aind_data_schema package#

Subpackages#

Submodules#

aind_data_schema.base module#

generic base class with supporting validators and fields for basic AIND schema

class aind_data_schema.base.AindCoreModel(*, describedBy: str, schema_version: str)#

Bases: aind_data_schema.base.AindModel

Generic base class to hold common fields/validators/etc for all basic AIND schema

classmethod default_filename()#: Returns standard filename in snakecase

describedBy: str#

schema_version: str#

write_standard_file(prefix=None)#: Writes schema to standard json file :param prefix: optional str for intended filepath with extra naming convention

class aind_data_schema.base.AindModel#

Bases: pydantic.main.BaseModel

BaseModel that disallows extra fields

class aind_data_schema.base.BaseName(*, name: str, abbreviation: Optional[str] = None)#

Bases: aind_data_schema.base.AindModel

A simple model associating a name with an abbreviation

abbreviation: Optional[str]#

name: str#

class aind_data_schema.base.BaseNameEnumMeta(cls, bases, classdict)#

Bases: enum.EnumMeta

Allows to create complicated enum based on attribute name.

class aind_data_schema.base.PIDName(*, name: aind_data_schema.base.BaseName, registry: aind_data_schema.base.BaseName, registry_identifier: str)#

Bases: aind_data_schema.base.AindModel

Model for associate a name with a persistent identifier (PID), the registry for that PID, and abbreviation for that registry

name: aind_data_schema.base.BaseName#

registry: aind_data_schema.base.BaseName#

registry_identifier: str#

aind_data_schema.base.build_described_by(cls, base_url='https://raw.githubusercontent.com/AllenNeuralDynamics/aind-data-schema/main/src/')#: construct a pydantic Field that refers to a specific file

aind_data_schema.data_description module#

Generic metadata classes for data

class aind_data_schema.data_description.DataDescription(label=None, *, describedBy: str = 'https://raw.githubusercontent.com/AllenNeuralDynamics/aind-data-schema/main/src/aind_data_schema/data_description.py', schema_version: str = '0.6.3', license: str = 'CC-BY-4.0', creation_time: datetime.time, creation_date: datetime.date, name: Optional[str] = None, institution: aind_data_schema.data_description.Institution, funding_source: List[aind_data_schema.data_description.Funding], data_level: aind_data_schema.data_description.DataLevel, group: Optional[aind_data_schema.data_description.Group] = None, investigators: List[str], project_name: Optional[str] = None, project_id: Optional[str] = None, restrictions: Optional[str] = None, modality: List[aind_data_schema.data_description.Modality], experiment_type: aind_data_schema.data_description.ExperimentType, subject_id: aind_data_schema.data_description.ConstrainedStrValue, related_data: Optional[List[aind_data_schema.data_description.RelatedData]] = [], data_summary: Optional[str] = None)#

Bases: aind_data_schema.base.AindCoreModel

Description of a logical collection of data files

creation_date: datetime.date#

creation_time: datetime.time#

data_level: aind_data_schema.data_description.DataLevel#

data_summary: Optional[str]#

experiment_type: aind_data_schema.data_description.ExperimentType#

funding_source: List[aind_data_schema.data_description.Funding]#

group: Optional[aind_data_schema.data_description.Group]#

institution: aind_data_schema.data_description.Institution#

investigators: List[str]#

license: str#

modality: List[aind_data_schema.data_description.Modality]#

name: Optional[str]#

classmethod parse_name(name)#: Decompose a DataDescription name string into component parts

project_id: Optional[str]#

project_name: Optional[str]#

related_data: Optional[List[aind_data_schema.data_description.RelatedData]]#

restrictions: Optional[str]#

schema_version: str#

subject_id: str#

class aind_data_schema.data_description.DataLevel(value)#

Bases: enum.Enum

Data level name

DERIVED_DATA = 'derived data'#

RAW_DATA = 'raw data'#

class aind_data_schema.data_description.DataRegex(value)#

Bases: enum.Enum

regular expression patterns for different kinds of data and their properties

DATA = '^(?P<label>.+?)_(?P<c_date>\\d{4}-\\d{2}-\\d{2})_(?P<c_time>\\d{2}-\\d{2}-\\d{2})$'#

DERIVED_DATA = '^(?P<input>.+?_\\d{4}-\\d{2}-\\d{2}_\\d{2}-\\d{2}-\\d{2})_(?P<process_name>.+?)_(?P<c_date>\\d{4}-\\d{2}-\\d{2})_(?P<c_time>\\d{2}-\\d{2}-\\d{2})'#

NO_UNDERSCORES = '^[^_]+$'#

RAW_DATA = '^(?P<experiment_type>.+?)_(?P<subject_id>.+?)_(?P<c_date>\\d{4}-\\d{2}-\\d{2})_(?P<c_time>\\d{2}-\\d{2}-\\d{2})$'#

class aind_data_schema.data_description.DerivedDataDescription(process_name, *, describedBy: str = 'https://raw.githubusercontent.com/AllenNeuralDynamics/aind-data-schema/main/src/aind_data_schema/data_description.py', schema_version: str = '0.6.3', license: str = 'CC-BY-4.0', creation_time: datetime.time, creation_date: datetime.date, name: Optional[str] = None, institution: aind_data_schema.data_description.Institution, funding_source: List[aind_data_schema.data_description.Funding], data_level: aind_data_schema.data_description.DataLevel = DataLevel.DERIVED_DATA, group: Optional[aind_data_schema.data_description.Group] = None, investigators: List[str], project_name: Optional[str] = None, project_id: Optional[str] = None, restrictions: Optional[str] = None, modality: List[aind_data_schema.data_description.Modality], experiment_type: aind_data_schema.data_description.ExperimentType, subject_id: aind_data_schema.data_description.ConstrainedStrValue, related_data: Optional[List[aind_data_schema.data_description.RelatedData]] = [], data_summary: Optional[str] = None, input_data_name: str)#

Bases: aind_data_schema.data_description.DataDescription

A logical collection of data files derived via processing

data_level: aind_data_schema.data_description.DataLevel#

input_data_name: str#

classmethod parse_name(name)#: decompose DerivedDataDescription name into parts

class aind_data_schema.data_description.ExperimentType(value)#

Bases: enum.Enum

Abbreviated name for data collection technique

CONFOCAL = 'confocal'#

DISPIM = 'diSPIM'#

ECEPHYS = 'ecephys'#

EXASPIM = 'exaSPIM'#

FIP = 'FIP'#

FMOST = 'fMOST'#

HSFP = 'HSFP'#

MERFISH = 'merfish'#

MESOSPIM = 'mesoSPIM'#

MRI = 'MRI'#

OTHER = 'Other'#

POPHYS = 'pophys'#

SLAP = 'slap'#

SMARTSPIM = 'SmartSPIM'#

class aind_data_schema.data_description.Funding(*, funder: str, grant_number: Optional[str] = None, fundee: Optional[str] = None)#

Bases: aind_data_schema.base.AindModel

Description of funding sources

fundee: Optional[str]#

funder: str#

grant_number: Optional[str]#

class aind_data_schema.data_description.Group(value)#

Bases: enum.Enum

Data collection group name

BEHAVIOR = 'behavior'#

EPHYS = 'ephys'#

MSMA = 'MSMA'#

OPHYS = 'ophys'#

class aind_data_schema.data_description.Institution(value, *args, **kw)#

Bases: enum.Enum

Institution name

AIBS = PIDName(name=BaseName(name='Allen Institute for Brain Science', abbreviation='AIBS'), registry=BaseName(name='Research Organization Registry', abbreviation='ROR'), registry_identifier='00dcv1019')#

AIND = PIDName(name=BaseName(name='Allen Institute for Neural Dynamics', abbreviation='AIND'), registry=BaseName(name='Research Organization Registry', abbreviation='ROR'), registry_identifier='04szwah67')#

COLUMBIA = PIDName(name=BaseName(name='Columbia University', abbreviation='Columbia'), registry=BaseName(name='Research Organization Registry', abbreviation='ROR'), registry_identifier='00hj8s172')#

HUST = PIDName(name=BaseName(name='Huazhong University of Science and Technology', abbreviation='HUST'), registry=BaseName(name='Research Organization Registry', abbreviation='ROR'), registry_identifier='00p991c53')#

NYU = PIDName(name=BaseName(name='New York University', abbreviation='NYU'), registry=BaseName(name='Research Organization Registry', abbreviation='ROR'), registry_identifier='0190ak572')#

class aind_data_schema.data_description.Modality(value, *args, **kw)#

Bases: enum.Enum

Data collection modality name

CONFOCAL = BaseName(name='Confocal microscopy', abbreviation='confocal')#

DISPIM = BaseName(name='Dual inverted selective plane illumination microscopy', abbreviation='diSPIM')#

ECEPHYS = BaseName(name='Extracellular electrophysiology', abbreviation='ecephys')#

EPHYS = BaseName(name='Electrophysiology', abbreviation='ephys')#

EXASPIM = BaseName(name='Expansion-assisted selective plane illumination microscopy', abbreviation='exaSPIM')#

FIB = BaseName(name='Fiber photometry', abbreviation='fib')#

FIP = BaseName(name='Frame-projected independent-fiber photometry', abbreviation='FIP')#

FISH = BaseName(name='Fluorescence in situ hybridization', abbreviation='fish')#

FMOST = BaseName(name='Fluorescence micro-optical sectioning tomography', abbreviation='fMOST')#

HSFP = BaseName(name='Hyperspectral fiber photometry', abbreviation='HSFP')#

ICEPHYS = BaseName(name='Intracellular electrophysiology', abbreviation='icephys')#

MERFISH = BaseName(name='Multiplexed error-robust fluorescence in situ hybridization', abbreviation='merfish')#

MESOSPIM = BaseName(name='Mesoscale selective plane illumination microscopy', abbreviation='mesoSPIM')#

MRI = BaseName(name='Magnetic resonance imaging', abbreviation='MRI')#

OPHYS = BaseName(name='Optical physiology', abbreviation='ophys')#

POPHYS = BaseName(name='Planar optical physiology', abbreviation='pophys')#

SLAP = BaseName(name='Scanned line projection', abbreviation='slap')#

SMARTSPIM = BaseName(name='Smart selective plane illumination microscopy', abbreviation='SmartSPIM')#

SPIM = BaseName(name='Selective plane illumination microscopy', abbreviation='SPIM')#

class aind_data_schema.data_description.RawDataDescription(experiment_type, subject_id, *, describedBy: str = 'https://raw.githubusercontent.com/AllenNeuralDynamics/aind-data-schema/main/src/aind_data_schema/data_description.py', schema_version: str = '0.6.3', license: str = 'CC-BY-4.0', creation_time: datetime.time, creation_date: datetime.date, name: Optional[str] = None, institution: aind_data_schema.data_description.Institution, funding_source: List[aind_data_schema.data_description.Funding], data_level: aind_data_schema.data_description.DataLevel = DataLevel.RAW_DATA, group: Optional[aind_data_schema.data_description.Group] = None, investigators: List[str], project_name: Optional[str] = None, project_id: Optional[str] = None, restrictions: Optional[str] = None, modality: List[aind_data_schema.data_description.Modality], related_data: Optional[List[aind_data_schema.data_description.RelatedData]] = [], data_summary: Optional[str] = None)#

Bases: aind_data_schema.data_description.DataDescription

A logical collection of data files as acquired from a rig or instrument

data_level: aind_data_schema.data_description.DataLevel#

classmethod parse_name(name)#: Decompose raw data description name into component parts

class aind_data_schema.data_description.RegexParts(value)#

Bases: enum.Enum

regular expression components to be re-used elsewhere

DATE = '\\d{4}-\\d{2}-\\d{2}'#

TIME = '\\d{2}-\\d{2}-\\d{2}'#

class aind_data_schema.data_description.RelatedData(*, related_data_path: str, relation: str)#

Bases: aind_data_schema.base.AindModel

Description of related data asset

related_data_path: str#

relation: str#

aind_data_schema.data_description.build_data_name(label, creation_date, creation_time)#: Construct a valid data description name

aind_data_schema.data_description.datetime_from_name_string(d, t)#: Take date and time strings, generate date and time objects

aind_data_schema.data_description.datetime_to_name_string(d, t)#: Take a date and time object, format it a as string

aind_data_schema.device module#

schema for various Devices

class aind_data_schema.device.AngleUnit(value)#

Bases: enum.Enum

orientation units

DEG = 'degree'#

class aind_data_schema.device.Camera(*, name: Optional[str] = None, serial_number: Optional[str] = None, manufacturer: typing_extensions.Literal[Allied, Basler, Edmund Optics, FLIR, Thorlabs, Other], model: Optional[str] = None, notes: Optional[str] = None, data_interface: aind_data_schema.device.DataInterface, computer_name: str, max_frame_rate: float, frame_rate_unit: aind_data_schema.device.FrequencyUnit = FrequencyUnit.HZ, pixel_width: int, pixel_height: int, size_unit: aind_data_schema.device.SizeUnit = SizeUnit.PX, chroma: aind_data_schema.device.CameraChroma, sensor_format: Optional[str] = None, format_unit: Optional[str] = None, recording_software: Optional[str] = None)#

Bases: aind_data_schema.device.Device

Device that acquires images and streams them to a computer

chroma: aind_data_schema.device.CameraChroma#

computer_name: str#

data_interface: aind_data_schema.device.DataInterface#

format_unit: Optional[str]#

frame_rate_unit: aind_data_schema.device.FrequencyUnit#

manufacturer: typing_extensions.Literal[Allied, Basler, Edmund Optics, FLIR, Thorlabs, Other]#

max_frame_rate: float#

pixel_height: int#

pixel_width: int#

recording_software: Optional[str]#

sensor_format: Optional[str]#

size_unit: aind_data_schema.device.SizeUnit#

class aind_data_schema.device.CameraAssembly(*, camera_assembly_name: str, camera_target: aind_data_schema.device.CameraTarget, camera: aind_data_schema.device.Camera, lens: aind_data_schema.device.Lens, filter: Optional[aind_data_schema.device.Filter] = None, position: Optional[aind_data_schema.device.RelativePosition] = None)#

Bases: aind_data_schema.base.AindModel

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

camera: aind_data_schema.device.Camera#

camera_assembly_name: str#

camera_target: aind_data_schema.device.CameraTarget#

filter: Optional[aind_data_schema.device.Filter]#

lens: aind_data_schema.device.Lens#

position: Optional[aind_data_schema.device.RelativePosition]#

class aind_data_schema.device.CameraChroma(value)#

Bases: enum.Enum

Color vs. black & white

BW = 'Monochrome'#

COLOR = 'Color'#

class aind_data_schema.device.CameraTarget(value)#

Bases: enum.Enum

Target of camera

BODY = 'Body'#

BOTTOM = 'Bottom'#

EYE = 'Eye'#

FACE = 'Face'#

OTHER = 'Other'#

SIDE = 'Side'#

TONGUE = 'Tongue'#

class aind_data_schema.device.Coordinates3d(*, x: float, y: float, z: float, unit: aind_data_schema.device.SizeUnit = SizeUnit.UM)#

Bases: aind_data_schema.base.AindModel

Coordinates in a 3D grid

unit: aind_data_schema.device.SizeUnit#

x: float#

y: float#

z: float#

class aind_data_schema.device.Coupling(value)#

Bases: enum.Enum

Laser coupling type

FREE_SPACE = 'Free-space'#

MMF = 'Multi-mode fiber'#

OTHER = 'Other'#

SMF = 'Single-mode fiber'#

class aind_data_schema.device.DAQChannel(*, channel_name: str, device_name: str, channel_type: aind_data_schema.device.DaqChannelType, port: Optional[int] = None, channel_index: Optional[int] = None, sample_rate: Optional[float] = None, sample_rate_unit: aind_data_schema.device.FrequencyUnit = FrequencyUnit.HZ, event_based_sampling: Optional[bool] = False)#

Bases: aind_data_schema.base.AindModel

Named input or output channel on a DAQ device

channel_index: Optional[int]#

channel_name: str#

channel_type: aind_data_schema.device.DaqChannelType#

device_name: str#

event_based_sampling: Optional[bool]#

port: Optional[int]#

sample_rate: Optional[float]#

sample_rate_unit: aind_data_schema.device.FrequencyUnit#

class aind_data_schema.device.DAQDevice(*, name: Optional[str] = None, serial_number: Optional[str] = None, manufacturer: typing_extensions.Literal[National Instruments, IMEC, OEPS, Other], model: Optional[str] = None, notes: Optional[str] = None, data_interface: aind_data_schema.device.DataInterface, computer_name: str, channels: Optional[List[aind_data_schema.device.DAQChannel]] = None)#

Bases: aind_data_schema.device.Device

Data acquisition device containing multiple I/O channels

channels: Optional[List[aind_data_schema.device.DAQChannel]]#

computer_name: str#

data_interface: aind_data_schema.device.DataInterface#

manufacturer: typing_extensions.Literal[National Instruments, IMEC, OEPS, Other]#

class aind_data_schema.device.DaqChannelType(value)#

Bases: enum.Enum

DAQ Channel type

AI = 'Analog Input'#

AO = 'Analog Output'#

DI = 'Digital Input'#

DO = 'Digital Output'#

class aind_data_schema.device.DataInterface(value)#

Bases: enum.Enum

Connection between a device and a PC

CAMERALINK = 'CameraLink'#

COAX = 'Coax'#

ETH = 'Ethernet'#

OTHER = 'Other'#

PCIE = 'PCIe'#

PXI = 'PXI'#

USB = 'USB'#

class aind_data_schema.device.Device(*, 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)#

Bases: aind_data_schema.base.AindModel

Generic device

manufacturer: Optional[aind_data_schema.device.Manufacturer]#

model: Optional[str]#

name: Optional[str]#

notes: Optional[str]#

serial_number: Optional[str]#

class aind_data_schema.device.Disc(*, 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, surface_material: Optional[str] = None, date_surface_replaced: Optional[datetime.datetime] = None, platform_type: str = 'Disc', radius: aind_data_schema.device.ConstrainedFloatValue, radius_unit: aind_data_schema.device.SizeUnit = SizeUnit.CM)#

Bases: aind_data_schema.device.MousePlatform

Description of a running disc

platform_type: str#

radius: float#

radius_unit: aind_data_schema.device.SizeUnit#

class aind_data_schema.device.Filter(*, name: Optional[str] = None, serial_number: Optional[str] = None, manufacturer: typing_extensions.Literal[Edmund Optics, Chroma, Semrock, Thorlabs, Other], model: Optional[str] = None, notes: Optional[str] = None, filter_type: aind_data_schema.device.FilterType, diameter: Optional[float] = None, diameter_unit: aind_data_schema.device.SizeUnit = SizeUnit.MM, thickness: Optional[aind_data_schema.device.ConstrainedFloatValue] = None, thickness_unit: aind_data_schema.device.SizeUnit = SizeUnit.MM, filter_wheel_index: Optional[int] = None, cut_off_wavelength: Optional[int] = None, cut_off_wavelength_unit: aind_data_schema.device.SizeUnit = SizeUnit.NM, cut_on_wavelength: Optional[int] = None, cut_on_wavelength_unit: aind_data_schema.device.SizeUnit = SizeUnit.NM, description: Optional[str] = None)#

Bases: aind_data_schema.device.Device

Filter used in a light path

cut_off_wavelength: Optional[int]#

cut_off_wavelength_unit: aind_data_schema.device.SizeUnit#

cut_on_wavelength: Optional[int]#

cut_on_wavelength_unit: aind_data_schema.device.SizeUnit#

description: Optional[str]#

diameter: Optional[float]#

diameter_unit: aind_data_schema.device.SizeUnit#

filter_type: aind_data_schema.device.FilterType#

filter_wheel_index: Optional[int]#

manufacturer: typing_extensions.Literal[Edmund Optics, Chroma, Semrock, Thorlabs, Other]#

thickness: Optional[float]#

thickness_unit: aind_data_schema.device.SizeUnit#

class aind_data_schema.device.FilterSize(value)#

Bases: enum.Enum

Filter size value

FILTER_SIZE_25 = 25#

FILTER_SIZE_32 = 32#

class aind_data_schema.device.FilterType(value)#

Bases: enum.Enum

Filter type

BANDPASS = 'Band pass'#

DICHROIC = 'Dichroic'#

LONGPASS = 'Long pass'#

MULTIBAND = 'Multiband'#

ND = 'Neutral density'#

NOTCH = 'Notch'#

SHORTPASS = 'Short pass'#

class aind_data_schema.device.FrequencyUnit(value)#

Bases: enum.Enum

Frequency units

HZ = 'Hertz'#

class aind_data_schema.device.HarpDevice(*, 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, harp_device_type: aind_data_schema.device.HarpDeviceType, harp_device_version: str)#

Bases: aind_data_schema.device.DAQDevice

DAQ that uses the Harp protocol for synchronization and data transmission

data_interface: aind_data_schema.device.DataInterface#

harp_device_type: aind_data_schema.device.HarpDeviceType#

harp_device_version: str#

manufacturer: aind_data_schema.device.Manufacturer#

class aind_data_schema.device.HarpDeviceType(value)#

Bases: enum.Enum

Harp device type

BEHAVIOR = 'Behavior'#

CAMERA_CONTROLLER = 'Camera Controller'#

INPUT_EXPANDER = 'Input Expander'#

LOAD_CELLS = 'Load Cells'#

SOUND_BOARD = 'Sound Board'#

TIMESTAMP_GENERATOR = 'Timestamp Generator'#

class aind_data_schema.device.Laser(*, name: Optional[str] = None, serial_number: Optional[str] = None, manufacturer: typing_extensions.Literal[Coherent Scientific, Hamamatsu, Oxxius, Quantifi, Other], model: Optional[str] = None, notes: Optional[str] = None, wavelength: int, wavelength_unit: aind_data_schema.device.SizeUnit = SizeUnit.NM, maximum_power: Optional[float] = None, power_unit: aind_data_schema.device.PowerUnit = PowerUnit.MW, coupling: Optional[aind_data_schema.device.Coupling] = None, coupling_efficiency: Optional[aind_data_schema.device.ConstrainedFloatValue] = None, coupling_efficiency_unit: Optional[str] = 'percent', item_number: Optional[str] = None, calibration_data: Optional[str] = None, calibration_date: Optional[datetime.datetime] = None)#

Bases: aind_data_schema.device.Device

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

calibration_data: Optional[str]#

calibration_date: Optional[datetime.datetime]#

coupling: Optional[aind_data_schema.device.Coupling]#

coupling_efficiency: Optional[float]#

coupling_efficiency_unit: Optional[str]#

item_number: Optional[str]#

manufacturer: typing_extensions.Literal[Coherent Scientific, Hamamatsu, Oxxius, Quantifi, Other]#

maximum_power: Optional[float]#

power_unit: aind_data_schema.device.PowerUnit#

wavelength: int#

wavelength_unit: aind_data_schema.device.SizeUnit#

class aind_data_schema.device.Lens(*, name: Optional[str] = None, serial_number: Optional[str] = None, manufacturer: typing_extensions.Literal[Edmund Optics, Thorlabs, Other], model: Optional[str] = None, notes: Optional[str] = None, focal_length: Optional[float] = None, focal_length_unit: aind_data_schema.device.SizeUnit = SizeUnit.MM, size: Optional[aind_data_schema.device.LensSize] = None, lens_size_unit: aind_data_schema.device.SizeUnit = SizeUnit.IN, optimized_wavelength_range: Optional[str] = None, wavelength_unit: aind_data_schema.device.SizeUnit = SizeUnit.NM, max_aperture: Optional[str] = None)#

Bases: aind_data_schema.device.Device

Lens used to focus light onto a camera sensor

focal_length: Optional[float]#

focal_length_unit: aind_data_schema.device.SizeUnit#

lens_size_unit: aind_data_schema.device.SizeUnit#

manufacturer: typing_extensions.Literal[Edmund Optics, Thorlabs, Other]#

max_aperture: Optional[str]#

optimized_wavelength_range: Optional[str]#

size: Optional[aind_data_schema.device.LensSize]#

wavelength_unit: aind_data_schema.device.SizeUnit#

class aind_data_schema.device.LensSize(value)#

Bases: enum.Enum

Lens size value

LENS_SIZE_1 = 1#

LENS_SIZE_2 = 2#

class aind_data_schema.device.LightEmittingDiode(*, name: Optional[str] = None, serial_number: Optional[str] = None, manufacturer: typing_extensions.Literal[Doric, Prizmatix, Thorlabs, Other], model: Optional[str] = None, notes: Optional[str] = None, wavelength: int, wavelength_unit: aind_data_schema.device.SizeUnit = SizeUnit.NM)#

Bases: aind_data_schema.device.Device

Description of a Light Emitting Diode (LED) device

manufacturer: typing_extensions.Literal[Doric, Prizmatix, Thorlabs, Other]#

wavelength: int#

wavelength_unit: aind_data_schema.device.SizeUnit#

class aind_data_schema.device.Manufacturer(value)#

Bases: enum.Enum

Device manufacturer name

ALLIED = 'Allied'#

ASI = 'Applied Scientific Instrumentation'#

BASLER = 'Basler'#

CAMBRIDGE_TECHNOLOGY = 'Cambridge Technology'#

CHROMA = 'Chroma'#

COHERENT_SCIENTIFIC = 'Coherent Scientific'#

CUSTOM = 'Custom'#

DORIC = 'Doric'#

EALING = 'Ealing'#

EDMUND_OPTICS = 'Edmund Optics'#

FLIR = 'FLIR'#

HAMAMATSU = 'Hamamatsu'#

IMEC = 'IMEC'#

JULABO = 'Julabo'#

LEICA = 'Leica'#

LG = 'LG'#

LIFECANVAS = 'LifeCanvas'#

MIGHTY_ZAP = 'IR Robot Co'#

MKS_NEWPORT = 'MKS Newport'#

MPI = 'MPI'#

NATIONAL_INSTRUMENTS = 'National Instruments'#

NEW_SCALE_TECHNOLOGIES = 'New Scale Technologies'#

NIKON = 'Nikon'#

OEPS = 'OEPS'#

OLYMPUS = 'Olympus'#

OPTOTUNE = 'Optotune'#

OTHER = 'Other'#

OXXIUS = 'Oxxius'#

PRIZMATIX = 'Prizmatix'#

QUANTIFI = 'Quantifi'#

SEMROCK = 'Semrock'#

THORLABS = 'Thorlabs'#

TMC = 'Technical Manufacturing Corporation'#

VIEWORKS = 'Vieworks'#

VORTRAN = 'Vortran'#

class aind_data_schema.device.ModuleOrientation2d(*, arc_angle: float, module_angle: float, unit: aind_data_schema.device.AngleUnit = AngleUnit.DEG)#

Bases: aind_data_schema.base.AindModel

2D module orientation of an object

arc_angle: float#

module_angle: float#

unit: aind_data_schema.device.AngleUnit#

class aind_data_schema.device.ModuleOrientation3d(*, arc_angle: float, module_angle: float, rotation_angle: float, unit: aind_data_schema.device.AngleUnit = AngleUnit.DEG)#

Bases: aind_data_schema.base.AindModel

3D module orientation of an object

arc_angle: float#

module_angle: float#

rotation_angle: float#

unit: aind_data_schema.device.AngleUnit#

class aind_data_schema.device.Monitor(*, name: Optional[str] = None, serial_number: Optional[str] = None, manufacturer: typing_extensions.Literal[LG], model: Optional[str] = None, notes: Optional[str] = None, refresh_rate: aind_data_schema.device.ConstrainedIntValue, width: int, height: int, size_unit: aind_data_schema.device.SizeUnit = SizeUnit.PX, viewing_distance: float, viewing_distance_unit: aind_data_schema.device.SizeUnit = SizeUnit.CM, contrast: Optional[aind_data_schema.device.ConstrainedIntValue], brightness: Optional[aind_data_schema.device.ConstrainedIntValue], position: Optional[aind_data_schema.device.RelativePosition] = None)#

Bases: aind_data_schema.device.Device

Visual display

brightness: Optional[int]#

contrast: Optional[int]#

height: int#

manufacturer: typing_extensions.Literal[LG]#

position: Optional[aind_data_schema.device.RelativePosition]#

refresh_rate: int#

size_unit: aind_data_schema.device.SizeUnit#

viewing_distance: float#

viewing_distance_unit: aind_data_schema.device.SizeUnit#

width: int#

class aind_data_schema.device.MotorizedStage(*, 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, travel: float, travel_unit: aind_data_schema.device.SizeUnit = SizeUnit.MM)#

Bases: aind_data_schema.device.Device

Description of motorized stage

travel: float#

travel_unit: aind_data_schema.device.SizeUnit#

class aind_data_schema.device.MousePlatform(*, 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, surface_material: Optional[str] = None, date_surface_replaced: Optional[datetime.datetime] = None)#

Bases: aind_data_schema.device.Device

Description of a mouse platform

date_surface_replaced: Optional[datetime.datetime]#

surface_material: Optional[str]#

class aind_data_schema.device.Orientation3d(*, pitch: aind_data_schema.device.ConstrainedFloatValue, yaw: aind_data_schema.device.ConstrainedFloatValue, roll: aind_data_schema.device.ConstrainedFloatValue, unit: aind_data_schema.device.AngleUnit = AngleUnit.DEG)#

Bases: aind_data_schema.base.AindModel

3D orientation of an object

pitch: float#

roll: float#

unit: aind_data_schema.device.AngleUnit#

yaw: float#

class aind_data_schema.device.PowerUnit(value)#

Bases: enum.Enum

Power units

MW = 'milliwatt'#

UW = 'microwatt'#

class aind_data_schema.device.RelativePosition(*, pitch: Optional[aind_data_schema.device.ConstrainedFloatValue] = None, yaw: Optional[aind_data_schema.device.ConstrainedFloatValue] = None, roll: Optional[aind_data_schema.device.ConstrainedFloatValue] = None, angle_unit: aind_data_schema.device.AngleUnit = AngleUnit.DEG, x: Optional[float] = None, y: Optional[float] = None, z: Optional[float] = None, position_unit: aind_data_schema.device.SizeUnit = SizeUnit.MM, coordinate_system: Optional[str] = None)#

Bases: aind_data_schema.base.AindModel

Set of 6 values describing relative position on a rig

angle_unit: aind_data_schema.device.AngleUnit#

coordinate_system: Optional[str]#

pitch: Optional[float]#

position_unit: aind_data_schema.device.SizeUnit#

roll: Optional[float]#

x: Optional[float]#

y: Optional[float]#

yaw: Optional[float]#

z: Optional[float]#

class aind_data_schema.device.Size2d(*, width: int, height: int, unit: aind_data_schema.device.SizeUnit = SizeUnit.PX)#

Bases: aind_data_schema.base.AindModel

2D size of an object

height: int#

unit: aind_data_schema.device.SizeUnit#

width: int#

class aind_data_schema.device.SizeUnit(value)#

Bases: enum.Enum

units for sizes

CM = 'centimeter'#

IN = 'inch'#

MM = 'millimeter'#

NM = 'nanometer'#

NONE = 'none'#

PX = 'pixel'#

UM = 'micrometer'#

class aind_data_schema.device.Treadmill(*, 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, surface_material: Optional[str] = None, date_surface_replaced: Optional[datetime.datetime] = None, platform_type: str = 'Treadmill', treadmill_width: float, width_unit: aind_data_schema.device.SizeUnit = SizeUnit.CM)#

Bases: aind_data_schema.device.MousePlatform

Description of treadmill platform

platform_type: str#

treadmill_width: float#

width_unit: aind_data_schema.device.SizeUnit#

class aind_data_schema.device.Tube(*, 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, surface_material: Optional[str] = None, date_surface_replaced: Optional[datetime.datetime] = None, platform_type: str = 'Tube', diameter: aind_data_schema.device.ConstrainedFloatValue, diameter_unit: aind_data_schema.device.SizeUnit = SizeUnit.CM)#

Bases: aind_data_schema.device.MousePlatform

Description of a tube platform

diameter: float#

diameter_unit: aind_data_schema.device.SizeUnit#

platform_type: str#

aind_data_schema.procedures module#

schema for various Procedures

class aind_data_schema.procedures.Anaesthetic(*, type: str, duration: float, duration_unit: aind_data_schema.procedures.TimeUnit = TimeUnit.M, level: aind_data_schema.procedures.ConstrainedFloatValue)#

Bases: aind_data_schema.base.AindModel

Description of an anaestheic

duration: float#

duration_unit: aind_data_schema.procedures.TimeUnit#

level: float#

type: str#

class aind_data_schema.procedures.BrainInjection(*, start_date: datetime.date, end_date: datetime.date, experimenter_full_name: str, protocol_id: str, iacuc_protocol: Optional[str] = None, animal_weight_prior: Optional[float] = None, animal_weight_post: Optional[float] = None, weight_unit: aind_data_schema.procedures.WeightUnit = WeightUnit.G, anaesthesia: Optional[aind_data_schema.procedures.Anaesthetic] = None, notes: Optional[str] = None, injection_materials: types.ConstrainedListValue[aind_data_schema.procedures.InjectionMaterial] = None, recovery_time: Optional[float] = None, recovery_time_unit: Optional[aind_data_schema.procedures.TimeUnit] = TimeUnit.M, injection_duration: Optional[float] = None, injection_duration_unit: Optional[aind_data_schema.procedures.TimeUnit] = TimeUnit.M, workstation_id: Optional[str] = None, instrument_id: Optional[str] = None, injection_coordinate_ml: float, injection_coordinate_ap: float, injection_coordinate_depth: float, injection_coordinate_unit: aind_data_schema.device.SizeUnit = SizeUnit.MM, injection_coordinate_reference: Optional[aind_data_schema.procedures.CoordinateReferenceLocation] = None, bregma_to_lambda_distance: Optional[float] = None, bregma_to_lambda_unit: aind_data_schema.device.SizeUnit = SizeUnit.MM, injection_angle: float, injection_angle_unit: aind_data_schema.device.AngleUnit = AngleUnit.DEG, targeted_structure: Optional[str] = None, injection_hemisphere: Optional[aind_data_schema.procedures.Side] = None)#

Bases: aind_data_schema.procedures.Injection

Description of a brain injection procedure

bregma_to_lambda_distance: Optional[float]#

bregma_to_lambda_unit: aind_data_schema.device.SizeUnit#

injection_angle: float#

injection_angle_unit: aind_data_schema.device.AngleUnit#

injection_coordinate_ap: float#

injection_coordinate_depth: float#

injection_coordinate_ml: float#

injection_coordinate_reference: Optional[aind_data_schema.procedures.CoordinateReferenceLocation]#

injection_coordinate_unit: aind_data_schema.device.SizeUnit#

injection_hemisphere: Optional[aind_data_schema.procedures.Side]#

targeted_structure: Optional[str]#

class aind_data_schema.procedures.CoordinateReferenceLocation(value)#

Bases: enum.Enum

Name of reference point for Coordinates

BREGMA = 'Bregma'#

LAMBDA = 'Lambda'#

class aind_data_schema.procedures.Craniotomy(*, start_date: datetime.date, end_date: datetime.date, experimenter_full_name: str, protocol_id: str, iacuc_protocol: Optional[str] = None, animal_weight_prior: Optional[float] = None, animal_weight_post: Optional[float] = None, weight_unit: aind_data_schema.procedures.WeightUnit = WeightUnit.G, anaesthesia: Optional[aind_data_schema.procedures.Anaesthetic] = None, notes: Optional[str] = None, procedure_type: str = 'Craniotomy', craniotomy_type: aind_data_schema.procedures.CraniotomyType, craniotomy_hemisphere: Optional[aind_data_schema.procedures.Side] = None, craniotomy_coordinates_ml: Optional[float] = None, craniotomy_coordinates_ap: Optional[float] = None, craniotomy_coordinates_unit: aind_data_schema.device.SizeUnit = SizeUnit.MM, craniotomy_coordinates_reference: Optional[aind_data_schema.procedures.CoordinateReferenceLocation] = None, bregma_to_lambda_distance: Optional[float] = None, bregma_to_lambda_unit: aind_data_schema.device.SizeUnit = SizeUnit.MM, craniotomy_size: float, craniotomy_size_unit: aind_data_schema.device.SizeUnit = SizeUnit.MM, implant_part_number: Optional[str] = None, dura_removed: Optional[bool] = None, protective_material: Optional[aind_data_schema.procedures.ProtectiveMaterial] = None, workstation_id: Optional[str] = None, recovery_time: Optional[float] = None, recovery_time_unit: Optional[aind_data_schema.procedures.TimeUnit] = TimeUnit.M)#

Bases: aind_data_schema.procedures.SubjectProcedure

Description of craniotomy procedure

bregma_to_lambda_distance: Optional[float]#

bregma_to_lambda_unit: aind_data_schema.device.SizeUnit#

craniotomy_coordinates_ap: Optional[float]#

craniotomy_coordinates_ml: Optional[float]#

craniotomy_coordinates_reference: Optional[aind_data_schema.procedures.CoordinateReferenceLocation]#

craniotomy_coordinates_unit: aind_data_schema.device.SizeUnit#

craniotomy_hemisphere: Optional[aind_data_schema.procedures.Side]#

craniotomy_size: float#

craniotomy_size_unit: aind_data_schema.device.SizeUnit#

craniotomy_type: aind_data_schema.procedures.CraniotomyType#

dura_removed: Optional[bool]#

implant_part_number: Optional[str]#

procedure_type: str#

protective_material: Optional[aind_data_schema.procedures.ProtectiveMaterial]#

recovery_time: Optional[float]#

recovery_time_unit: Optional[aind_data_schema.procedures.TimeUnit]#

workstation_id: Optional[str]#

class aind_data_schema.procedures.CraniotomyType(value)#

Bases: enum.Enum

Name of craniotomy Type

FIVE_MM = '5 mm'#

OTHER = 'Other'#

THREE_MM = '3 mm'#

VISCTX = 'Visual Cortex'#

WHC = 'Whole hemisphere craniotomy'#

class aind_data_schema.procedures.CurrentUnit(value)#

Bases: enum.Enum

Current units

UA = 'microamps'#

class aind_data_schema.procedures.FerruleMaterial(value)#

Bases: enum.Enum

Probe ferrule material type name

CERAMIC = 'Ceramic'#

STAINLESS_STEEL = 'Stainless steel'#

class aind_data_schema.procedures.FiberImplant(*, start_date: datetime.date, end_date: datetime.date, experimenter_full_name: str, protocol_id: str, iacuc_protocol: Optional[str] = None, animal_weight_prior: Optional[float] = None, animal_weight_post: Optional[float] = None, weight_unit: aind_data_schema.procedures.WeightUnit = WeightUnit.G, anaesthesia: Optional[aind_data_schema.procedures.Anaesthetic] = None, notes: Optional[str] = None, procedure_type: str = 'Fiber implant', probes: types.ConstrainedListValue[aind_data_schema.procedures.OphysProbe])#

Bases: aind_data_schema.procedures.SubjectProcedure

Description of an implant procedure

probes: List[aind_data_schema.procedures.OphysProbe]#

procedure_type: str#

class aind_data_schema.procedures.Fluorophore(value)#

Bases: enum.Enum

Fluorophores used in HCR

ALEXA_546 = 'Alexa Fluor 546'#

ALEXA_594 = 'Alexa Fluor 594'#

ALEXA_647 = 'Alexa Fluor 647'#

class aind_data_schema.procedures.HCRProbe(*, name: str, source: str, rrid: Optional[str] = None, lot_number: str, expiration_date: Optional[datetime.date] = None, species: aind_data_schema.subject.Species, gene_name: str, gene_accession_number: str, probe_sequences: List[str], readout: aind_data_schema.procedures.HCRReadout, channel_index: int, initiator_name: str)#

Bases: aind_data_schema.procedures.OligoProbe

Description of a HCR probe

initiator_name: str#

readout: aind_data_schema.procedures.HCRReadout#

class aind_data_schema.procedures.HCRReadout(*, name: str, source: str, rrid: Optional[str] = None, lot_number: str, expiration_date: Optional[datetime.date] = None, fluorophore: aind_data_schema.procedures.Fluorophore, excitation_wavelength: int, stain_type: aind_data_schema.procedures.StainType, excitation_wavelength_unit: aind_data_schema.device.SizeUnit = SizeUnit.NM, SizeUnit: aind_data_schema.device.SizeUnit = SizeUnit.NM, initiator_name: str)#

Bases: aind_data_schema.procedures.Readout

Description of a readout for HCR

initiator_name: str#

class aind_data_schema.procedures.HCRSeries(*, specimen_id: str, procedure_type: aind_data_schema.procedures.SpecimenProcedureName, start_date: datetime.date, end_date: datetime.date, experimenter_full_name: str, protocol_id: str, reagents: Optional[List[aind_data_schema.procedures.Reagent]] = None, notes: Optional[str] = None, codebook_name: str, number_of_rounds: int, hcr_rounds: List[aind_data_schema.procedures.HybridizationChainReaction], strip_qc_compatible: bool)#

Bases: aind_data_schema.procedures.SpecimenProcedure

Description of series of HCR rounds for mFISH

codebook_name: str#

hcr_rounds: List[aind_data_schema.procedures.HybridizationChainReaction]#

number_of_rounds: int#

strip_qc_compatible: bool#

class aind_data_schema.procedures.Headframe(*, start_date: datetime.date, end_date: datetime.date, experimenter_full_name: str, protocol_id: str, iacuc_protocol: Optional[str] = None, animal_weight_prior: Optional[float] = None, animal_weight_post: Optional[float] = None, weight_unit: aind_data_schema.procedures.WeightUnit = WeightUnit.G, anaesthesia: Optional[aind_data_schema.procedures.Anaesthetic] = None, notes: Optional[str] = None, procedure_type: str = 'Headframe', headframe_type: str, headframe_part_number: str, headframe_material: Optional[aind_data_schema.procedures.HeadframeMaterial] = None, well_part_number: Optional[str] = None, well_type: Optional[str] = None)#

Bases: aind_data_schema.procedures.SubjectProcedure

Description of headframe procedure

headframe_material: Optional[aind_data_schema.procedures.HeadframeMaterial]#

headframe_part_number: str#

headframe_type: str#

procedure_type: str#

well_part_number: Optional[str]#

well_type: Optional[str]#

class aind_data_schema.procedures.HeadframeMaterial(value)#

Bases: enum.Enum

Headframe material name

STEEL = 'Steel'#

TITANIUM = 'Titanium'#

WHITE_ZIRCONIA = 'White Zirconia'#

class aind_data_schema.procedures.HybridizationChainReaction(*, round_index: int, start_time: datetime.datetime, end_time: datetime.datetime, HCR_probes: List[aind_data_schema.procedures.HCRProbe], other_probes: Optional[List[aind_data_schema.procedures.OligoProbe]] = None, probe_concentration: float, probe_concentration_unit: str = 'M', intrument_id: str)#

Bases: aind_data_schema.base.AindModel

Description of an HCR round

HCR_probes: List[aind_data_schema.procedures.HCRProbe]#

end_time: datetime.datetime#

intrument_id: str#

other_probes: Optional[List[aind_data_schema.procedures.OligoProbe]]#

probe_concentration: float#

probe_concentration_unit: str#

round_index: int#

start_time: datetime.datetime#

class aind_data_schema.procedures.Injection(*, start_date: datetime.date, end_date: datetime.date, experimenter_full_name: str, protocol_id: str, iacuc_protocol: Optional[str] = None, animal_weight_prior: Optional[float] = None, animal_weight_post: Optional[float] = None, weight_unit: aind_data_schema.procedures.WeightUnit = WeightUnit.G, anaesthesia: Optional[aind_data_schema.procedures.Anaesthetic] = None, notes: Optional[str] = None, injection_materials: types.ConstrainedListValue[aind_data_schema.procedures.InjectionMaterial] = None, recovery_time: Optional[float] = None, recovery_time_unit: Optional[aind_data_schema.procedures.TimeUnit] = TimeUnit.M, injection_duration: Optional[float] = None, injection_duration_unit: Optional[aind_data_schema.procedures.TimeUnit] = TimeUnit.M, workstation_id: Optional[str] = None, instrument_id: Optional[str] = None)#

Bases: aind_data_schema.procedures.SubjectProcedure

Description of an injection procedure

injection_duration: Optional[float]#

injection_duration_unit: Optional[aind_data_schema.procedures.TimeUnit]#

injection_materials: List[aind_data_schema.procedures.InjectionMaterial]#

instrument_id: Optional[str]#

recovery_time: Optional[float]#

recovery_time_unit: Optional[aind_data_schema.procedures.TimeUnit]#

workstation_id: Optional[str]#

class aind_data_schema.procedures.InjectionMaterial(*, name: str, material_id: Optional[str] = None, full_genome_name: Optional[str] = None, plasmid_name: Optional[str] = None, genome_copy: Optional[float] = None, titer: Optional[float] = None, titer_unit: Optional[str] = 'gc/mL', prep_lot_number: Optional[str] = None, prep_date: Optional[datetime.date] = None, prep_type: Optional[aind_data_schema.procedures.VirusPrepType] = None, prep_protocol: Optional[str] = None)#

Bases: aind_data_schema.base.AindModel

Description of injection material

full_genome_name: Optional[str]#

genome_copy: Optional[float]#

material_id: Optional[str]#

name: str#

plasmid_name: Optional[str]#

prep_date: Optional[datetime.date]#

prep_lot_number: Optional[str]#

prep_protocol: Optional[str]#

prep_type: Optional[aind_data_schema.procedures.VirusPrepType]#

titer: Optional[float]#

titer_unit: Optional[str]#

class aind_data_schema.procedures.IntraCerebellarVentricleInjection(*, start_date: datetime.date, end_date: datetime.date, experimenter_full_name: str, protocol_id: str, iacuc_protocol: Optional[str] = None, animal_weight_prior: Optional[float] = None, animal_weight_post: Optional[float] = None, weight_unit: aind_data_schema.procedures.WeightUnit = WeightUnit.G, anaesthesia: Optional[aind_data_schema.procedures.Anaesthetic] = None, notes: Optional[str] = None, injection_materials: types.ConstrainedListValue[aind_data_schema.procedures.InjectionMaterial] = None, recovery_time: Optional[float] = None, recovery_time_unit: Optional[aind_data_schema.procedures.TimeUnit] = TimeUnit.M, injection_duration: Optional[float] = None, injection_duration_unit: Optional[aind_data_schema.procedures.TimeUnit] = TimeUnit.M, workstation_id: Optional[str] = None, instrument_id: Optional[str] = None, injection_coordinate_ml: float, injection_coordinate_ap: float, injection_coordinate_depth: float, injection_coordinate_unit: aind_data_schema.device.SizeUnit = SizeUnit.MM, injection_coordinate_reference: Optional[aind_data_schema.procedures.CoordinateReferenceLocation] = None, bregma_to_lambda_distance: Optional[float] = None, bregma_to_lambda_unit: aind_data_schema.device.SizeUnit = SizeUnit.MM, injection_angle: float, injection_angle_unit: aind_data_schema.device.AngleUnit = AngleUnit.DEG, targeted_structure: Optional[str] = None, injection_hemisphere: Optional[aind_data_schema.procedures.Side] = None, procedure_type: str = 'ICV injection', injection_volume: float, injection_volume_unit: aind_data_schema.procedures.VolumeUnit = VolumeUnit.NL)#

Bases: aind_data_schema.procedures.BrainInjection

Description of an interacerebellar ventricle injection

injection_volume: float#

injection_volume_unit: aind_data_schema.procedures.VolumeUnit#

procedure_type: str#

class aind_data_schema.procedures.IntraCisternalMagnaInjection(*, start_date: datetime.date, end_date: datetime.date, experimenter_full_name: str, protocol_id: str, iacuc_protocol: Optional[str] = None, animal_weight_prior: Optional[float] = None, animal_weight_post: Optional[float] = None, weight_unit: aind_data_schema.procedures.WeightUnit = WeightUnit.G, anaesthesia: Optional[aind_data_schema.procedures.Anaesthetic] = None, notes: Optional[str] = None, injection_materials: types.ConstrainedListValue[aind_data_schema.procedures.InjectionMaterial] = None, recovery_time: Optional[float] = None, recovery_time_unit: Optional[aind_data_schema.procedures.TimeUnit] = TimeUnit.M, injection_duration: Optional[float] = None, injection_duration_unit: Optional[aind_data_schema.procedures.TimeUnit] = TimeUnit.M, workstation_id: Optional[str] = None, instrument_id: Optional[str] = None, injection_coordinate_ml: float, injection_coordinate_ap: float, injection_coordinate_depth: float, injection_coordinate_unit: aind_data_schema.device.SizeUnit = SizeUnit.MM, injection_coordinate_reference: Optional[aind_data_schema.procedures.CoordinateReferenceLocation] = None, bregma_to_lambda_distance: Optional[float] = None, bregma_to_lambda_unit: aind_data_schema.device.SizeUnit = SizeUnit.MM, injection_angle: float, injection_angle_unit: aind_data_schema.device.AngleUnit = AngleUnit.DEG, targeted_structure: Optional[str] = None, injection_hemisphere: Optional[aind_data_schema.procedures.Side] = None, procedure_type: str = 'ICM injection', injection_volume: float, injection_volume_unit: aind_data_schema.procedures.VolumeUnit = VolumeUnit.NL)#

Bases: aind_data_schema.procedures.BrainInjection

Description of an interacisternal magna injection

injection_volume: float#

injection_volume_unit: aind_data_schema.procedures.VolumeUnit#

procedure_type: str#

class aind_data_schema.procedures.IontophoresisInjection(*, start_date: datetime.date, end_date: datetime.date, experimenter_full_name: str, protocol_id: str, iacuc_protocol: Optional[str] = None, animal_weight_prior: Optional[float] = None, animal_weight_post: Optional[float] = None, weight_unit: aind_data_schema.procedures.WeightUnit = WeightUnit.G, anaesthesia: Optional[aind_data_schema.procedures.Anaesthetic] = None, notes: Optional[str] = None, injection_materials: types.ConstrainedListValue[aind_data_schema.procedures.InjectionMaterial] = None, recovery_time: Optional[float] = None, recovery_time_unit: Optional[aind_data_schema.procedures.TimeUnit] = TimeUnit.M, injection_duration: Optional[float] = None, injection_duration_unit: Optional[aind_data_schema.procedures.TimeUnit] = TimeUnit.M, workstation_id: Optional[str] = None, instrument_id: Optional[str] = None, injection_coordinate_ml: float, injection_coordinate_ap: float, injection_coordinate_depth: float, injection_coordinate_unit: aind_data_schema.device.SizeUnit = SizeUnit.MM, injection_coordinate_reference: Optional[aind_data_schema.procedures.CoordinateReferenceLocation] = None, bregma_to_lambda_distance: Optional[float] = None, bregma_to_lambda_unit: aind_data_schema.device.SizeUnit = SizeUnit.MM, injection_angle: float, injection_angle_unit: aind_data_schema.device.AngleUnit = AngleUnit.DEG, targeted_structure: Optional[str] = None, injection_hemisphere: Optional[aind_data_schema.procedures.Side] = None, procedure_type: str = 'Iontophoresis injection', injection_current: float, injection_current_unit: aind_data_schema.procedures.CurrentUnit = CurrentUnit.UA, alternating_current: str)#

Bases: aind_data_schema.procedures.BrainInjection

Description of an iotophoresis injection procedure

alternating_current: str#

injection_current: float#

injection_current_unit: aind_data_schema.procedures.CurrentUnit#

procedure_type: str#

class aind_data_schema.procedures.NanojectInjection(*, start_date: datetime.date, end_date: datetime.date, experimenter_full_name: str, protocol_id: str, iacuc_protocol: Optional[str] = None, animal_weight_prior: Optional[float] = None, animal_weight_post: Optional[float] = None, weight_unit: aind_data_schema.procedures.WeightUnit = WeightUnit.G, anaesthesia: Optional[aind_data_schema.procedures.Anaesthetic] = None, notes: Optional[str] = None, injection_materials: types.ConstrainedListValue[aind_data_schema.procedures.InjectionMaterial] = None, recovery_time: Optional[float] = None, recovery_time_unit: Optional[aind_data_schema.procedures.TimeUnit] = TimeUnit.M, injection_duration: Optional[float] = None, injection_duration_unit: Optional[aind_data_schema.procedures.TimeUnit] = TimeUnit.M, workstation_id: Optional[str] = None, instrument_id: Optional[str] = None, injection_coordinate_ml: float, injection_coordinate_ap: float, injection_coordinate_depth: float, injection_coordinate_unit: aind_data_schema.device.SizeUnit = SizeUnit.MM, injection_coordinate_reference: Optional[aind_data_schema.procedures.CoordinateReferenceLocation] = None, bregma_to_lambda_distance: Optional[float] = None, bregma_to_lambda_unit: aind_data_schema.device.SizeUnit = SizeUnit.MM, injection_angle: float, injection_angle_unit: aind_data_schema.device.AngleUnit = AngleUnit.DEG, targeted_structure: Optional[str] = None, injection_hemisphere: Optional[aind_data_schema.procedures.Side] = None, procedure_type: str = 'Nanoject injection', injection_volume: float, injection_volume_unit: aind_data_schema.procedures.VolumeUnit = VolumeUnit.NL)#

Bases: aind_data_schema.procedures.BrainInjection

Description of a nanoject injection procedure

injection_volume: float#

injection_volume_unit: aind_data_schema.procedures.VolumeUnit#

procedure_type: str#

class aind_data_schema.procedures.OligoProbe(*, name: str, source: str, rrid: Optional[str] = None, lot_number: str, expiration_date: Optional[datetime.date] = None, species: aind_data_schema.subject.Species, gene_name: str, gene_accession_number: str, probe_sequences: List[str], readout: aind_data_schema.procedures.Readout, channel_index: int)#

Bases: aind_data_schema.procedures.Reagent

Description of an oligo probe

channel_index: int#

gene_accession_number: str#

gene_name: str#

probe_sequences: List[str]#

readout: aind_data_schema.procedures.Readout#

species: aind_data_schema.subject.Species#

class aind_data_schema.procedures.OphysProbe(*, name: aind_data_schema.procedures.ProbeName, manufacturer: str, part_number: str, core_diameter: float, core_diameter_unit: str = 'μm', numerical_aperture: float, ferrule_material: Optional[aind_data_schema.procedures.FerruleMaterial] = None, targeted_structure: str, stereotactic_coordinate_ap: float, stereotactic_coordinate_ml: float, stereotactic_coordinate_dv: float, stereotactic_coordinate_unit: aind_data_schema.device.SizeUnit = SizeUnit.MM, stereotactic_coordinate_reference: Optional[aind_data_schema.procedures.CoordinateReferenceLocation] = None, bregma_to_lambda_distance: Optional[float] = None, bregma_to_lambda_unit: aind_data_schema.device.SizeUnit = SizeUnit.MM, angle: float, angle_unit: aind_data_schema.device.AngleUnit = AngleUnit.DEG, notes: Optional[str] = None)#

Bases: aind_data_schema.base.AindModel

Description of an ophys probe

angle: float#

angle_unit: aind_data_schema.device.AngleUnit#

bregma_to_lambda_distance: Optional[float]#

bregma_to_lambda_unit: aind_data_schema.device.SizeUnit#

core_diameter: float#

core_diameter_unit: str#

ferrule_material: Optional[aind_data_schema.procedures.FerruleMaterial]#

manufacturer: str#

name: aind_data_schema.procedures.ProbeName#

notes: Optional[str]#

numerical_aperture: float#

part_number: str#

stereotactic_coordinate_ap: float#

stereotactic_coordinate_dv: float#

stereotactic_coordinate_ml: float#

stereotactic_coordinate_reference: Optional[aind_data_schema.procedures.CoordinateReferenceLocation]#

stereotactic_coordinate_unit: aind_data_schema.device.SizeUnit#

targeted_structure: str#

class aind_data_schema.procedures.Perfusion(*, start_date: datetime.date, end_date: datetime.date, experimenter_full_name: str, protocol_id: str, iacuc_protocol: Optional[str] = None, animal_weight_prior: Optional[float] = None, animal_weight_post: Optional[float] = None, weight_unit: aind_data_schema.procedures.WeightUnit = WeightUnit.G, anaesthesia: Optional[aind_data_schema.procedures.Anaesthetic] = None, notes: Optional[str] = None, procedure_type: str = 'Perfusion', output_specimen_ids: types.ConstrainedListValue[str])#

Bases: aind_data_schema.procedures.SubjectProcedure

Description of a perfusion procedure that creates a specimen

output_specimen_ids: List[str]#

procedure_type: str#

class aind_data_schema.procedures.ProbeName(value)#

Bases: enum.Enum

Probe name

PROBE_A = 'Probe A'#

PROBE_B = 'Probe B'#

PROBE_C = 'Probe C'#

PROBE_D = 'Probe D'#

Bases: aind_data_schema.base.AindCoreModel

Description of all procedures performed on a subject

notes: Optional[str]#

schema_version: str#

specimen_procedures: Optional[List[Union[aind_data_schema.procedures.HCRSeries, aind_data_schema.procedures.SpecimenProcedure]]]#

subject_id: str#

subject_procedures: Optional[List[Union[aind_data_schema.procedures.Headframe, aind_data_schema.procedures.Craniotomy, aind_data_schema.procedures.RetroOrbitalInjection, aind_data_schema.procedures.NanojectInjection, aind_data_schema.procedures.IontophoresisInjection, aind_data_schema.procedures.IntraCerebellarVentricleInjection, aind_data_schema.procedures.IntraCisternalMagnaInjection, aind_data_schema.procedures.FiberImplant, aind_data_schema.procedures.WaterRestriction, aind_data_schema.procedures.TrainingProtocol, aind_data_schema.procedures.Perfusion, aind_data_schema.procedures.SubjectProcedure]]]#

class aind_data_schema.procedures.ProtectiveMaterial(value)#

Bases: enum.Enum

Name of material applied to craniotomy

DURAGEL = 'Duragel'#

KWIK_CAST = 'Kwik-Cast'#

OTHER = 'Other - see notes'#

SORTA_CLEAR = 'SORTA-clear'#

class aind_data_schema.procedures.Readout(*, name: str, source: str, rrid: Optional[str] = None, lot_number: str, expiration_date: Optional[datetime.date] = None, fluorophore: aind_data_schema.procedures.Fluorophore, excitation_wavelength: int, stain_type: aind_data_schema.procedures.StainType, excitation_wavelength_unit: aind_data_schema.device.SizeUnit = SizeUnit.NM, SizeUnit: aind_data_schema.device.SizeUnit = SizeUnit.NM)#

Bases: aind_data_schema.procedures.Reagent

Description of a readout

excitation_wavelength: int#

fluorophore: aind_data_schema.procedures.Fluorophore#

stain_type: aind_data_schema.procedures.StainType#

class aind_data_schema.procedures.Reagent(*, name: str, source: str, rrid: Optional[str] = None, lot_number: str, expiration_date: Optional[datetime.date] = None)#

Bases: aind_data_schema.base.AindModel

Description of reagents used in procedure

expiration_date: Optional[datetime.date]#

lot_number: str#

name: str#

rrid: Optional[str]#

source: str#

class aind_data_schema.procedures.RetroOrbitalInjection(*, start_date: datetime.date, end_date: datetime.date, experimenter_full_name: str, protocol_id: str, iacuc_protocol: Optional[str] = None, animal_weight_prior: Optional[float] = None, animal_weight_post: Optional[float] = None, weight_unit: aind_data_schema.procedures.WeightUnit = WeightUnit.G, anaesthesia: Optional[aind_data_schema.procedures.Anaesthetic] = None, notes: Optional[str] = None, injection_materials: types.ConstrainedListValue[aind_data_schema.procedures.InjectionMaterial] = None, recovery_time: Optional[float] = None, recovery_time_unit: Optional[aind_data_schema.procedures.TimeUnit] = TimeUnit.M, injection_duration: Optional[float] = None, injection_duration_unit: Optional[aind_data_schema.procedures.TimeUnit] = TimeUnit.M, workstation_id: Optional[str] = None, instrument_id: Optional[str] = None, procedure_type: str = 'Retro-orbital injection', injection_volume: float, injection_volume_unit: aind_data_schema.procedures.VolumeUnit = VolumeUnit.UL, injection_eye: aind_data_schema.procedures.Side)#

Bases: aind_data_schema.procedures.Injection

Description of a retro-orbital injection procedure

injection_eye: aind_data_schema.procedures.Side#

injection_volume: float#

injection_volume_unit: aind_data_schema.procedures.VolumeUnit#

procedure_type: str#

class aind_data_schema.procedures.Side(value)#

Bases: enum.Enum

Side of animal

LEFT = 'Left'#

RIGHT = 'Right'#

class aind_data_schema.procedures.SpecimenProcedure(*, specimen_id: str, procedure_type: aind_data_schema.procedures.SpecimenProcedureName, start_date: datetime.date, end_date: datetime.date, experimenter_full_name: str, protocol_id: str, reagents: Optional[List[aind_data_schema.procedures.Reagent]] = None, notes: Optional[str] = None)#

Bases: aind_data_schema.base.AindModel

Description of surgical or other procedure performed on a specimen

end_date: datetime.date#

experimenter_full_name: str#

notes: Optional[str]#

procedure_type: aind_data_schema.procedures.SpecimenProcedureName#

protocol_id: str#

reagents: Optional[List[aind_data_schema.procedures.Reagent]]#

specimen_id: str#

start_date: datetime.date#

class aind_data_schema.procedures.SpecimenProcedureName(value)#

Bases: enum.Enum

Specimen procedure type name

ACTIVE_DELIPIDATION = 'Active delipidation'#

CLEARING = 'Clearing'#

DCM_DELIPIDATION = 'DCM delipidation'#

DOUBLE_DELIPIDATION = 'Double delipidation'#

EMBEDDING = 'Embedding'#

FIXATION = 'Fixation'#

FIXATION_PERMEABILIZATION = 'Fixation and permeabilization'#

GELATION = 'Gelation'#

HYBRIDIZATION_AMPLIFICATION = 'Hybridication and amplification'#

IMMUNOSTAINING = 'Immunostaining'#

OTHER = 'Other - see notes'#

SOAK = 'Soak'#

STORAGE = 'Storage'#

STRIPPING = 'Stripping'#

class aind_data_schema.procedures.StainType(value)#

Bases: enum.Enum

Stain Types for HCR probes

RNA = 'RNA'#

class aind_data_schema.procedures.SubjectProcedure(*, start_date: datetime.date, end_date: datetime.date, experimenter_full_name: str, protocol_id: str, iacuc_protocol: Optional[str] = None, animal_weight_prior: Optional[float] = None, animal_weight_post: Optional[float] = None, weight_unit: aind_data_schema.procedures.WeightUnit = WeightUnit.G, anaesthesia: Optional[aind_data_schema.procedures.Anaesthetic] = None, notes: Optional[str] = None)#

Bases: aind_data_schema.base.AindModel

Description of surgical or other procedure performed on a subject

anaesthesia: Optional[aind_data_schema.procedures.Anaesthetic]#

animal_weight_post: Optional[float]#

animal_weight_prior: Optional[float]#

end_date: datetime.date#

experimenter_full_name: str#

iacuc_protocol: Optional[str]#

notes: Optional[str]#

protocol_id: str#

start_date: datetime.date#

weight_unit: aind_data_schema.procedures.WeightUnit#

class aind_data_schema.procedures.TimeUnit(value)#

Bases: enum.Enum

Time units

M = 'minute'#

MS = 'millisecond'#

S = 'second'#

class aind_data_schema.procedures.TrainingProtocol(*, procedure_type: str = 'Training', training_name: str, protocol_id: str, training_protocol_start_date: datetime.date, training_protocol_end_date: Optional[datetime.date] = None, notes: Optional[str] = None)#

Bases: aind_data_schema.base.AindModel

Description of an animal training protocol

notes: Optional[str]#

procedure_type: str#

protocol_id: str#

training_name: str#

training_protocol_end_date: Optional[datetime.date]#

training_protocol_start_date: datetime.date#

class aind_data_schema.procedures.VirusPrepType(value)#

Bases: enum.Enum

Type of virus preparation

CRUDE = 'Crude'#

PURIFIED = 'Purified'#

class aind_data_schema.procedures.VolumeUnit(value)#

Bases: enum.Enum

Volume units

NL = 'nanoliter'#

UL = 'microliter'#

class aind_data_schema.procedures.WaterRestriction(*, procedure_type: str = 'Water restriction', protocol_id: Optional[str] = None, baseline_weight: float, weight_unit: aind_data_schema.procedures.WeightUnit = WeightUnit.G, start_date: datetime.date, end_date: datetime.date)#

Bases: aind_data_schema.base.AindModel

Description of a water restriction procedure

baseline_weight: float#

end_date: datetime.date#

procedure_type: str#

protocol_id: Optional[str]#

start_date: datetime.date#

weight_unit: aind_data_schema.procedures.WeightUnit#

class aind_data_schema.procedures.WeightUnit(value)#

Bases: enum.Enum

Weight units

G = 'gram'#

aind_data_schema.processing module#

schema for processing

class aind_data_schema.processing.DataProcess(*, name: aind_data_schema.processing.ProcessName, version: str, start_date_time: datetime.datetime, end_date_time: datetime.datetime, input_location: str, output_location: str, code_url: str, code_version: Optional[str] = None, parameters: Dict[str, Any], outputs: Optional[Dict[str, Any]] = None, notes: Optional[str] = None)#

Bases: aind_data_schema.base.AindModel

Description of a single processing step

code_url: str#

code_version: Optional[str]#

end_date_time: datetime.datetime#

input_location: str#

name: aind_data_schema.processing.ProcessName#

notes: Optional[str]#

output_location: str#

outputs: Optional[Dict[str, Any]]#

parameters: Dict[str, Any]#

start_date_time: datetime.datetime#

version: str#

class aind_data_schema.processing.ProcessName(value)#

Bases: enum.Enum

Data processing type labels

EPHYS_CURATION = 'Ephys curation'#

EPHYS_POSTPROCESSING = 'Ephys postprocessing'#

EPHYS_PREPROCESSING = 'Ephys preprocessing'#

EPHYS_VISUALIZATION = 'Ephys visualization'#

FILE_CONVERSION = 'File format conversion'#

IMAGE_ATLAS_ALIGNMENT = 'Image atlas alignment'#

IMAGE_BACKGROUND_SUBTRACTION = 'Image background subtraction'#

IMAGE_CELL_SEGMENTATION = 'Image cell segmentation'#

IMAGE_DESTRIPING = 'Image destriping'#

IMAGE_IMPORTING = 'Image importing'#

IMAGE_THRESHOLDING = 'Image thresholding'#

IMAGE_TILE_ALIGNMENT = 'Image tile alignment'#

IMAGE_TILE_FUSING = 'Image tile fusing'#

IMAGE_TILE_PROJECTION = 'Image tile projection'#

OTHER = 'Other'#

SPIKE_SORTING = 'Spike sorting'#

class aind_data_schema.processing.Processing(*, describedBy: str = 'https://raw.githubusercontent.com/AllenNeuralDynamics/aind-data-schema/main/src/aind_data_schema/processing.py', schema_version: str = '0.2.1', pipeline_version: Optional[str] = None, pipeline_url: Optional[str] = None, data_processes: types.ConstrainedListValue[aind_data_schema.processing.DataProcess])#

Bases: aind_data_schema.base.AindCoreModel

Description of all processes run on data

data_processes: List[aind_data_schema.processing.DataProcess]#

pipeline_url: Optional[str]#

pipeline_version: Optional[str]#

schema_version: str#

class aind_data_schema.processing.Registration(*, name: aind_data_schema.processing.ProcessName, version: str, start_date_time: datetime.datetime, end_date_time: datetime.datetime, input_location: str, output_location: str, code_url: str, code_version: Optional[str] = None, parameters: Dict[str, Any], outputs: Optional[Dict[str, Any]] = None, notes: Optional[str] = None, registration_type: aind_data_schema.processing.RegistrationType, registration_channel: Optional[int] = None, tiles: List[aind_data_schema.imaging.tile.Tile])#

Bases: aind_data_schema.processing.DataProcess

Description of tile alignment coordinate transformations

registration_channel: Optional[int]#

registration_type: aind_data_schema.processing.RegistrationType#

tiles: List[aind_data_schema.imaging.tile.Tile]#

class aind_data_schema.processing.RegistrationType(value)#

Bases: enum.Enum

Types of registration

INTER = 'Inter-channel'#

INTRA = 'Intra-channel'#

aind_data_schema.stimulus module#

schema for session stimulus

class aind_data_schema.stimulus.OptoStim(*, stimulus_name: str, pulse_shape: aind_data_schema.stimulus.PulseShape, pulse_frequency: int, pulse_frequency_unit: aind_data_schema.device.FrequencyUnit = FrequencyUnit.HZ, number_pulse_trains: int, pulse_width: int, pulse_width_unit: aind_data_schema.procedures.TimeUnit = TimeUnit.MS, pulse_train_duration: float, pulse_train_duration_unit: aind_data_schema.procedures.TimeUnit = TimeUnit.S, fixed_pulse_train_interval: bool, pulse_train_interval: Optional[float] = None, pulse_train_interval_unit: aind_data_schema.procedures.TimeUnit = TimeUnit.S, baseline_duration: float, baseline_duration_unit: aind_data_schema.procedures.TimeUnit = TimeUnit.S, other_parameters: Optional[Dict[str, Any]] = None, notes: Optional[str] = None)#

Bases: aind_data_schema.base.AindModel

Description of opto stimulation parameters

baseline_duration: float#

baseline_duration_unit: aind_data_schema.procedures.TimeUnit#

fixed_pulse_train_interval: bool#

notes: Optional[str]#

number_pulse_trains: int#

other_parameters: Optional[Dict[str, Any]]#

pulse_frequency: int#

pulse_frequency_unit: aind_data_schema.device.FrequencyUnit#

pulse_shape: aind_data_schema.stimulus.PulseShape#

pulse_train_duration: float#

pulse_train_duration_unit: aind_data_schema.procedures.TimeUnit#

pulse_train_interval: Optional[float]#

pulse_train_interval_unit: aind_data_schema.procedures.TimeUnit#

pulse_width: int#

pulse_width_unit: aind_data_schema.procedures.TimeUnit#

stimulus_name: str#

class aind_data_schema.stimulus.PulseShape(value)#

Bases: enum.Enum

Types of Opto stim pulse shapes

RAMP = 'Ramp'#

SINE = 'Sinusoidal'#

SQUARE = 'Square'#

class aind_data_schema.stimulus.StimulusPresentation(*, stimulus: Union[aind_data_schema.stimulus.OptoStim, aind_data_schema.stimulus.VisualStim], stimulus_start_time: datetime.time, stimulus_end_time: datetime.time)#

Bases: aind_data_schema.base.AindModel

Description of stimulus used during session

stimulus: Union[aind_data_schema.stimulus.OptoStim, aind_data_schema.stimulus.VisualStim]#

stimulus_end_time: datetime.time#

stimulus_start_time: datetime.time#

class aind_data_schema.stimulus.VisualStim(*, stimulus_name: str, stimulus_parameters: Optional[Dict[str, Any]] = None, stimulus_template_name: Optional[List[str]] = None, stimulus_software: str, stimulus_software_version: str, stimulus_script: str, stimulus_script_version: str, notes: Optional[str] = None)#

Bases: aind_data_schema.base.AindModel

Description of visual stimulus parameters. Provides a high level description of stimulus.

notes: Optional[str]#

stimulus_name: str#

stimulus_parameters: Optional[Dict[str, Any]]#

stimulus_script: str#

stimulus_script_version: str#

stimulus_software: str#

stimulus_software_version: str#

stimulus_template_name: Optional[List[str]]#

aind_data_schema.subject module#

schema for mostly mouse metadata

class aind_data_schema.subject.BackgroundStrain(value)#

Bases: enum.Enum

Animal background strain name

BALB_c = 'BALB/c'#

C57BL_6J = 'C57BL/6J'#

class aind_data_schema.subject.HomeCageEnrichment(value)#

Bases: enum.Enum

Materials provided in animal home cage

NONE = 'None'#

OTHER = 'Other'#

PLASTIC_SHELTER = 'Plastic shelter'#

PLASTIC_TUBE = 'Plastic tube'#

RUNNING_WHEEL = 'Running wheel'#

class aind_data_schema.subject.Housing(*, cage_id: Optional[str] = None, room_id: Optional[str] = None, light_cycle: Optional[aind_data_schema.subject.LightCycle] = None, home_cage_enrichment: Optional[List[aind_data_schema.subject.HomeCageEnrichment]] = None, cohoused_subjects: Optional[List[str]] = None)#

Bases: aind_data_schema.base.AindModel

Description of subject housing

cage_id: Optional[str]#

cohoused_subjects: Optional[List[str]]#

home_cage_enrichment: Optional[List[aind_data_schema.subject.HomeCageEnrichment]]#

light_cycle: Optional[aind_data_schema.subject.LightCycle]#

room_id: Optional[str]#

class aind_data_schema.subject.LightCycle(*, lights_on_time: datetime.time, lights_off_time: datetime.time)#

Bases: aind_data_schema.base.AindModel

Description of vivarium light cycle times

lights_off_time: datetime.time#

lights_on_time: datetime.time#

class aind_data_schema.subject.MgiAlleleId(*, allele_name: str, mgi_id: str)#

Bases: aind_data_schema.base.AindModel

Mouse Genome Informatics IDs for genotype alleles

allele_name: str#

mgi_id: str#

class aind_data_schema.subject.Sex(value)#

Bases: enum.Enum

Subject sex name

FEMALE = 'Female'#

MALE = 'Male'#

class aind_data_schema.subject.Species(value)#

Bases: enum.Enum

Species latin name

CALLITHRIX_JACCHUS = PIDName(name=BaseName(name='Callithrix jacchus', abbreviation=None), registry=BaseName(name='National Center for Biotechnology Information', abbreviation='NCBI'), registry_identifier='9483')#

HOMO_SAPIENS = PIDName(name=BaseName(name='Homo sapiens', abbreviation=None), registry=BaseName(name='National Center for Biotechnology Information', abbreviation='NCBI'), registry_identifier='9606')#

MACACA_MULATTA = PIDName(name=BaseName(name='Macaca mulatta', abbreviation=None), registry=BaseName(name='National Center for Biotechnology Information', abbreviation='NCBI'), registry_identifier='9544')#

MUS_MUSCULUS = PIDName(name=BaseName(name='Mus musculus', abbreviation=None), registry=BaseName(name='National Center for Biotechnology Information', abbreviation='NCBI'), registry_identifier='10090')#

class aind_data_schema.subject.Subject(*, describedBy: str = 'https://raw.githubusercontent.com/AllenNeuralDynamics/aind-data-schema/main/src/aind_data_schema/subject.py', schema_version: str = '0.3.2', species: aind_data_schema.subject.Species, subject_id: str, sex: aind_data_schema.subject.Sex, date_of_birth: datetime.date, genotype: str, mgi_allele_ids: Optional[List[aind_data_schema.subject.MgiAlleleId]] = None, background_strain: Optional[aind_data_schema.subject.BackgroundStrain] = None, source: Optional[str] = None, rrid: Optional[str] = None, restrictions: Optional[str] = None, breeding_group: Optional[str] = None, maternal_id: Optional[str] = None, maternal_genotype: Optional[str] = None, paternal_id: Optional[str] = None, paternal_genotype: Optional[str] = None, wellness_reports: Optional[List[aind_data_schema.subject.WellnessReport]] = None, housing: Optional[aind_data_schema.subject.Housing] = None, notes: Optional[str] = None)#

Bases: aind_data_schema.base.AindCoreModel

Description of a subject of data collection

background_strain: Optional[aind_data_schema.subject.BackgroundStrain]#

breeding_group: Optional[str]#

date_of_birth: datetime.date#

genotype: str#

housing: Optional[aind_data_schema.subject.Housing]#

maternal_genotype: Optional[str]#

maternal_id: Optional[str]#

mgi_allele_ids: Optional[List[aind_data_schema.subject.MgiAlleleId]]#

notes: Optional[str]#

paternal_genotype: Optional[str]#

paternal_id: Optional[str]#

restrictions: Optional[str]#

rrid: Optional[str]#

schema_version: str#

sex: aind_data_schema.subject.Sex#

source: Optional[str]#

species: aind_data_schema.subject.Species#

subject_id: str#

wellness_reports: Optional[List[aind_data_schema.subject.WellnessReport]]#

class aind_data_schema.subject.WellnessReport(*, date: datetime.date, report: str)#

Bases: aind_data_schema.base.AindModel

Wellness report on animal health

date: datetime.date#

report: str#

Module contents#

imports for AindModel subclasses

class aind_data_schema.Acquisition(*, describedBy: str = 'https://raw.githubusercontent.com/AllenNeuralDynamics/aind-data-schema/main/src/aind_data_schema/imaging/acquisition.py', schema_version: str = '0.4.5', experimenter_full_name: List[str], specimen_id: str, subject_id: Optional[str] = None, instrument_id: str, session_start_time: datetime.datetime, session_end_time: datetime.datetime, session_type: Optional[str] = None, tiles: List[aind_data_schema.imaging.tile.AcquisitionTile], axes: List[aind_data_schema.imaging.acquisition.Axis], chamber_immersion: aind_data_schema.imaging.acquisition.Immersion, sample_immersion: Optional[aind_data_schema.imaging.acquisition.Immersion] = None, active_objectives: Optional[List[str]] = None, local_storage_directory: Optional[str] = None, external_storage_directory: Optional[str] = None, processing_steps: Optional[List[aind_data_schema.imaging.acquisition.ProcessingSteps]] = None, notes: Optional[str] = None)#

Bases: aind_data_schema.base.AindCoreModel

Description of an imaging acquisition session

active_objectives: Optional[List[str]]#

axes: List[aind_data_schema.imaging.acquisition.Axis]#

chamber_immersion: aind_data_schema.imaging.acquisition.Immersion#

experimenter_full_name: List[str]#

external_storage_directory: Optional[str]#

instrument_id: str#

local_storage_directory: Optional[str]#

notes: Optional[str]#

processing_steps: Optional[List[aind_data_schema.imaging.acquisition.ProcessingSteps]]#

sample_immersion: Optional[aind_data_schema.imaging.acquisition.Immersion]#

schema_version: str#

session_end_time: datetime.datetime#

session_start_time: datetime.datetime#

session_type: Optional[str]#

specimen_id: str#

subject_id: Optional[str]#

tiles: List[aind_data_schema.imaging.tile.AcquisitionTile]#

class aind_data_schema.Axis(*, name: aind_data_schema.imaging.acquisition.AxisName, dimension: int, direction: aind_data_schema.imaging.acquisition.Direction, unit: aind_data_schema.device.SizeUnit = SizeUnit.UM)#

Bases: aind_data_schema.base.AindModel

Description of an image axis

dimension: int#

direction: aind_data_schema.imaging.acquisition.Direction#

static from_direction_code(code) → List[aind_data_schema.imaging.acquisition.Axis]#: Convert direction codes like ‘RAS’ or ‘PLA’ into a set of axis objects

name: aind_data_schema.imaging.acquisition.AxisName#

unit: aind_data_schema.device.SizeUnit#

class aind_data_schema.BehaviorRig(*, describedBy: str = 'https://raw.githubusercontent.com/AllenNeuralDynamics/aind-data-schema/main/src/aind_data_schema/behavior/behavior_rig.py', schema_version: str = '0.0.2', rig_id: str, 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.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 behavior 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.device.DAQDevice]]]#

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#

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

class aind_data_schema.BehaviorSession(*, describedBy: str = 'https://raw.githubusercontent.com/AllenNeuralDynamics/aind-data-schema/main/src/aind_data_schema/behavior/behavior_session.py', schema_version: str = '0.0.1', experimenter_full_name: str, session_start_time: datetime.datetime, session_end_time: datetime.datetime, subject_id: int, animal_weight_prior: Optional[float] = None, animal_weight_post: Optional[float] = None, weight_unit: aind_data_schema.procedures.WeightUnit = WeightUnit.G, behavior_type: str, behavior_code: str, code_version: str, input_parameters: Dict[str, Any], output_parameters: Dict[str, Any], water_consumed: float, water_consumed_unit: aind_data_schema.procedures.VolumeUnit = VolumeUnit.UL, notes: Optional[str] = None)#

Bases: aind_data_schema.base.AindCoreModel

Description of a behavior session

animal_weight_post: Optional[float]#

animal_weight_prior: Optional[float]#

behavior_code: str#

behavior_type: str#

code_version: str#

experimenter_full_name: str#

input_parameters: Dict[str, Any]#

notes: Optional[str]#

output_parameters: Dict[str, Any]#

schema_version: str#

session_end_time: datetime.datetime#

session_start_time: datetime.datetime#

subject_id: int#

water_consumed: float#

water_consumed_unit: aind_data_schema.procedures.VolumeUnit#

weight_unit: aind_data_schema.procedures.WeightUnit#

class aind_data_schema.DataDescription(label=None, *, describedBy: str = 'https://raw.githubusercontent.com/AllenNeuralDynamics/aind-data-schema/main/src/aind_data_schema/data_description.py', schema_version: str = '0.6.3', license: str = 'CC-BY-4.0', creation_time: datetime.time, creation_date: datetime.date, name: Optional[str] = None, institution: aind_data_schema.data_description.Institution, funding_source: List[aind_data_schema.data_description.Funding], data_level: aind_data_schema.data_description.DataLevel, group: Optional[aind_data_schema.data_description.Group] = None, investigators: List[str], project_name: Optional[str] = None, project_id: Optional[str] = None, restrictions: Optional[str] = None, modality: List[aind_data_schema.data_description.Modality], experiment_type: aind_data_schema.data_description.ExperimentType, subject_id: aind_data_schema.data_description.ConstrainedStrValue, related_data: Optional[List[aind_data_schema.data_description.RelatedData]] = [], data_summary: Optional[str] = None)#

Bases: aind_data_schema.base.AindCoreModel

Description of a logical collection of data files

creation_date: datetime.date#

creation_time: datetime.time#

data_level: aind_data_schema.data_description.DataLevel#

data_summary: Optional[str]#

describedBy: str#

experiment_type: aind_data_schema.data_description.ExperimentType#

funding_source: List[aind_data_schema.data_description.Funding]#

group: Optional[aind_data_schema.data_description.Group]#

institution: aind_data_schema.data_description.Institution#

investigators: List[str]#

license: str#

modality: List[aind_data_schema.data_description.Modality]#

name: Optional[str]#

classmethod parse_name(name)#: Decompose a DataDescription name string into component parts

project_id: Optional[str]#

project_name: Optional[str]#

related_data: Optional[List[aind_data_schema.data_description.RelatedData]]#

restrictions: Optional[str]#

schema_version: str#

subject_id: str#

class aind_data_schema.DataProcess(*, name: aind_data_schema.processing.ProcessName, version: str, start_date_time: datetime.datetime, end_date_time: datetime.datetime, input_location: str, output_location: str, code_url: str, code_version: Optional[str] = None, parameters: Dict[str, Any], outputs: Optional[Dict[str, Any]] = None, notes: Optional[str] = None)#

Bases: aind_data_schema.base.AindModel

Description of a single processing step

code_url: str#

code_version: Optional[str]#

end_date_time: datetime.datetime#

input_location: str#

name: aind_data_schema.processing.ProcessName#

notes: Optional[str]#

output_location: str#

outputs: Optional[Dict[str, Any]]#

parameters: Dict[str, Any]#

start_date_time: datetime.datetime#

version: str#

class aind_data_schema.DerivedDataDescription(process_name, *, describedBy: str = 'https://raw.githubusercontent.com/AllenNeuralDynamics/aind-data-schema/main/src/aind_data_schema/data_description.py', schema_version: str = '0.6.3', license: str = 'CC-BY-4.0', creation_time: datetime.time, creation_date: datetime.date, name: Optional[str] = None, institution: aind_data_schema.data_description.Institution, funding_source: List[aind_data_schema.data_description.Funding], data_level: aind_data_schema.data_description.DataLevel = DataLevel.DERIVED_DATA, group: Optional[aind_data_schema.data_description.Group] = None, investigators: List[str], project_name: Optional[str] = None, project_id: Optional[str] = None, restrictions: Optional[str] = None, modality: List[aind_data_schema.data_description.Modality], experiment_type: aind_data_schema.data_description.ExperimentType, subject_id: aind_data_schema.data_description.ConstrainedStrValue, related_data: Optional[List[aind_data_schema.data_description.RelatedData]] = [], data_summary: Optional[str] = None, input_data_name: str)#

Bases: aind_data_schema.data_description.DataDescription

A logical collection of data files derived via processing

creation_date: datetime.date#

creation_time: datetime.time#

data_level: aind_data_schema.data_description.DataLevel#

data_summary: Optional[str]#

describedBy: str#

experiment_type: aind_data_schema.data_description.ExperimentType#

funding_source: List[aind_data_schema.data_description.Funding]#

group: Optional[aind_data_schema.data_description.Group]#

input_data_name: str#

institution: aind_data_schema.data_description.Institution#

investigators: List[str]#

license: str#

modality: List[aind_data_schema.data_description.Modality]#

name: Optional[str]#

classmethod parse_name(name)#: decompose DerivedDataDescription name into parts

project_id: Optional[str]#

project_name: Optional[str]#

related_data: Optional[List[aind_data_schema.data_description.RelatedData]]#

restrictions: Optional[str]#

schema_version: str#

subject_id: str#

class aind_data_schema.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]]]#

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.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]#

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.Funding(*, funder: str, grant_number: Optional[str] = None, fundee: Optional[str] = None)#

Bases: aind_data_schema.base.AindModel

Description of funding sources

fundee: Optional[str]#

funder: str#

grant_number: Optional[str]#

class aind_data_schema.Instrument(*, describedBy: str = 'https://raw.githubusercontent.com/AllenNeuralDynamics/aind-data-schema/main/src/aind_data_schema/imaging/instrument.py', schema_version: str = '0.6.1', instrument_id: Optional[str] = None, instrument_type: aind_data_schema.imaging.instrument.ImagingInstrumentType, manufacturer: aind_data_schema.device.Manufacturer, temperature_control: Optional[bool] = None, humidity_control: Optional[bool] = None, optical_tables: List[aind_data_schema.imaging.instrument.OpticalTable] = None, objectives: types.ConstrainedListValue[aind_data_schema.imaging.instrument.Objective], detectors: Optional[types.ConstrainedListValue[aind_data_schema.imaging.instrument.Detector]] = None, light_sources: Optional[types.ConstrainedListValue[aind_data_schema.imaging.instrument.Lightsource]] = None, fluorescence_filters: Optional[types.ConstrainedListValue[aind_data_schema.device.Filter]] = None, motorized_stages: Optional[types.ConstrainedListValue[aind_data_schema.device.MotorizedStage]] = None, scanning_stages: Optional[types.ConstrainedListValue[aind_data_schema.imaging.instrument.ScanningStage]] = None, daqs: Optional[types.ConstrainedListValue[aind_data_schema.device.DAQDevice]] = None, additional_devices: Optional[types.ConstrainedListValue[aind_data_schema.imaging.instrument.AdditionalImagingDevice]] = None, calibration_date: Optional[datetime.date] = None, calibration_data: Optional[str] = None, com_ports: Optional[types.ConstrainedListValue[aind_data_schema.imaging.instrument.Com]] = None, notes: Optional[str] = None)#

Bases: aind_data_schema.base.AindCoreModel

Description of an instrument, which is a collection of devices

additional_devices: Optional[List[aind_data_schema.imaging.instrument.AdditionalImagingDevice]]#

calibration_data: Optional[str]#

calibration_date: Optional[datetime.date]#

com_ports: Optional[List[aind_data_schema.imaging.instrument.Com]]#

daqs: Optional[List[aind_data_schema.device.DAQDevice]]#

detectors: Optional[List[aind_data_schema.imaging.instrument.Detector]]#

fluorescence_filters: Optional[List[aind_data_schema.device.Filter]]#

humidity_control: Optional[bool]#

instrument_id: Optional[str]#

instrument_type: aind_data_schema.imaging.instrument.ImagingInstrumentType#

light_sources: Optional[List[aind_data_schema.imaging.instrument.Lightsource]]#

manufacturer: aind_data_schema.device.Manufacturer#

motorized_stages: Optional[List[aind_data_schema.device.MotorizedStage]]#

notes: Optional[str]#

objectives: List[aind_data_schema.imaging.instrument.Objective]#

optical_tables: List[aind_data_schema.imaging.instrument.OpticalTable]#

scanning_stages: Optional[List[aind_data_schema.imaging.instrument.ScanningStage]]#

schema_version: str#

temperature_control: Optional[bool]#

class aind_data_schema.LightCycle(*, lights_on_time: datetime.time, lights_off_time: datetime.time)#

Bases: aind_data_schema.base.AindModel

Description of vivarium light cycle times

lights_off_time: datetime.time#

lights_on_time: datetime.time#

class aind_data_schema.MriSession(*, describedBy: str = 'https://raw.githubusercontent.com/AllenNeuralDynamics/aind-data-schema/main/src/aind_data_schema/imaging/mri_session.py', schema_version: str = '0.0.3', subject_id: str, session_start_time: datetime.datetime, session_end_time: Optional[datetime.datetime] = None, experimenter_full_name: List[str], protocol_id: str, iacuc_protocol: Optional[str] = None, animal_weight_prior: Optional[float] = None, animal_weight_post: Optional[float] = None, weight_unit: aind_data_schema.procedures.WeightUnit = WeightUnit.G, anaesthesia: Optional[aind_data_schema.procedures.Anaesthetic] = None, scan_sequence: aind_data_schema.imaging.mri_session.MriScanSequence, mri_scanner: aind_data_schema.imaging.mri_session.Scanner, axes: List[aind_data_schema.imaging.acquisition.Axis], voxel_sizes: aind_data_schema.imaging.tile.Scale3dTransform, notes: Optional[str] = None)#

Bases: aind_data_schema.base.AindCoreModel

Description of an MRI scan

anaesthesia: Optional[aind_data_schema.procedures.Anaesthetic]#

animal_weight_post: Optional[float]#

animal_weight_prior: Optional[float]#

axes: List[aind_data_schema.imaging.acquisition.Axis]#

experimenter_full_name: List[str]#

iacuc_protocol: Optional[str]#

mri_scanner: aind_data_schema.imaging.mri_session.Scanner#

notes: Optional[str]#

protocol_id: str#

scan_sequence: aind_data_schema.imaging.mri_session.MriScanSequence#

schema_version: str#

session_end_time: Optional[datetime.datetime]#

session_start_time: datetime.datetime#

subject_id: str#

voxel_sizes: aind_data_schema.imaging.tile.Scale3dTransform#

weight_unit: aind_data_schema.procedures.WeightUnit#

class aind_data_schema.OphysRig(*, describedBy: str = 'https://raw.githubusercontent.com/AllenNeuralDynamics/aind-data-schema/main/src/aind_data_schema/ophys/ophys_rig.py', schema_version: str = '0.5.1', rig_id: str, temperature_control: Optional[bool] = None, humidity_control: Optional[bool] = None, vibration_control: Optional[bool] = None, patch_cords: Optional[types.ConstrainedListValue[aind_data_schema.ophys.ophys_rig.Patch]], light_sources: types.ConstrainedListValue[Union[aind_data_schema.device.Laser, aind_data_schema.device.LightEmittingDiode]], detectors: Optional[types.ConstrainedListValue[aind_data_schema.ophys.ophys_rig.Detector]] = None, filters: Optional[types.ConstrainedListValue[aind_data_schema.device.Filter]] = None, lenses: Optional[types.ConstrainedListValue[aind_data_schema.device.Lens]] = None, cameras: Optional[types.ConstrainedListValue[aind_data_schema.device.CameraAssembly]] = None, mouse_platform: Optional[Union[aind_data_schema.device.Tube, aind_data_schema.device.Treadmill, aind_data_schema.device.Disc]] = None, visual_monitors: Optional[types.ConstrainedListValue[aind_data_schema.device.Monitor]] = None, daqs: Optional[List[Union[aind_data_schema.device.HarpDevice, aind_data_schema.device.DAQDevice]]] = None, additional_devices: Optional[types.ConstrainedListValue[aind_data_schema.device.Device]] = None, light_path_diagram: Optional[str] = None, notes: Optional[str] = None)#

Bases: aind_data_schema.base.AindCoreModel

Description of an optical physiology 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.device.DAQDevice]]]#

detectors: Optional[List[aind_data_schema.ophys.ophys_rig.Detector]]#

filters: Optional[List[aind_data_schema.device.Filter]]#

humidity_control: Optional[bool]#

lenses: Optional[List[aind_data_schema.device.Lens]]#

light_path_diagram: Optional[str]#

light_sources: List[Union[aind_data_schema.device.Laser, aind_data_schema.device.LightEmittingDiode]]#

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

notes: Optional[str]#

patch_cords: Optional[List[aind_data_schema.ophys.ophys_rig.Patch]]#

rig_id: str#

schema_version: str#

temperature_control: Optional[bool]#

vibration_control: Optional[bool]#

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

class aind_data_schema.OphysSession(*, describedBy: str = 'https://raw.githubusercontent.com/AllenNeuralDynamics/aind-data-schema/main/src/aind_data_schema/ophys/ophys_session.py', schema_version: str = '0.2.3', experimenter_full_name: List[str], session_start_time: datetime.datetime, session_end_time: Optional[datetime.datetime] = None, subject_id: int, session_type: str, iacuc_protocol: Optional[str] = None, rig_id: str, light_sources: types.ConstrainedListValue[Union[aind_data_schema.ophys.ophys_session.Laser, aind_data_schema.ophys.ophys_session.LightEmittingDiode]], detectors: Optional[types.ConstrainedListValue[aind_data_schema.ophys.ophys_session.Detector]] = None, cameras: Optional[types.ConstrainedListValue[aind_data_schema.ophys.ophys_session.Camera]] = None, stimulus_presentations: Optional[List[aind_data_schema.stimulus.StimulusPresentation]] = None, notes: Optional[str] = None)#

Bases: aind_data_schema.base.AindCoreModel

Description of an ophys session

cameras: Optional[List[aind_data_schema.ophys.ophys_session.Camera]]#

detectors: Optional[List[aind_data_schema.ophys.ophys_session.Detector]]#

experimenter_full_name: List[str]#

iacuc_protocol: Optional[str]#

light_sources: List[Union[aind_data_schema.ophys.ophys_session.Laser, aind_data_schema.ophys.ophys_session.LightEmittingDiode]]#

notes: Optional[str]#

rig_id: str#

schema_version: str#

session_end_time: Optional[datetime.datetime]#

session_start_time: datetime.datetime#

session_type: str#

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

subject_id: int#

Bases: aind_data_schema.base.AindCoreModel

Description of all procedures performed on a subject

describedBy: str#

notes: Optional[str]#

schema_version: str#

specimen_procedures: Optional[List[Union[aind_data_schema.procedures.HCRSeries, aind_data_schema.procedures.SpecimenProcedure]]]#

subject_id: str#

subject_procedures: Optional[List[Union[aind_data_schema.procedures.Headframe, aind_data_schema.procedures.Craniotomy, aind_data_schema.procedures.RetroOrbitalInjection, aind_data_schema.procedures.NanojectInjection, aind_data_schema.procedures.IontophoresisInjection, aind_data_schema.procedures.IntraCerebellarVentricleInjection, aind_data_schema.procedures.IntraCisternalMagnaInjection, aind_data_schema.procedures.FiberImplant, aind_data_schema.procedures.WaterRestriction, aind_data_schema.procedures.TrainingProtocol, aind_data_schema.procedures.Perfusion, aind_data_schema.procedures.SubjectProcedure]]]#

class aind_data_schema.Processing(*, describedBy: str = 'https://raw.githubusercontent.com/AllenNeuralDynamics/aind-data-schema/main/src/aind_data_schema/processing.py', schema_version: str = '0.2.1', pipeline_version: Optional[str] = None, pipeline_url: Optional[str] = None, data_processes: types.ConstrainedListValue[aind_data_schema.processing.DataProcess])#

Bases: aind_data_schema.base.AindCoreModel

Description of all processes run on data

data_processes: List[aind_data_schema.processing.DataProcess]#

describedBy: str#

pipeline_url: Optional[str]#

pipeline_version: Optional[str]#

schema_version: str#

class aind_data_schema.RawDataDescription(experiment_type, subject_id, *, describedBy: str = 'https://raw.githubusercontent.com/AllenNeuralDynamics/aind-data-schema/main/src/aind_data_schema/data_description.py', schema_version: str = '0.6.3', license: str = 'CC-BY-4.0', creation_time: datetime.time, creation_date: datetime.date, name: Optional[str] = None, institution: aind_data_schema.data_description.Institution, funding_source: List[aind_data_schema.data_description.Funding], data_level: aind_data_schema.data_description.DataLevel = DataLevel.RAW_DATA, group: Optional[aind_data_schema.data_description.Group] = None, investigators: List[str], project_name: Optional[str] = None, project_id: Optional[str] = None, restrictions: Optional[str] = None, modality: List[aind_data_schema.data_description.Modality], related_data: Optional[List[aind_data_schema.data_description.RelatedData]] = [], data_summary: Optional[str] = None)#

Bases: aind_data_schema.data_description.DataDescription

A logical collection of data files as acquired from a rig or instrument

creation_date: datetime.date#

creation_time: datetime.time#

data_level: aind_data_schema.data_description.DataLevel#

data_summary: Optional[str]#

describedBy: str#

experiment_type: aind_data_schema.data_description.ExperimentType#

funding_source: List[aind_data_schema.data_description.Funding]#

group: Optional[aind_data_schema.data_description.Group]#