aind_data_schema.imaging package

Submodules

aind_data_schema.imaging.acquisition module

schema describing imaging acquisition

class aind_data_schema.imaging.acquisition.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

describedBy: str

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.imaging.acquisition.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.imaging.acquisition.AxisName(value)

Bases: enum.Enum

Image axis name

X = 'X'

Y = 'Y'

Z = 'Z'

class aind_data_schema.imaging.acquisition.Direction(value)

Bases: enum.Enum

Anatomical direction name

AP = 'Anterior_to_posterior'

IS = 'Inferior_to_superior'

LR = 'Left_to_right'

OTHER = 'Other'

PA = 'Posterior_to_anterior'

RL = 'Right_to_left'

SI = 'Superior_to_inferior'

class aind_data_schema.imaging.acquisition.Immersion(*, medium: str, refractive_index: float)

Bases: aind_data_schema.base.AindModel

Description of immersion media

medium: str

refractive_index: float

class aind_data_schema.imaging.acquisition.ProcessingSteps(*, channel_name: str, process_name: List[typing_extensions.Literal[Image importing, Image background subtraction, Image cell segmentation, Image destriping, Image thresholding, Image tile alignment, Image tile fusing, Image tile projection, File format conversion]])

Bases: aind_data_schema.base.AindModel

Description of downstream processing steps

channel_name: str

process_name: List[typing_extensions.Literal[Image importing, Image background subtraction, Image cell segmentation, Image destriping, Image thresholding, Image tile alignment, Image tile fusing, Image tile projection, File format conversion]]

aind_data_schema.imaging.instrument module

schema describing imaging instrument

class aind_data_schema.imaging.instrument.AdditionalImagingDevice(*, 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, type: aind_data_schema.imaging.instrument.ImagingDeviceType)

Bases: aind_data_schema.device.Device

Description of additional devices

type: aind_data_schema.imaging.instrument.ImagingDeviceType

class aind_data_schema.imaging.instrument.CameraType(value)

Bases: enum.Enum

Camera type name

CAMERA = 'Camera'

OTHER = 'other'

PMT = 'PMT'

class aind_data_schema.imaging.instrument.Com(*, hardware_name: str, com_port: str)

Bases: aind_data_schema.base.AindModel

Description of a communication system

com_port: str

hardware_name: str

class aind_data_schema.imaging.instrument.Cooling(value)

Bases: enum.Enum

Cooling medium name

AIR = 'air'

WATER = 'water'

class aind_data_schema.imaging.instrument.Detector(*, 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, type: aind_data_schema.imaging.instrument.CameraType, data_interface: aind_data_schema.device.DataInterface, cooling: aind_data_schema.imaging.instrument.Cooling)

Bases: aind_data_schema.device.Device

Description of a detector device

cooling: aind_data_schema.imaging.instrument.Cooling

data_interface: aind_data_schema.device.DataInterface

type: aind_data_schema.imaging.instrument.CameraType

class aind_data_schema.imaging.instrument.ImagingDeviceType(value)

Bases: enum.Enum

Imaginge device type name

BEAM_EXPANDER = 'Beam expander'

DIFFUSER = 'Diffuser'

GALVO = 'Galvo'

LASER_COMBINER = 'Laser combiner'

LASER_COUPLER = 'Laser coupler'

OBJECTIVE = 'Objective'

OTHER = 'Other'

PRISM = 'Prism'

ROTATION_MOUNT = 'Rotation mount'

SLIT = 'Slit'

TUNABLE_LENS = 'Tunable lens'

class aind_data_schema.imaging.instrument.ImagingInstrumentType(value)

Bases: enum.Enum

Experiment type name

CONFOCAL = 'confocal'

DISPIM = 'diSPIM'

ECEPHYS = 'ecephys'

EXASPIM = 'exaSPIM'

MESOSPIM = 'mesoSPIM'

OTHER = 'Other'

SMARTSPIM = 'SmartSPIM'

TWO_PHOTON = 'Two photon'

class aind_data_schema.imaging.instrument.Immersion(value)

Bases: enum.Enum

Immersion media name

AIR = 'air'

MULTI = 'multi'

OIL = 'oil'

OTHER = 'other'

WATER = 'water'

class aind_data_schema.imaging.instrument.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]]

describedBy: str

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.imaging.instrument.Lightsource(*, 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, type: aind_data_schema.imaging.instrument.LightsourceType, coupling: aind_data_schema.device.Coupling, wavelength: aind_data_schema.imaging.instrument.ConstrainedFloatValue, wavelength_unit: aind_data_schema.device.SizeUnit = SizeUnit.NM, max_power: float, power_unit: aind_data_schema.device.PowerUnit = PowerUnit.MW)

Bases: aind_data_schema.device.Device

Description of lightsource device

coupling: aind_data_schema.device.Coupling

max_power: float

power_unit: aind_data_schema.device.PowerUnit

type: aind_data_schema.imaging.instrument.LightsourceType

wavelength: float

wavelength_unit: aind_data_schema.device.SizeUnit

class aind_data_schema.imaging.instrument.LightsourceType(value)

Bases: enum.Enum

Light source type name

LAMP = 'lamp'

LASER = 'laser'

LED = 'LED'

OTHER = 'other'

class aind_data_schema.imaging.instrument.Objective(*, 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, numerical_aperture: float, magnification: float, immersion: aind_data_schema.imaging.instrument.Immersion)

Bases: aind_data_schema.device.Device

Description of an objective device

immersion: aind_data_schema.imaging.instrument.Immersion

magnification: float

numerical_aperture: float

class aind_data_schema.imaging.instrument.OpticalTable(*, 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, length: Optional[aind_data_schema.imaging.instrument.ConstrainedFloatValue] = None, width: Optional[aind_data_schema.imaging.instrument.ConstrainedFloatValue] = None, table_size_unit: aind_data_schema.device.SizeUnit = SizeUnit.IN, vibration_control: Optional[bool] = None)

Bases: aind_data_schema.device.Device

Description of Optical Table

length: Optional[float]

table_size_unit: aind_data_schema.device.SizeUnit

vibration_control: Optional[bool]

width: Optional[float]

class aind_data_schema.imaging.instrument.ScanningStage(*, 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, stage_axis_direction: aind_data_schema.imaging.instrument.StageAxisDirection, stage_axis_name: aind_data_schema.imaging.instrument.StageAxisName)

Bases: aind_data_schema.device.MotorizedStage

Description of a scanning motorized stages

stage_axis_direction: aind_data_schema.imaging.instrument.StageAxisDirection

stage_axis_name: aind_data_schema.imaging.instrument.StageAxisName

class aind_data_schema.imaging.instrument.StageAxisDirection(value)

Bases: enum.Enum

Direction of motion for motorized stage

DETECTION_AXIS = 'Detection axis'

ILLUMINATION_AXIS = 'Illumination axis'

PERPENDICULAR_AXIS = 'Perpendicular axis'

class aind_data_schema.imaging.instrument.StageAxisName(value)

Bases: enum.Enum

Axis names for motorized stages as configured by hardware

X = 'X'

Y = 'Y'

Z = 'Z'

aind_data_schema.imaging.mri_session module

schema for MRI Scan

class aind_data_schema.imaging.mri_session.MagneticStrength(value)

Bases: enum.Enum

Strength of magnet

MRI_14T = 14

MRI_7T = 7

class aind_data_schema.imaging.mri_session.MriScanSequence(value)

Bases: enum.Enum

MRI scan sequence

RARE = 'RARE'

class aind_data_schema.imaging.mri_session.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]

describedBy: str

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.imaging.mri_session.Scanner(*, 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, scanner_location: aind_data_schema.imaging.mri_session.ScannerLocation, magnetic_strength: aind_data_schema.imaging.mri_session.MagneticStrength, magnetic_strength_unit: str = 'T')

Bases: aind_data_schema.device.Device

Description of a MRI Scanner

magnetic_strength: aind_data_schema.imaging.mri_session.MagneticStrength

magnetic_strength_unit: str

scanner_location: aind_data_schema.imaging.mri_session.ScannerLocation

class aind_data_schema.imaging.mri_session.ScannerLocation(value)

Bases: enum.Enum

location of scanner

FRED_HUTCH = 'Fred Hutch'

UW_SLU = 'UW SLU'

aind_data_schema.imaging.tile module

Models related to imaging tiles and their transformations

class aind_data_schema.imaging.tile.AcquisitionTile(*, coordinate_transformations: List[Union[aind_data_schema.imaging.tile.Scale3dTransform, aind_data_schema.imaging.tile.Translation3dTransform, aind_data_schema.imaging.tile.Rotation3dTransform, aind_data_schema.imaging.tile.Affine3dTransform]], file_name: Optional[str] = None, channel: aind_data_schema.imaging.tile.Channel, notes: Optional[str] = None, imaging_angle: int = 0, imaging_angle_unit: aind_data_schema.device.AngleUnit = AngleUnit.DEG)

Bases: aind_data_schema.imaging.tile.Tile

Description of acquisition tile

channel: aind_data_schema.imaging.tile.Channel

imaging_angle: int

imaging_angle_unit: aind_data_schema.device.AngleUnit

notes: Optional[str]

class aind_data_schema.imaging.tile.Affine3dTransform(*, type: str = 'affine', affine_transform: types.ConstrainedListValue[float])

Bases: aind_data_schema.imaging.tile.CoordinateTransform

Values to be vector-added to a 3D position. Often needed to specify a Tile’s origin.

affine_transform: types.ConstrainedListValue[float]

type: str

class aind_data_schema.imaging.tile.Channel(*, channel_name: str, laser_wavelength: aind_data_schema.imaging.tile.ConstrainedIntValue, laser_wavelength_unit: aind_data_schema.device.SizeUnit = SizeUnit.NM, laser_power: aind_data_schema.imaging.tile.ConstrainedFloatValue, laser_power_unit: aind_data_schema.device.PowerUnit = PowerUnit.MW, filter_wheel_index: int)

Bases: aind_data_schema.base.AindModel

Description of a channel

channel_name: str

filter_wheel_index: int

laser_power: float

laser_power_unit: aind_data_schema.device.PowerUnit

laser_wavelength: int

laser_wavelength_unit: aind_data_schema.device.SizeUnit

class aind_data_schema.imaging.tile.CoordinateTransform(*, type: str)

Bases: aind_data_schema.base.AindModel

Generic base class for coordinate transform subtypes

type: str

class aind_data_schema.imaging.tile.Rotation3dTransform(*, type: str = 'rotation', rotation: types.ConstrainedListValue[float])

Bases: aind_data_schema.imaging.tile.CoordinateTransform

Values to be vector-added to a 3D position. Often needed to specify a Tile’s origin.

rotation: types.ConstrainedListValue[float]

type: str

class aind_data_schema.imaging.tile.Scale3dTransform(*, type: str = 'scale', scale: types.ConstrainedListValue[float])

Bases: aind_data_schema.imaging.tile.CoordinateTransform

Values to be vector-multiplied with a 3D position, equivalent to the diagonals of a 3x3 transform matrix. Represents voxel spacing if used as the first applied coordinate transform.

scale: types.ConstrainedListValue[float]

type: str

class aind_data_schema.imaging.tile.Tile(*, coordinate_transformations: List[Union[aind_data_schema.imaging.tile.Scale3dTransform, aind_data_schema.imaging.tile.Translation3dTransform, aind_data_schema.imaging.tile.Rotation3dTransform, aind_data_schema.imaging.tile.Affine3dTransform]], file_name: Optional[str] = None)

Bases: aind_data_schema.base.AindModel

Description of an image tile

coordinate_transformations: List[Union[aind_data_schema.imaging.tile.Scale3dTransform, aind_data_schema.imaging.tile.Translation3dTransform, aind_data_schema.imaging.tile.Rotation3dTransform, aind_data_schema.imaging.tile.Affine3dTransform]]

file_name: Optional[str]

class aind_data_schema.imaging.tile.Translation3dTransform(*, type: str = 'translation', translation: types.ConstrainedListValue[float])

Bases: aind_data_schema.imaging.tile.CoordinateTransform

Values to be vector-added to a 3D position. Often needed to specify a Tile’s origin.

translation: types.ConstrainedListValue[float]

type: str

Module contents

imports for imaging subpackage