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.software
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()
DerivedDataDescription
Funding
RawDataDescription
RelatedData
- 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
- 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_ratio
FieldOfView.power_unit
FieldOfView.scanfield_z
FieldOfView.scanfield_z_unit
FieldOfView.scanimage_roi_index
FieldOfView.targeted_structure
LaserConfig
LightEmittingDiodeConfig
MRIScan
MRIScan.additional_scan_parameters
MRIScan.echo_time
MRIScan.echo_time_unit
MRIScan.effective_echo_time
MRIScan.mri_scanner
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
ManipulatorModule
MriScanSequence
RewardDeliveryConfig
RewardSolution
RewardSpoutConfig
ScanType
Session
Session.active_mouse_platform
Session.anaesthesia
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.mri_scans
Stream.notes
Stream.ophys_fovs
Stream.slap_fovs
Stream.software
Stream.stack_parameters
Stream.stick_microscopes
Stream.stream_end_time
Stream.stream_modalities
Stream.stream_start_time
Stream.validate_stream_modalities
SubjectPosition
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
- aind_data_schema.models package
- Submodules
- aind_data_schema.models.coordinates module
- aind_data_schema.models.devices module
- aind_data_schema.models.harp_types module
- aind_data_schema.models.modalities module
- aind_data_schema.models.organizations module
- aind_data_schema.models.pid_names module
- aind_data_schema.models.platforms module
- aind_data_schema.models.process_names module
- aind_data_schema.models.reagent module
- aind_data_schema.models.registry module
- aind_data_schema.models.species module
- aind_data_schema.models.stimulus module
- 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