrophysiology DAQ

data_interface: DataInterface

manufacturer: Manufacturer

ports: List[ProbePort]

class aind_data_schema.ephys.ephys_rig.ProbeModel(value)

Bases: enum.Enum

Probe model name

MI_ULED_PROBE = 'Michigan uLED Probe (Version 1)'

MP_PHOTONIC_V1 = 'MPI Photonic Probe (Version 1)'

NP1 = 'Neuropixels 1.0'

NP2_MULTI_SHANK = 'Neuropixels 2.0 (Multi Shank)'

NP2_QUAD_BASE = 'Neuropixels 2.0 (Quad Base)'

NP2_SINGLE_SHANK = 'Neuropixels 2.0 (Single Shank)'

NP_OPTO_DEMONSTRATOR = 'Neuropixels Opto (Demonstrator)'

NP_UHD_FIXED = 'Neuropixels UHD (Fixed)'

NP_UHD_SWITCHABLE = 'Neuropixels UHD (Switchable)'

class aind_data_schema.ephys.ephys_rig.ProbePort(*, index: int, probes: List[str])

Bases: aind_data_schema.base.AindModel

Port for a probe connection

index: int

probes: List[str]

class aind_data_schema.ephys.ephys_rig.StickMicroscopeAssembly(*, scope_assembly_name: str, camera: aind_data_schema.device.Camera, lens: aind_data_schema.device.Lens)

Bases: aind_data_schema.base.AindModel

Stick microscope used to monitor probes during insertion

camera: aind_data_schema.device.Camera

lens: aind_data_schema.device.Lens

scope_assembly_name: str

aind_data_schema.ephys.ephys_session module

ephys session description and related objects

class aind_data_schema.ephys.ephys_session.Camera(*, name: str)

Bases: aind_data_schema.base.AindModel

Camera recorded in a Stream

name: str

class aind_data_schema.ephys.ephys_session.CcfCoords(*, ml: float, ap: float, dv: float, unit: aind_data_schema.device.SizeUnit = SizeUnit.UM, ccf_version: aind_data_schema.ephys.ephys_session.CcfVersion = CcfVersion.CCFv3)

Bases: aind_data_schema.base.AindModel

Coordinates in CCF template space

ap: float

ccf_version: aind_data_schema.ephys.ephys_session.CcfVersion

dv: float

ml: float

unit: aind_data_schema.device.SizeUnit

class aind_data_schema.ephys.ephys_session.CcfVersion(value)

Bases: enum.Enum

CCF version

CCFv3 = 'CCFv3'

class aind_data_schema.ephys.ephys_session.DAQDevice(*, name: str)

Bases: aind_data_schema.base.AindModel

Data acquisition device recorded in a Stream

name: str

class aind_data_schema.ephys.ephys_session.DomeModule(*, assembly_name: str, arc_angle: float, module_angle: float, angle_unit: aind_data_schema.device.AngleUnit = AngleUnit.DEG, rotation_angle: Optional[float] = 0.0, coordinate_transform: Optional[str] = None, calibration_date: Optional[datetime.datetime] = None, notes: Optional[str] = None)

Bases: aind_data_schema.base.AindModel

Movable module that is mounted on the ephys dome insertion system

angle_unit: aind_data_schema.device.AngleUnit

arc_angle: float

assembly_name: str

calibration_date: Optional[datetime.datetime]

coordinate_transform: Optional[str]

module_angle: float

notes: Optional[str]

rotation_angle: Optional[float]

class aind_data_schema.ephys.ephys_session.EphysModule(*, assembly_name: str, arc_angle: float, module_angle: float, angle_unit: aind_data_schema.device.AngleUnit = AngleUnit.DEG, rotation_angle: Optional[float] = 0.0, coordinate_transform: Optional[str] = None, calibration_date: Optional[datetime.datetime] = None, notes: Optional[str] = None, primary_targeted_structure: str, targeted_ccf_coordinates: Optional[List[aind_data_schema.ephys.ephys_session.CcfCoords]] = None, manipulator_coordinates: aind_data_schema.device.Coordinates3d, ephys_probes: List[aind_data_schema.ephys.ephys_session.EphysProbe])

Bases: aind_data_schema.ephys.ephys_session.ManipulatorModule

Probe recorded in a Stream

ephys_probes: List[aind_data_schema.ephys.ephys_session.EphysProbe]

class aind_data_schema.ephys.ephys_session.EphysProbe(*, name: str, other_targeted_structures: Optional[List[str]] = None)

Bases: aind_data_schema.base.AindModel

Probes in a EphysProbeModule

name: str

other_targeted_structures: Optional[List[str]]

class aind_data_schema.ephys.ephys_session.EphysSession(*, describedBy: str = 'https://raw.githubusercontent.com/AllenNeuralDynamics/aind-data-schema/main/src/aind_data_schema/ephys/ephys_session.py', schema_version: str = '0.4.5', experimenter_full_name: List[str], session_start_time: datetime.datetime, session_end_time: datetime.datetime, subject_id: str, session_type: aind_data_schema.ephys.ephys_session.SessionType, session_description: Optional[str] = None, iacuc_protocol: Optional[str] = None, rig_id: str, stick_microscopes: Optional[List[aind_data_schema.ephys.ephys_session.DomeModule]], data_streams: types.ConstrainedListValue[aind_data_schema.ephys.ephys_session.Stream], ccf_coordinate_transform: Optional[str] = None, notes: Optional[str] = None)

Bases: aind_data_schema.base.AindCoreModel

Description of an ephys recording session

ccf_coordinate_transform: Optional[str]

data_streams: List[aind_data_schema.ephys.ephys_session.Stream]

describedBy: str

experimenter_full_name: List[str]

iacuc_protocol: Optional[str]

notes: Optional[str]

rig_id: str

schema_version: str

session_description: Optional[str]

session_end_time: datetime.datetime

session_start_time: datetime.datetime

session_type: aind_data_schema.ephys.ephys_session.SessionType

stick_microscopes: Optional[List[aind_data_schema.ephys.ephys_session.DomeModule]]

subject_id: str

class aind_data_schema.ephys.ephys_session.Laser(*, name: str, power_level: float, power_unit: aind_data_schema.device.PowerUnit = PowerUnit.MW)

Bases: aind_data_schema.base.AindModel

Laser used in a LaserModule

name: str

power_level: float

power_unit: aind_data_schema.device.PowerUnit

class aind_data_schema.ephys.ephys_session.LaserModule(*, assembly_name: str, arc_angle: float, module_angle: float, angle_unit: aind_data_schema.device.AngleUnit = AngleUnit.DEG, rotation_angle: Optional[float] = 0.0, coordinate_transform: Optional[str] = None, calibration_date: Optional[datetime.datetime] = None, notes: Optional[str] = None, primary_targeted_structure: str, targeted_ccf_coordinates: Optional[List[aind_data_schema.ephys.ephys_session.CcfCoords]] = None, manipulator_coordinates: aind_data_schema.device.Coordinates3d, lasers: List[aind_data_schema.ephys.ephys_session.Laser])

Bases: aind_data_schema.ephys.ephys_session.ManipulatorModule

Laser Module used in a Stream

lasers: List[aind_data_schema.ephys.ephys_session.Laser]

class aind_data_schema.ephys.ephys_session.ManipulatorModule(*, assembly_name: str, arc_angle: float, module_angle: float, angle_unit: aind_data_schema.device.AngleUnit = AngleUnit.DEG, rotation_angle: Optional[float] = 0.0, coordinate_transform: Optional[str] = None, calibration_date: Optional[datetime.datetime] = None, notes: Optional[str] = None, primary_targeted_structure: str, targeted_ccf_coordinates: Optional[List[aind_data_schema.ephys.ephys_session.CcfCoords]] = None, manipulator_coordinates: aind_data_schema.device.Coordinates3d)

Bases: aind_data_schema.ephys.ephys_session.DomeModule

A module connected to a 3-axis manipulator

manipulator_coordinates: aind_data_schema.device.Coordinates3d

primary_targeted_structure: str

targeted_ccf_coordinates: Optional[List[aind_data_schema.ephys.ephys_session.CcfCoords]]

class aind_data_schema.ephys.ephys_session.SessionType(value)

Bases: enum.Enum

Session type name

OPTO = 'Optotagging'

RF_MAPPING = 'Receptive field mapping'

TEST = 'Test'

class aind_data_schema.ephys.ephys_session.Stream(*, stream_start_time: datetime.datetime, stream_end_time: datetime.datetime, ephys_modules: Optional[types.ConstrainedListValue[aind_data_schema.ephys.ephys_session.EphysModule]] = None, laser_modules: Optional[types.ConstrainedListValue[aind_data_schema.ephys.ephys_session.LaserModule]] = None, daqs: Optional[types.ConstrainedListValue[aind_data_schema.ephys.ephys_session.DAQDevice]] = None, cameras: Optional[types.ConstrainedListValue[aind_data_schema.ephys.ephys_session.Camera]] = None, stimulus_presentations: Optional[List[aind_data_schema.stimulus.StimulusPresentation]] = None, notes: Optional[str] = None)

Bases: aind_data_schema.base.AindModel

Stream of data with a start and stop time

cameras: Optional[List[aind_data_schema.ephys.ephys_session.Camera]]

daqs: Optional[List[aind_data_schema.ephys.ephys_session.DAQDevice]]

ephys_modules: Optional[List[aind_data_schema.ephys.ephys_session.EphysModule]]

laser_modules: Optional[List[aind_data_schema.ephys.ephys_session.LaserModule]]

notes: Optional[str]

stimulus_presentations: Optional[List[aind_data_schema.stimulus.StimulusPresentation]]

stream_end_time: datetime.datetime

stream_start_time: datetime.datetime

Module contents

ephys schemas