aind_data_schema package#
Subpackages#
- aind_data_schema.core package
- Submodules
- aind_data_schema.core.acquisition module
Acquisition
Acquisition.active_objectives
Acquisition.axes
Acquisition.calibrations
Acquisition.chamber_immersion
Acquisition.describedBy
Acquisition.experimenter_full_name
Acquisition.external_storage_directory
Acquisition.instrument_id
Acquisition.local_storage_directory
Acquisition.maintenance
Acquisition.notes
Acquisition.processing_steps
Acquisition.protocol_id
Acquisition.sample_immersion
Acquisition.schema_version
Acquisition.session_end_time
Acquisition.session_start_time
Acquisition.session_type
Acquisition.specimen_id
Acquisition.subject_id
Acquisition.tiles
Acquisition.from_direction_code
Acquisition.model_post_init()
Immersion
ProcessingSteps
- aind_data_schema.core.data_description module
AnalysisDescription
DataDescription
DataDescription.creation_time
DataDescription.data_level
DataDescription.data_summary
DataDescription.describedBy
DataDescription.funding_source
DataDescription.group
DataDescription.institution
DataDescription.investigators
DataDescription.label
DataDescription.license
DataDescription.modality
DataDescription.name
DataDescription.platform
DataDescription.project_name
DataDescription.related_data
DataDescription.restrictions
DataDescription.schema_version
DataDescription.subject_id
DataDescription.build_name
DataDescription.model_post_init()
DataDescription.parse_name()
DataLevel
DataRegex
DerivedDataDescription
Funding
Group
RawDataDescription
RegexParts
RelatedData
build_data_name()
datetime_from_name_string()
datetime_to_name_string()
- aind_data_schema.core.instrument module
Com
Instrument
Instrument.additional_devices
Instrument.calibration_data
Instrument.calibration_date
Instrument.com_ports
Instrument.daqs
Instrument.describedBy
Instrument.detectors
Instrument.enclosure
Instrument.fluorescence_filters
Instrument.humidity_control
Instrument.instrument_id
Instrument.instrument_type
Instrument.lenses
Instrument.light_sources
Instrument.manufacturer
Instrument.modification_date
Instrument.motorized_stages
Instrument.notes
Instrument.objectives
Instrument.optical_tables
Instrument.scanning_stages
Instrument.schema_version
Instrument.temperature_control
Instrument.model_post_init()
Instrument.validate_device_names
Instrument.validate_other
- aind_data_schema.core.metadata module
ExternalPlatforms
Metadata
Metadata.acquisition
Metadata.created
Metadata.data_description
Metadata.describedBy
Metadata.external_links
Metadata.id
Metadata.instrument
Metadata.last_modified
Metadata.location
Metadata.metadata_status
Metadata.name
Metadata.procedures
Metadata.processing
Metadata.rig
Metadata.schema_version
Metadata.session
Metadata.subject
Metadata.model_post_init()
Metadata.validate_core_fields
Metadata.validate_ecephys_metadata
Metadata.validate_metadata
Metadata.validate_smartspim_metadata
MetadataStatus
- aind_data_schema.core.mri_session module
MRIScan
MRIScan.additional_scan_parameters
MRIScan.echo_time
MRIScan.echo_time_unit
MRIScan.effective_echo_time
MRIScan.notes
MRIScan.primary_scan
MRIScan.processing_steps
MRIScan.rare_factor
MRIScan.repetition_time
MRIScan.repetition_time_unit
MRIScan.scan_index
MRIScan.scan_sequence_type
MRIScan.scan_type
MRIScan.subject_position
MRIScan.vc_orientation
MRIScan.vc_position
MRIScan.voxel_sizes
MRIScan.validate_other
MRIScan.validate_primary_scan
MriScanSequence
MriSession
MriSession.anaesthesia
MriSession.animal_weight_post
MriSession.animal_weight_prior
MriSession.describedBy
MriSession.experimenter_full_name
MriSession.iacuc_protocol
MriSession.mri_scanner
MriSession.notes
MriSession.protocol_id
MriSession.scans
MriSession.schema_version
MriSession.session_end_time
MriSession.session_start_time
MriSession.subject_id
MriSession.weight_unit
MriSession.model_post_init()
ScanType
SubjectPosition
- aind_data_schema.core.procedures module
Anaesthetic
Antibody
BrainInjection
BrainInjection.bregma_to_lambda_distance
BrainInjection.bregma_to_lambda_unit
BrainInjection.injection_angle
BrainInjection.injection_angle_unit
BrainInjection.injection_coordinate_ap
BrainInjection.injection_coordinate_depth
BrainInjection.injection_coordinate_ml
BrainInjection.injection_coordinate_reference
BrainInjection.injection_coordinate_unit
BrainInjection.injection_hemisphere
BrainInjection.targeted_structure
CoordinateReferenceLocation
Craniotomy
Craniotomy.bregma_to_lambda_distance
Craniotomy.bregma_to_lambda_unit
Craniotomy.craniotomy_hemisphere
Craniotomy.craniotomy_type
Craniotomy.dura_removed
Craniotomy.implant_part_number
Craniotomy.procedure_type
Craniotomy.protective_material
Craniotomy.protocol_id
Craniotomy.recovery_time
Craniotomy.recovery_time_unit
CraniotomyType
FiberImplant
Fluorophore
GroundWireMaterial
HCRProbe
HCRReadout
HCRSeries
Headframe
HeadframeMaterial
HybridizationChainReaction
HybridizationChainReaction.HCR_probes
HybridizationChainReaction.end_time
HybridizationChainReaction.instrument_id
HybridizationChainReaction.other_probes
HybridizationChainReaction.other_stains
HybridizationChainReaction.probe_concentration
HybridizationChainReaction.probe_concentration_unit
HybridizationChainReaction.round_index
HybridizationChainReaction.start_time
ImmunolabelClass
Injection
IntraCerebellarVentricleInjection
IntraCisternalMagnaInjection
IntraperitonealInjection
IontophoresisInjection
NanojectInjection
NonViralMaterial
OligoProbe
OphysProbe
OphysProbe.angle
OphysProbe.angle_unit
OphysProbe.bregma_to_lambda_distance
OphysProbe.bregma_to_lambda_unit
OphysProbe.notes
OphysProbe.ophys_probe
OphysProbe.stereotactic_coordinate_ap
OphysProbe.stereotactic_coordinate_dv
OphysProbe.stereotactic_coordinate_ml
OphysProbe.stereotactic_coordinate_reference
OphysProbe.stereotactic_coordinate_unit
OphysProbe.targeted_structure
OtherSubjectProcedure
Perfusion
Procedures
ProtectiveMaterial
ProtectiveMaterialReplacement
ProtectiveMaterialReplacement.ground_wire_diameter
ProtectiveMaterialReplacement.ground_wire_diameter_unit
ProtectiveMaterialReplacement.ground_wire_hole
ProtectiveMaterialReplacement.ground_wire_material
ProtectiveMaterialReplacement.procedure_type
ProtectiveMaterialReplacement.protective_material
ProtectiveMaterialReplacement.protocol_id
ProtectiveMaterialReplacement.well_part_number
ProtectiveMaterialReplacement.well_type
Readout
RetroOrbitalInjection
SectionOrientation
SectionStrategy
Sectioning
Sectioning.number_of_slices
Sectioning.output_specimen_ids
Sectioning.procedure_type
Sectioning.reference_location
Sectioning.section_distance_from_reference
Sectioning.section_distance_unit
Sectioning.section_orientation
Sectioning.section_strategy
Sectioning.section_thickness
Sectioning.section_thickness_unit
Sectioning.targeted_structure
Sectioning.check_output_id_length
Side
SpecimenProcedure
SpecimenProcedure.antibodies
SpecimenProcedure.end_date
SpecimenProcedure.experimenter_full_name
SpecimenProcedure.hcr_series
SpecimenProcedure.notes
SpecimenProcedure.procedure_name
SpecimenProcedure.procedure_type
SpecimenProcedure.protocol_id
SpecimenProcedure.reagents
SpecimenProcedure.sectioning
SpecimenProcedure.specimen_id
SpecimenProcedure.start_date
SpecimenProcedure.validate_procedure_type
SpecimenProcedureType
SpecimenProcedureType.CLEARING
SpecimenProcedureType.DELIPIDATION
SpecimenProcedureType.EMBEDDING
SpecimenProcedureType.FIXATION
SpecimenProcedureType.FIXATION_PERMEABILIZATION
SpecimenProcedureType.GELATION
SpecimenProcedureType.HCR
SpecimenProcedureType.HYBRIDIZATION_AMPLIFICATION
SpecimenProcedureType.IMMUNOLABELING
SpecimenProcedureType.MOUNTING
SpecimenProcedureType.OTHER
SpecimenProcedureType.REFRACTIVE_INDEX_MATCHING
SpecimenProcedureType.SECTIONING
SpecimenProcedureType.SOAK
SpecimenProcedureType.STORAGE
SpecimenProcedureType.STRIPPING
Stain
StainType
Surgery
TarsVirusIdentifiers
TrainingProtocol
ViralMaterial
VirusPrepType
WaterRestriction
WaterRestriction.baseline_weight
WaterRestriction.end_date
WaterRestriction.iacuc_protocol
WaterRestriction.minimum_water_per_day
WaterRestriction.minimum_water_per_day_unit
WaterRestriction.procedure_type
WaterRestriction.start_date
WaterRestriction.target_fraction_weight
WaterRestriction.target_fraction_weight_unit
WaterRestriction.weight_unit
- aind_data_schema.core.processing module
- aind_data_schema.core.rig module
Rig
Rig.additional_devices
Rig.calibrations
Rig.cameras
Rig.ccf_coordinate_transform
Rig.daqs
Rig.describedBy
Rig.detectors
Rig.digital_micromirror_devices
Rig.enclosure
Rig.ephys_assemblies
Rig.fiber_assemblies
Rig.filters
Rig.laser_assemblies
Rig.lenses
Rig.light_sources
Rig.modalities
Rig.modification_date
Rig.mouse_platform
Rig.notes
Rig.objectives
Rig.origin
Rig.patch_cords
Rig.pockels_cells
Rig.polygonal_scanners
Rig.rig_axes
Rig.rig_id
Rig.schema_version
Rig.stick_microscopes
Rig.stimulus_devices
Rig.model_post_init()
Rig.validate_cameras_other
Rig.validate_device_names
Rig.validate_modalities
- aind_data_schema.core.session module
DetectorConfig
DomeModule
EphysModule
EphysProbeConfig
FiberConnectionConfig
FiberModule
FieldOfView
FieldOfView.coupled_fov_index
FieldOfView.fov_coordinate_ap
FieldOfView.fov_coordinate_ml
FieldOfView.fov_coordinate_unit
FieldOfView.fov_height
FieldOfView.fov_reference
FieldOfView.fov_scale_factor
FieldOfView.fov_scale_factor_unit
FieldOfView.fov_size_unit
FieldOfView.fov_width
FieldOfView.frame_rate
FieldOfView.frame_rate_unit
FieldOfView.imaging_depth
FieldOfView.imaging_depth_unit
FieldOfView.index
FieldOfView.magnification
FieldOfView.notes
FieldOfView.power
FieldOfView.power_unit
FieldOfView.scanfield_z
FieldOfView.scanfield_z_unit
FieldOfView.scanimage_roi_index
FieldOfView.targeted_structure
LaserConfig
LightEmittingDiodeConfig
ManipulatorModule
RewardDeliveryConfig
RewardSolution
RewardSpoutConfig
Session
Session.active_mouse_platform
Session.animal_weight_post
Session.animal_weight_prior
Session.calibrations
Session.data_streams
Session.describedBy
Session.experimenter_full_name
Session.iacuc_protocol
Session.maintenance
Session.mouse_platform_name
Session.notes
Session.protocol_id
Session.reward_consumed_total
Session.reward_consumed_unit
Session.reward_delivery
Session.rig_id
Session.schema_version
Session.session_end_time
Session.session_start_time
Session.session_type
Session.stimulus_epochs
Session.subject_id
Session.weight_unit
Session.model_post_init()
SlapFieldOfView
SlapSessionType
SpeakerConfig
Stack
Stack.channels
Stack.fov_coordinate_ap
Stack.fov_coordinate_ml
Stack.fov_coordinate_unit
Stack.fov_height
Stack.fov_reference
Stack.fov_scale_factor
Stack.fov_scale_factor_unit
Stack.fov_size_unit
Stack.fov_width
Stack.frame_rate
Stack.frame_rate_unit
Stack.magnification
Stack.number_of_plane_repeats_per_volume
Stack.number_of_planes
Stack.number_of_volume_repeats
Stack.step_size
Stack.step_size_unit
Stack.targeted_structure
StackChannel
StimulusEpoch
StimulusEpoch.light_source_config
StimulusEpoch.notes
StimulusEpoch.output_parameters
StimulusEpoch.reward_consumed_during_epoch
StimulusEpoch.reward_consumed_unit
StimulusEpoch.script
StimulusEpoch.session_number
StimulusEpoch.software
StimulusEpoch.speaker_config
StimulusEpoch.stimulus_device_names
StimulusEpoch.stimulus_end_time
StimulusEpoch.stimulus_modalities
StimulusEpoch.stimulus_name
StimulusEpoch.stimulus_parameters
StimulusEpoch.stimulus_start_time
StimulusEpoch.trials_finished
StimulusEpoch.trials_rewarded
StimulusEpoch.trials_total
StimulusModality
Stream
Stream.camera_names
Stream.daq_names
Stream.detectors
Stream.ephys_modules
Stream.fiber_connections
Stream.fiber_modules
Stream.light_sources
Stream.manipulator_modules
Stream.notes
Stream.ophys_fovs
Stream.slap_fovs
Stream.stack_parameters
Stream.stick_microscopes
Stream.stream_end_time
Stream.stream_modalities
Stream.stream_start_time
Stream.validate_stream_modalities
TriggerType
- aind_data_schema.core.subject module
BackgroundStrain
BreedingInfo
HomeCageEnrichment
Housing
LightCycle
Sex
Subject
Subject.alleles
Subject.background_strain
Subject.breeding_info
Subject.date_of_birth
Subject.describedBy
Subject.genotype
Subject.housing
Subject.notes
Subject.restrictions
Subject.rrid
Subject.schema_version
Subject.sex
Subject.source
Subject.species
Subject.subject_id
Subject.wellness_reports
Subject.model_post_init()
Subject.validate_genotype
Subject.validate_inhouse_breeding_info
WellnessReport
- Module contents
- aind_data_schema.imaging package
- Submodules
- aind_data_schema.imaging.tile module
AcquisitionTile
Channel
Channel.additional_device_names
Channel.channel_name
Channel.description
Channel.detector_name
Channel.dilation
Channel.dilation_unit
Channel.excitation_power
Channel.excitation_power_unit
Channel.excitation_wavelength
Channel.excitation_wavelength_unit
Channel.filter_names
Channel.filter_wheel_index
Channel.light_source_name
Tile
- Module contents
- aind_data_schema.models package
- Submodules
- aind_data_schema.models.coordinates module
- aind_data_schema.models.devices module
AdditionalImagingDevice
BinMode
Calibration
Camera
Camera.bin_height
Camera.bin_mode
Camera.bin_unit
Camera.bin_width
Camera.bit_depth
Camera.chroma
Camera.computer_name
Camera.cooling
Camera.crop_height
Camera.crop_unit
Camera.crop_width
Camera.data_interface
Camera.detector_type
Camera.device_type
Camera.driver
Camera.driver_version
Camera.frame_rate_unit
Camera.gain
Camera.immersion
Camera.manufacturer
Camera.max_frame_rate
Camera.recording_software
Camera.sensor_format
Camera.sensor_format_unit
Camera.sensor_height
Camera.sensor_width
Camera.size_unit
CameraAssembly
CameraChroma
CameraTarget
ChannelType
Cooling
Coupling
DAQChannel
DAQDevice
DaqChannelType
DataInterface
Detector
Detector.bin_height
Detector.bin_mode
Detector.bin_unit
Detector.bin_width
Detector.bit_depth
Detector.chroma
Detector.computer_name
Detector.cooling
Detector.crop_height
Detector.crop_unit
Detector.crop_width
Detector.data_interface
Detector.detector_type
Detector.device_type
Detector.driver
Detector.driver_version
Detector.frame_rate_unit
Detector.gain
Detector.immersion
Detector.manufacturer
Detector.max_frame_rate
Detector.recording_software
Detector.sensor_format
Detector.sensor_format_unit
Detector.sensor_height
Detector.sensor_width
Detector.size_unit
Detector.validate_other
DetectorType
Device
DeviceDriver
DigitalMicromirrorDevice
DigitalMicromirrorDevice.device_type
DigitalMicromirrorDevice.dmd_curtain
DigitalMicromirrorDevice.dmd_curtain_unit
DigitalMicromirrorDevice.dmd_flip
DigitalMicromirrorDevice.double_bounce_design
DigitalMicromirrorDevice.invert_pixel_values
DigitalMicromirrorDevice.line_shear
DigitalMicromirrorDevice.line_shear_units
DigitalMicromirrorDevice.max_dmd_patterns
DigitalMicromirrorDevice.motion_padding_x
DigitalMicromirrorDevice.motion_padding_y
DigitalMicromirrorDevice.padding_unit
DigitalMicromirrorDevice.pixel_size
DigitalMicromirrorDevice.pixel_size_unit
DigitalMicromirrorDevice.start_phase
Disc
Enclosure
EphysAssembly
EphysProbe
FerruleMaterial
FiberAssembly
FiberProbe
Filter
Filter.center_wavelength
Filter.cut_off_wavelength
Filter.cut_on_wavelength
Filter.description
Filter.device_type
Filter.diameter
Filter.filter_type
Filter.filter_wheel_index
Filter.height
Filter.manufacturer
Filter.size_unit
Filter.thickness
Filter.thickness_unit
Filter.wavelength_unit
Filter.width
FilterSize
FilterType
HarpDevice
Headstage
ImagingDeviceType
ImagingDeviceType.BEAM_EXPANDER
ImagingDeviceType.DIFFUSER
ImagingDeviceType.GALVO
ImagingDeviceType.LASER_COMBINER
ImagingDeviceType.LASER_COUPLER
ImagingDeviceType.OBJECTIVE
ImagingDeviceType.OTHER
ImagingDeviceType.PRISM
ImagingDeviceType.ROTATION_MOUNT
ImagingDeviceType.SAMPLE_CHAMBER
ImagingDeviceType.SLIT
ImagingDeviceType.TUNABLE_LENS
ImagingInstrumentType
ImmersionMedium
Lamp
Laser
LaserAssembly
Lens
LensSize
LickSensorType
LightEmittingDiode
MagneticStrength
Maintenance
Manipulator
Monitor
MotorizedStage
MousePlatform
NeuropixelsBasestation
Objective
ObjectiveType
Olfactometer
OlfactometerChannel
OpenEphysAcquisitionBoard
OpticalTable
Patch
PockelsCell
PolygonalScanner
ProbeModel
ProbePort
RewardDelivery
RewardSpout
Scanner
ScannerLocation
ScanningStage
Software
Speaker
SpoutSide
StageAxisDirection
StageAxisName
Treadmill
Tube
Wheel
- aind_data_schema.models.harp_types module
Behavior
CameraController
ClockSynchronizer
Cuttlefish
GenericHarpDevice
HarpDeviceType
HarpDeviceType.BEHAVIOR
HarpDeviceType.CAMERA_CONTROLLER
HarpDeviceType.CLOCK_SYNCHRONIZER
HarpDeviceType.CUTTLEFISH
HarpDeviceType.GENERIC_HARP_DEVICE
HarpDeviceType.INPUT_EXPANDER
HarpDeviceType.LICKETY_SPLIT
HarpDeviceType.LOAD_CELLS
HarpDeviceType.OLFACTOMETER
HarpDeviceType.ONE_OF
HarpDeviceType.SNIFF_DETECTOR
HarpDeviceType.SOUND_CARD
HarpDeviceType.STEPPER_DRIVER
HarpDeviceType.SYNCHRONIZER
HarpDeviceType.TIMESTAMP_GENERATOR_1
HarpDeviceType.TIMESTAMP_GENERATOR_3
HarpDeviceType.TREADMILL
InputExpander
LicketySplit
LoadCells
Olfactometer
SniffDetector
SoundCard
StepperDriver
Synchronizer
TimestampGeneratorGen1
TimestampGeneratorGen3
Treadmill
- aind_data_schema.models.modalities module
- aind_data_schema.models.organizations module
AAOptoElectronic
Abcam
AilipuTechnologyCo
AllenInstitute
AllenInstituteForBrainScience
AllenInstituteForNeuralDynamics
Allied
AmsOsram
AppliedScientificInstrumentation
ArecontVisionCostar
Asus
Basler
CambridgeTechnology
CarlZeiss
ChampalimaudFoundation
Chroma
CoherentScientific
ColumbiaUniversity
Computar
Conoptics
Custom
Dodotronic
Doric
Ealing
EdmundOptics
Euresys
Fujinon
Hamamatsu
Hamilton
HuazhongUniversityOfScienceAndTechnology
IRRobotCo
ISLProductsInternational
InfinityPhotoOptical
InteruniversityMicroelectronicsCenter
JacksonLaboratory
Julabo
Leica
Lg
LifeCanvas
MKSNewport
MeadowlarkOptics
Mitutuyo
Mpi
NResearch
NationalInstituteOfNeurologicalDisordersAndStroke
NationalInstruments
Navitar
Neurophotometrics
NewScaleTechnologies
NewYorkUniversity
Nikon
Olympus
OpenEphysProductionSite
Optotune
Organization
Organization.AA_OPTO
Organization.ABCAM
Organization.AI
Organization.AIBS
Organization.AILIPU
Organization.AIND
Organization.ALLIED
Organization.ASI
Organization.ASUS
Organization.AVCOSTAR
Organization.BASLER
Organization.CAMBRIDGE_TECHNOLOGY
Organization.CHAMPALIMAUD
Organization.CHROMA
Organization.COHERENT_SCIENTIFIC
Organization.COLUMBIA
Organization.COMPUTAR
Organization.CONOPTICS
Organization.CUSTOM
Organization.DAQ_DEVICE_MANUFACTURERS
Organization.DETECTOR_MANUFACTURERS
Organization.DODOTRONIC
Organization.DORIC
Organization.EALING
Organization.EDMUND_OPTICS
Organization.EURESYS
Organization.FILTER_MANUFACTURERS
Organization.FLIR
Organization.FUJINON
Organization.FUNDERS
Organization.HAMAMATSU
Organization.HAMILTON
Organization.HUST
Organization.IMAGING_SOURCE
Organization.IMEC
Organization.INFINITY_PHOTO_OPTICAL
Organization.ISL
Organization.JAX
Organization.JULABO
Organization.LASER_MANUFACTURERS
Organization.LED_MANUFACTURERS
Organization.LEE
Organization.LEICA
Organization.LENS_MANUFACTURERS
Organization.LG
Organization.LIFECANVAS
Organization.MANIPULATOR_MANUFACTURERS
Organization.MEADOWLARK
Organization.MIGHTY_ZAP
Organization.MITUTUYO
Organization.MKS_NEWPORT
Organization.MONITOR_MANUFACTURERS
Organization.MPI
Organization.NATIONAL_INSTRUMENTS
Organization.NAVITAR
Organization.NEUROPHOTOMETRICS
Organization.NEW_SCALE_TECHNOLOGIES
Organization.NIKON
Organization.NINDS
Organization.NRESEARCH
Organization.NYU
Organization.OEPS
Organization.OLYMPUS
Organization.ONE_OF
Organization.OPTOTUNE
Organization.OSRAM
Organization.OTHER
Organization.OXXIUS
Organization.PRIZMATIX
Organization.QUANTIFI
Organization.RASPBERRYPI
Organization.RESEARCH_INSTITUTIONS
Organization.SCHNEIDER_KREUZNACH
Organization.SEMROCK
Organization.SIGMA
Organization.SIMONS
Organization.SPEAKER_MANUFACTURERS
Organization.SPINNAKER
Organization.SUBJECT_SOURCES
Organization.TAMRON
Organization.THERMOFISHER
Organization.THORLABS
Organization.TMC
Organization.TYMPHANY
Organization.VIEWORKS
Organization.VORTRAN
Organization.ZEISS
Organization.from_abbreviation()
Organization.from_name()
Organization.name_map
Other
Oxxius
Prizmatix
Quantifi
RaspberryPi
SchneiderKreuznach
SecondOrderEffects
Semrock
SigmaAldritch
SimonsFoundation
Spinnaker
TMC
Tamron
TeledyneFLIR
TheImagingSource
TheLeeCompany
Thermofisher
Thorlabs
Tymphany
Vieworks
Vortran
- aind_data_schema.models.pid_names module
- aind_data_schema.models.platforms module
Behavior
Confocal
Ecephys
ExaSpim
Fip
Hcr
Hsfp
Isi
Merfish
MesoSpim
Mri
MultiplaneOphys
Platform
Platform.BEHAVIOR
Platform.CONFOCAL
Platform.ECEPHYS
Platform.EXASPIM
Platform.FIP
Platform.HCR
Platform.HSFP
Platform.ISI
Platform.MERFISH
Platform.MESOSPIM
Platform.MRI
Platform.MULTIPLANE_OPHYS
Platform.ONE_OF
Platform.SINGLE_PLANE_OPHYS
Platform.SLAP2
Platform.SMARTSPIM
Platform.from_abbreviation()
SingleplaneOphys
Slap2
SmartSpim
- aind_data_schema.models.process_names module
ProcessName
ProcessName.ANALYSIS
ProcessName.COMPRESSION
ProcessName.DENOISING
ProcessName.DFF_ESTIMATION
ProcessName.EPHYS_CURATION
ProcessName.EPHYS_POSTPROCESSING
ProcessName.EPHYS_PREPROCESSING
ProcessName.EPHYS_VISUALIZATION
ProcessName.FIDUCIAL_SEGMENTATION
ProcessName.FILE_CONVERSION
ProcessName.FLUORESCENCE_EVENT_DETECTION
ProcessName.IMAGE_ATLAS_ALIGNMENT
ProcessName.IMAGE_BACKGROUND_SUBTRACTION
ProcessName.IMAGE_CELL_QUANTIFICATION
ProcessName.IMAGE_CELL_SEGMENTATION
ProcessName.IMAGE_DESTRIPING
ProcessName.IMAGE_FLATFIELD_CORRECTION
ProcessName.IMAGE_IMPORTING
ProcessName.IMAGE_THRESHOLDING
ProcessName.IMAGE_TILE_ALIGNMENT
ProcessName.IMAGE_TILE_FUSING
ProcessName.IMAGE_TILE_PROJECTION
ProcessName.MANUAL_ANNOTATION
ProcessName.NEUROPIL_SUBTRACTION
ProcessName.OTHER
ProcessName.QUALITY_CONTROL_AND_ASSESSMENT
ProcessName.SKULL_STRIPPING
ProcessName.SPATIAL_TIMESERIES_DEMIXING
ProcessName.SPIKE_SORTING
ProcessName.VIDEO_MOTION_CORRECTION
ProcessName.VIDEO_PLANE_DECROSSTALK
ProcessName.VIDEO_ROI_CLASSIFICATION
ProcessName.VIDEO_ROI_SEGMENTATION
ProcessName.VIDEO_ROI_TIMESERIES_EXTRACTION
- aind_data_schema.models.reagent module
- aind_data_schema.models.registry module
- aind_data_schema.models.species module
- aind_data_schema.models.stimulus module
AuditoryStimulation
AuditoryStimulation.amplitude_modulation_frequency
AuditoryStimulation.bandpass_filter_type
AuditoryStimulation.bandpass_high_frequency
AuditoryStimulation.bandpass_low_frequency
AuditoryStimulation.bandpass_order
AuditoryStimulation.frequency_unit
AuditoryStimulation.notes
AuditoryStimulation.sample_frequency
AuditoryStimulation.sitmulus_name
AuditoryStimulation.stimulus_type
FilterType
OlfactometerChannelConfig
OlfactoryStimulation
OptoStimulation
OptoStimulation.baseline_duration
OptoStimulation.baseline_duration_unit
OptoStimulation.fixed_pulse_train_interval
OptoStimulation.notes
OptoStimulation.number_pulse_trains
OptoStimulation.other_parameters
OptoStimulation.pulse_frequency
OptoStimulation.pulse_frequency_unit
OptoStimulation.pulse_shape
OptoStimulation.pulse_train_duration
OptoStimulation.pulse_train_duration_unit
OptoStimulation.pulse_train_interval
OptoStimulation.pulse_train_interval_unit
OptoStimulation.pulse_width
OptoStimulation.pulse_width_unit
OptoStimulation.stimulus_name
OptoStimulation.stimulus_type
PhotoStimulation
PhotoStimulationGroup
PhotoStimulationGroup.group_index
PhotoStimulationGroup.inter_spiral_interval
PhotoStimulationGroup.inter_spiral_interval_unit
PhotoStimulationGroup.notes
PhotoStimulationGroup.number_of_neurons
PhotoStimulationGroup.number_spirals
PhotoStimulationGroup.number_trials
PhotoStimulationGroup.other_parameters
PhotoStimulationGroup.spiral_duration
PhotoStimulationGroup.spiral_duration_unit
PhotoStimulationGroup.stimulation_laser_power
PhotoStimulationGroup.stimulation_laser_power_unit
PulseShape
VisualStimulation
- aind_data_schema.models.units module
- Module contents
- aind_data_schema.utils package
Submodules#
aind_data_schema.base module#
generic base class with supporting validators and fields for basic AIND schema
- pydantic model aind_data_schema.base.AindCoreModel#
Bases:
AindModel
Generic base class to hold common fields/validators/etc for all basic AIND schema
Show JSON schema
{ "title": "AindCoreModel", "description": "Generic base class to hold common fields/validators/etc for all basic AIND schema", "type": "object", "properties": { "describedBy": { "title": "Describedby", "type": "string" }, "schema_version": { "description": "schema version", "pattern": "^\\d+.\\d+.\\d+$", "title": "Version", "type": "string" } }, "additionalProperties": false, "required": [ "describedBy", "schema_version" ] }
- Config:
extra: str = forbid
use_enum_values: bool = True
- Fields:
- field describedBy: str [Required]#
- field schema_version: str [Required]#
schema version
- Constraints:
pattern = ^d+.d+.d+$
- classmethod default_filename()#
Returns standard filename in snakecase
- model_post_init(__context: Any) None #
This function is meant to behave like a BaseModel method to initialise private attributes.
It takes context as an argument since that’s what pydantic-core passes when calling it.
- Parameters:
self – The BaseModel instance.
__context – The context.
- write_standard_file(output_directory: Path | None = None, prefix: str | None = None, suffix: str | None = None)#
Writes schema to standard json file :param output_directory: optional Path object for output directory.
Default: None
- Parameters:
prefix (Optional[str]) – optional str for intended filepath with extra naming convention Default: None
suffix (Optional[str]) – optional str for intended filepath with extra naming convention Default: None
- pydantic model aind_data_schema.base.AindGeneric#
Bases:
BaseModel
Base class for generic types that can be used in AIND schema
Show JSON schema
{ "title": "AindGeneric", "description": "Base class for generic types that can be used in AIND schema", "type": "object", "properties": {}, "additionalProperties": true }
- Config:
extra: str = allow
- pydantic model aind_data_schema.base.AindModel#
Bases:
BaseModel
,Generic
[AindGenericType
]BaseModel that disallows extra fields
Show JSON schema
{ "title": "AindModel", "description": "BaseModel that disallows extra fields", "type": "object", "properties": {}, "additionalProperties": false }
- Config:
extra: str = forbid
use_enum_values: bool = True
Module contents#
imports for AindModel subclasses