aind_data_schema.core package¶
Submodules¶
aind_data_schema.core.acquisition module¶
schema describing imaging acquisition
- pydantic model aind_data_schema.core.acquisition.Acquisition¶
Bases:
AindCoreModelDescription of an imaging acquisition session
Show JSON schema
{ "title": "Acquisition", "description": "Description of an imaging acquisition session", "type": "object", "properties": { "describedBy": { "const": "https://raw.githubusercontent.com/AllenNeuralDynamics/aind-data-schema/main/src/aind_data_schema/core/acquisition.py", "default": "https://raw.githubusercontent.com/AllenNeuralDynamics/aind-data-schema/main/src/aind_data_schema/core/acquisition.py", "title": "Describedby", "type": "string" }, "schema_version": { "const": "1.0.4", "default": "1.0.4", "title": "Schema Version", "type": "string" }, "protocol_id": { "default": [], "description": "DOI for protocols.io", "items": { "type": "string" }, "title": "Protocol ID", "type": "array" }, "experimenter_full_name": { "description": "First and last name of the experimenter(s).", "items": { "type": "string" }, "title": "Experimenter(s) full name", "type": "array" }, "specimen_id": { "title": "Specimen ID", "type": "string" }, "subject_id": { "anyOf": [ { "type": "string" }, { "type": "null" } ], "default": null, "title": "Subject ID" }, "instrument_id": { "title": "Instrument ID", "type": "string" }, "calibrations": { "default": [], "description": "List of calibration measurements taken prior to acquisition.", "items": { "$ref": "#/$defs/Calibration" }, "title": "Calibrations", "type": "array" }, "maintenance": { "default": [], "description": "List of maintenance on rig prior to acquisition.", "items": { "$ref": "#/$defs/Maintenance" }, "title": "Maintenance", "type": "array" }, "session_start_time": { "format": "date-time", "title": "Session start time", "type": "string" }, "session_end_time": { "format": "date-time", "title": "Session end time", "type": "string" }, "session_type": { "anyOf": [ { "type": "string" }, { "type": "null" } ], "default": null, "title": "Session type" }, "tiles": { "items": { "$ref": "#/$defs/AcquisitionTile" }, "title": "Acquisition tiles", "type": "array" }, "axes": { "items": { "$ref": "#/$defs/ImageAxis" }, "title": "Acquisition axes", "type": "array" }, "chamber_immersion": { "$ref": "#/$defs/Immersion", "title": "Acquisition chamber immersion data" }, "sample_immersion": { "anyOf": [ { "$ref": "#/$defs/Immersion" }, { "type": "null" } ], "default": null, "title": "Acquisition sample immersion data" }, "active_objectives": { "anyOf": [ { "items": { "type": "string" }, "type": "array" }, { "type": "null" } ], "default": null, "title": "List of objectives used in this acquisition." }, "local_storage_directory": { "anyOf": [ { "type": "string" }, { "type": "null" } ], "default": null, "title": "Local storage directory" }, "external_storage_directory": { "anyOf": [ { "type": "string" }, { "type": "null" } ], "default": null, "title": "External storage directory" }, "processing_steps": { "default": [], "description": "List of downstream processing steps planned for each channel", "items": { "$ref": "#/$defs/ProcessingSteps" }, "title": "Processing steps", "type": "array" }, "software": { "anyOf": [ { "items": { "$ref": "#/$defs/Software" }, "type": "array" }, { "type": "null" } ], "default": [], "title": "Acquisition software version data" }, "notes": { "anyOf": [ { "type": "string" }, { "type": "null" } ], "default": null, "title": "Notes" } }, "$defs": { "AcquisitionTile": { "additionalProperties": false, "description": "Description of acquisition tile", "properties": { "coordinate_transformations": { "items": { "discriminator": { "mapping": { "affine": "#/$defs/Affine3dTransform", "rotation": "#/$defs/Rotation3dTransform", "scale": "#/$defs/Scale3dTransform", "translation": "#/$defs/Translation3dTransform" }, "propertyName": "type" }, "oneOf": [ { "$ref": "#/$defs/Scale3dTransform" }, { "$ref": "#/$defs/Translation3dTransform" }, { "$ref": "#/$defs/Rotation3dTransform" }, { "$ref": "#/$defs/Affine3dTransform" } ] }, "title": "Tile coordinate transformations", "type": "array" }, "file_name": { "anyOf": [ { "type": "string" }, { "type": "null" } ], "default": null, "title": "File name" }, "channel": { "$ref": "#/$defs/Channel" }, "notes": { "anyOf": [ { "type": "string" }, { "type": "null" } ], "default": null, "title": "Notes" }, "imaging_angle": { "default": 0, "title": "Imaging angle", "type": "integer" }, "imaging_angle_unit": { "$ref": "#/$defs/AngleUnit", "default": "degrees", "title": "Imaging angle unit" }, "acquisition_start_time": { "anyOf": [ { "format": "date-time", "type": "string" }, { "type": "null" } ], "default": null, "title": "Acquisition start time" }, "acquisition_end_time": { "anyOf": [ { "format": "date-time", "type": "string" }, { "type": "null" } ], "default": null, "title": "Acquisition end time" } }, "required": [ "coordinate_transformations", "channel" ], "title": "AcquisitionTile", "type": "object" }, "Affine3dTransform": { "additionalProperties": false, "description": "Values to be vector-added to a 3D position. Often needed to specify a Tile's origin.", "properties": { "type": { "const": "affine", "default": "affine", "title": "Type", "type": "string" }, "affine_transform": { "items": { "anyOf": [ { "type": "number" }, { "type": "string" } ] }, "maxItems": 12, "minItems": 12, "title": "Affine transform matrix values (top 3x4 matrix)", "type": "array" } }, "required": [ "affine_transform" ], "title": "Affine3dTransform", "type": "object" }, "AindGeneric": { "additionalProperties": true, "description": "Base class for generic types that can be used in AIND schema", "properties": {}, "title": "AindGeneric", "type": "object" }, "AnatomicalDirection": { "description": "Anatomical direction name", "enum": [ "Left_to_right", "Right_to_left", "Anterior_to_posterior", "Posterior_to_anterior", "Inferior_to_superior", "Superior_to_inferior", "Other" ], "title": "AnatomicalDirection", "type": "string" }, "AngleUnit": { "description": "Enumeration of Angle Measurements", "enum": [ "radians", "degrees" ], "title": "AngleUnit", "type": "string" }, "AxisName": { "description": "Image axis name", "enum": [ "X", "Y", "Z" ], "title": "AxisName", "type": "string" }, "BaseName": { "additionalProperties": false, "description": "A simple model associating a name with an abbreviation", "properties": { "name": { "title": "Name", "type": "string" }, "abbreviation": { "anyOf": [ { "type": "string" }, { "type": "null" } ], "default": null, "title": "Abbreviation" } }, "required": [ "name" ], "title": "BaseName", "type": "object" }, "Calibration": { "additionalProperties": false, "description": "Generic calibration class", "properties": { "calibration_date": { "format": "date-time", "title": "Date and time of calibration", "type": "string" }, "device_name": { "description": "Must match a device name in rig/instrument", "title": "Device name", "type": "string" }, "description": { "description": "Brief description of what is being calibrated", "title": "Description", "type": "string" }, "input": { "$ref": "#/$defs/AindGeneric", "default": {}, "description": "Calibration input", "title": "inputs" }, "output": { "$ref": "#/$defs/AindGeneric", "default": {}, "description": "Calibration output", "title": "outputs" }, "notes": { "anyOf": [ { "type": "string" }, { "type": "null" } ], "default": null, "title": "Notes" } }, "required": [ "calibration_date", "device_name", "description" ], "title": "Calibration", "type": "object" }, "Channel": { "additionalProperties": false, "description": "Description of a channel", "properties": { "channel_name": { "title": "Channel", "type": "string" }, "light_source_name": { "description": "Must match device name", "title": "Light source name", "type": "string" }, "filter_names": { "description": "Must match device names", "items": { "type": "string" }, "title": "Filter names", "type": "array" }, "detector_name": { "description": "Must match device name", "title": "Detector name", "type": "string" }, "additional_device_names": { "default": [], "items": { "type": "string" }, "title": "Additional device names", "type": "array" }, "excitation_wavelength": { "maximum": 1000, "minimum": 300, "title": "Wavelength", "type": "integer" }, "excitation_wavelength_unit": { "$ref": "#/$defs/SizeUnit", "default": "nanometer", "title": "Laser wavelength unit" }, "excitation_power": { "maximum": 2000.0, "title": "Laser power", "type": "number" }, "excitation_power_unit": { "$ref": "#/$defs/PowerUnit", "default": "milliwatt", "title": "Laser power unit" }, "filter_wheel_index": { "title": "Filter wheel index", "type": "integer" }, "dilation": { "anyOf": [ { "type": "integer" }, { "type": "null" } ], "default": null, "title": "Dilation (pixels)" }, "dilation_unit": { "$ref": "#/$defs/SizeUnit", "default": "pixel", "title": "Dilation unit" }, "description": { "anyOf": [ { "type": "string" }, { "type": "null" } ], "default": null, "title": "Description" } }, "required": [ "channel_name", "light_source_name", "filter_names", "detector_name", "excitation_wavelength", "excitation_power", "filter_wheel_index" ], "title": "Channel", "type": "object" }, "ImageAxis": { "additionalProperties": false, "description": "Description of an image axis", "properties": { "name": { "$ref": "#/$defs/AxisName", "title": "Name" }, "direction": { "$ref": "#/$defs/AnatomicalDirection", "description": "Tissue direction as the value of axis increases. If Other describe in notes." }, "dimension": { "description": "Reference axis number for stitching", "title": "Dimension", "type": "integer" }, "unit": { "$ref": "#/$defs/SizeUnit", "default": "micrometer", "title": "Axis physical units" } }, "required": [ "name", "direction", "dimension" ], "title": "ImageAxis", "type": "object" }, "Immersion": { "additionalProperties": false, "description": "Description of immersion medium", "properties": { "medium": { "$ref": "#/$defs/ImmersionMedium", "title": "Immersion medium" }, "refractive_index": { "anyOf": [ { "type": "number" }, { "type": "string" } ], "title": "Index of refraction" } }, "required": [ "medium", "refractive_index" ], "title": "Immersion", "type": "object" }, "ImmersionMedium": { "description": "Immersion medium name", "enum": [ "air", "multi", "oil", "PBS", "water", "other", "easy index", "ethyl cinnimate", "aqueous clearing buffer" ], "title": "ImmersionMedium", "type": "string" }, "Maintenance": { "additionalProperties": false, "description": "Generic maintenance class", "properties": { "maintenance_date": { "format": "date-time", "title": "Date and time of maintenance", "type": "string" }, "device_name": { "description": "Must match a device name in rig/instrument", "title": "Device name", "type": "string" }, "description": { "description": "Description on maintenance procedure", "title": "Description", "type": "string" }, "protocol_id": { "anyOf": [ { "type": "string" }, { "type": "null" } ], "default": null, "title": "Protocol ID" }, "reagents": { "default": [], "items": { "$ref": "#/$defs/Reagent" }, "title": "Reagents", "type": "array" }, "notes": { "anyOf": [ { "type": "string" }, { "type": "null" } ], "default": null, "title": "Notes" } }, "required": [ "maintenance_date", "device_name", "description" ], "title": "Maintenance", "type": "object" }, "PIDName": { "additionalProperties": false, "description": "Model for associate a name with a persistent identifier (PID),\nthe registry for that PID, and abbreviation for that registry", "properties": { "name": { "title": "Name", "type": "string" }, "abbreviation": { "anyOf": [ { "type": "string" }, { "type": "null" } ], "default": null, "title": "Abbreviation" }, "registry": { "anyOf": [ { "$ref": "#/$defs/BaseName" }, { "type": "null" } ], "default": null, "title": "Registry" }, "registry_identifier": { "anyOf": [ { "type": "string" }, { "type": "null" } ], "default": null, "title": "Registry identifier" } }, "required": [ "name" ], "title": "PIDName", "type": "object" }, "PowerUnit": { "description": "Unit for power, set or measured", "enum": [ "microwatt", "milliwatt", "percent" ], "title": "PowerUnit", "type": "string" }, "ProcessingSteps": { "additionalProperties": false, "description": "Description of downstream processing steps", "properties": { "channel_name": { "title": "Channel name", "type": "string" }, "process_name": { "items": { "enum": [ "Image atlas alignment", "Image background subtraction", "Image cell segmentation", "Image destriping", "Image flat-field correction", "Image importing", "Image thresholding", "Image tile alignment", "Image tile fusing", "Image tile projection", "File format conversion" ], "type": "string" }, "title": "Process Name", "type": "array" } }, "required": [ "channel_name", "process_name" ], "title": "ProcessingSteps", "type": "object" }, "Reagent": { "additionalProperties": false, "description": "Description of reagent used in procedure", "properties": { "name": { "title": "Name", "type": "string" }, "source": { "discriminator": { "mapping": { "AA Opto Electronic": "#/$defs/_Aa_Opto_Electronic", "ASUS": "#/$defs/_Asus", "Abcam": "#/$defs/_Abcam", "Addgene": "#/$defs/aind_data_schema_models__organizations___Addgene", "Ailipu Technology Co": "#/$defs/_Ailipu_Technology_Co", "Allen Institute": "#/$defs/_Allen_Institute", "Allen Institute for Brain Science": "#/$defs/_Allen_Institute_For_Brain_Science", "Allen Institute for Neural Dynamics": "#/$defs/_Allen_Institute_For_Neural_Dynamics", "Allied": "#/$defs/_Allied", "Applied Scientific Instrumentation": "#/$defs/_Applied_Scientific_Instrumentation", "Arecont Vision Costar": "#/$defs/_Arecont_Vision_Costar", "Basler": "#/$defs/_Basler", "Cambridge Technology": "#/$defs/_Cambridge_Technology", "Carl Zeiss": "#/$defs/_Carl_Zeiss", "Champalimaud Foundation": "#/$defs/_Champalimaud_Foundation", "Chan Zuckerberg Initiative": "#/$defs/_Chan_Zuckerberg_Initiative", "Charles River Laboratories": "#/$defs/_Charles_River_Laboratories", "Chroma": "#/$defs/_Chroma", "Coherent Scientific": "#/$defs/_Coherent_Scientific", "Columbia University": "#/$defs/_Columbia_University", "Computar": "#/$defs/_Computar", "Conoptics": "#/$defs/_Conoptics", "Custom": "#/$defs/_Custom", "DigiKey": "#/$defs/_Digikey", "Dodotronic": "#/$defs/_Dodotronic", "Doric": "#/$defs/_Doric", "Ealing": "#/$defs/_Ealing", "Edmund Optics": "#/$defs/_Edmund_Optics", "Emory University": "#/$defs/_Emory_University", "Euresys": "#/$defs/_Euresys", "Fujinon": "#/$defs/_Fujinon", "Hamamatsu": "#/$defs/_Hamamatsu", "Hamilton": "#/$defs/_Hamilton", "Huazhong University of Science and Technology": "#/$defs/_Huazhong_University_Of_Science_And_Technology", "IR Robot Co": "#/$defs/_Ir_Robot_Co", "ISL Products International": "#/$defs/_Isl_Products_International", "Infinity Photo-Optical": "#/$defs/_Infinity_Photo_Optical", "Integrated DNA Technologies": "#/$defs/_Integrated_Dna_Technologies", "Interuniversity Microelectronics Center": "#/$defs/_Interuniversity_Microelectronics_Center", "Invitrogen": "#/$defs/_Invitrogen", "Item": "#/$defs/_Item", "Jackson Laboratory": "#/$defs/_Jackson_Laboratory", "Janelia Research Campus": "#/$defs/_Janelia_Research_Campus", "Julabo": "#/$defs/_Julabo", "Kowa": "#/$defs/_Kowa", "LG": "#/$defs/_Lg", "Leica": "#/$defs/_Leica", "LifeCanvas": "#/$defs/_Lifecanvas", "Lumen Dynamics": "#/$defs/_Lumen_Dynamics", "MBF Bioscience": "#/$defs/_Mbf_Bioscience", "MKS Newport": "#/$defs/_Mks_Newport", "MPI": "#/$defs/_Mpi", "Meadowlark Optics": "#/$defs/_Meadowlark_Optics", "Michael J. Fox Foundation for Parkinson's Research": "#/$defs/_Michael_J_Fox_Foundation_For_Parkinson_S_Research", "Midwest Optical Systems, Inc.": "#/$defs/_Midwest_Optical_Systems_Inc_", "Mitutuyo": "#/$defs/_Mitutuyo", "NResearch Inc": "#/$defs/_Nresearch_Inc", "National Center for Complementary and Integrative Health": "#/$defs/_National_Center_For_Complementary_And_Integrative_Health", "National Institute of Mental Health": "#/$defs/_National_Institute_Of_Mental_Health", "National Institute of Neurological Disorders and Stroke": "#/$defs/_National_Institute_Of_Neurological_Disorders_And_Stroke", "National Instruments": "#/$defs/_National_Instruments", "Navitar": "#/$defs/_Navitar", "Neurophotometrics": "#/$defs/_Neurophotometrics", "New Scale Technologies": "#/$defs/_New_Scale_Technologies", "New York University": "#/$defs/_New_York_University", "Nikon": "#/$defs/_Nikon", "Olympus": "#/$defs/_Olympus", "Open Ephys Production Site": "#/$defs/_Open_Ephys_Production_Site", "Optotune": "#/$defs/_Optotune", "Other": "#/$defs/_Other", "Oxxius": "#/$defs/_Oxxius", "Placid Industries": "#/$defs/_Placid_Industries", "Prizmatix": "#/$defs/_Prizmatix", "Quantifi": "#/$defs/_Quantifi", "Raspberry Pi": "#/$defs/_Raspberry_Pi", "SICGEN": "#/$defs/_Sicgen", "Same Sky": "#/$defs/_Same_Sky", "Schneider-Kreuznach": "#/$defs/_Schneider_Kreuznach", "Second Order Effects": "#/$defs/_Second_Order_Effects", "Semrock": "#/$defs/_Semrock", "Sigma-Aldrich": "#/$defs/_Sigma_Aldrich", "Simons Foundation": "#/$defs/_Simons_Foundation", "Spinnaker": "#/$defs/_Spinnaker", "Tamron": "#/$defs/_Tamron", "Technical Manufacturing Corporation": "#/$defs/_Technical_Manufacturing_Corporation", "Teledyne FLIR": "#/$defs/_Teledyne_Flir", "Templeton World Charity Foundation": "#/$defs/_Templeton_World_Charity_Foundation", "The Imaging Source": "#/$defs/_The_Imaging_Source", "The Lee Company": "#/$defs/_The_Lee_Company", "Thermo Fisher Scientific": "#/$defs/_Thermo_Fisher_Scientific", "Thorlabs": "#/$defs/_Thorlabs", "Transducer Techniques": "#/$defs/_Transducer_Techniques", "Tymphany": "#/$defs/_Tymphany", "Vieworks": "#/$defs/_Vieworks", "Vortran": "#/$defs/_Vortran", "ams OSRAM": "#/$defs/_Ams_Osram" }, "propertyName": "name" }, "oneOf": [ { "$ref": "#/$defs/_Aa_Opto_Electronic" }, { "$ref": "#/$defs/_Asus" }, { "$ref": "#/$defs/_Abcam" }, { "$ref": "#/$defs/aind_data_schema_models__organizations___Addgene" }, { "$ref": "#/$defs/_Ailipu_Technology_Co" }, { "$ref": "#/$defs/_Allen_Institute" }, { "$ref": "#/$defs/_Allen_Institute_For_Brain_Science" }, { "$ref": "#/$defs/_Allen_Institute_For_Neural_Dynamics" }, { "$ref": "#/$defs/_Allied" }, { "$ref": "#/$defs/_Applied_Scientific_Instrumentation" }, { "$ref": "#/$defs/_Arecont_Vision_Costar" }, { "$ref": "#/$defs/_Basler" }, { "$ref": "#/$defs/_Cambridge_Technology" }, { "$ref": "#/$defs/_Carl_Zeiss" }, { "$ref": "#/$defs/_Champalimaud_Foundation" }, { "$ref": "#/$defs/_Chan_Zuckerberg_Initiative" }, { "$ref": "#/$defs/_Charles_River_Laboratories" }, { "$ref": "#/$defs/_Chroma" }, { "$ref": "#/$defs/_Coherent_Scientific" }, { "$ref": "#/$defs/_Columbia_University" }, { "$ref": "#/$defs/_Computar" }, { "$ref": "#/$defs/_Conoptics" }, { "$ref": "#/$defs/_Custom" }, { "$ref": "#/$defs/_Digikey" }, { "$ref": "#/$defs/_Dodotronic" }, { "$ref": "#/$defs/_Doric" }, { "$ref": "#/$defs/_Ealing" }, { "$ref": "#/$defs/_Edmund_Optics" }, { "$ref": "#/$defs/_Emory_University" }, { "$ref": "#/$defs/_Euresys" }, { "$ref": "#/$defs/_Fujinon" }, { "$ref": "#/$defs/_Hamamatsu" }, { "$ref": "#/$defs/_Hamilton" }, { "$ref": "#/$defs/_Huazhong_University_Of_Science_And_Technology" }, { "$ref": "#/$defs/_Ir_Robot_Co" }, { "$ref": "#/$defs/_Isl_Products_International" }, { "$ref": "#/$defs/_Infinity_Photo_Optical" }, { "$ref": "#/$defs/_Integrated_Dna_Technologies" }, { "$ref": "#/$defs/_Interuniversity_Microelectronics_Center" }, { "$ref": "#/$defs/_Invitrogen" }, { "$ref": "#/$defs/_Item" }, { "$ref": "#/$defs/_Jackson_Laboratory" }, { "$ref": "#/$defs/_Janelia_Research_Campus" }, { "$ref": "#/$defs/_Julabo" }, { "$ref": "#/$defs/_Kowa" }, { "$ref": "#/$defs/_Lg" }, { "$ref": "#/$defs/_Leica" }, { "$ref": "#/$defs/_Lumen_Dynamics" }, { "$ref": "#/$defs/_Lifecanvas" }, { "$ref": "#/$defs/_Mbf_Bioscience" }, { "$ref": "#/$defs/_Mks_Newport" }, { "$ref": "#/$defs/_Mpi" }, { "$ref": "#/$defs/_Meadowlark_Optics" }, { "$ref": "#/$defs/_Michael_J_Fox_Foundation_For_Parkinson_S_Research" }, { "$ref": "#/$defs/_Midwest_Optical_Systems_Inc_" }, { "$ref": "#/$defs/_Mitutuyo" }, { "$ref": "#/$defs/_Nresearch_Inc" }, { "$ref": "#/$defs/_National_Center_For_Complementary_And_Integrative_Health" }, { "$ref": "#/$defs/_National_Institute_Of_Mental_Health" }, { "$ref": "#/$defs/_National_Institute_Of_Neurological_Disorders_And_Stroke" }, { "$ref": "#/$defs/_National_Instruments" }, { "$ref": "#/$defs/_Navitar" }, { "$ref": "#/$defs/_Neurophotometrics" }, { "$ref": "#/$defs/_New_Scale_Technologies" }, { "$ref": "#/$defs/_New_York_University" }, { "$ref": "#/$defs/_Nikon" }, { "$ref": "#/$defs/_Olympus" }, { "$ref": "#/$defs/_Open_Ephys_Production_Site" }, { "$ref": "#/$defs/_Optotune" }, { "$ref": "#/$defs/_Other" }, { "$ref": "#/$defs/_Oxxius" }, { "$ref": "#/$defs/_Placid_Industries" }, { "$ref": "#/$defs/_Prizmatix" }, { "$ref": "#/$defs/_Quantifi" }, { "$ref": "#/$defs/_Raspberry_Pi" }, { "$ref": "#/$defs/_Same_Sky" }, { "$ref": "#/$defs/_Sicgen" }, { "$ref": "#/$defs/_Schneider_Kreuznach" }, { "$ref": "#/$defs/_Second_Order_Effects" }, { "$ref": "#/$defs/_Semrock" }, { "$ref": "#/$defs/_Sigma_Aldrich" }, { "$ref": "#/$defs/_Simons_Foundation" }, { "$ref": "#/$defs/_Spinnaker" }, { "$ref": "#/$defs/_Tamron" }, { "$ref": "#/$defs/_Technical_Manufacturing_Corporation" }, { "$ref": "#/$defs/_Teledyne_Flir" }, { "$ref": "#/$defs/_Templeton_World_Charity_Foundation" }, { "$ref": "#/$defs/_The_Imaging_Source" }, { "$ref": "#/$defs/_The_Lee_Company" }, { "$ref": "#/$defs/_Thermo_Fisher_Scientific" }, { "$ref": "#/$defs/_Thorlabs" }, { "$ref": "#/$defs/_Transducer_Techniques" }, { "$ref": "#/$defs/_Tymphany" }, { "$ref": "#/$defs/_Vieworks" }, { "$ref": "#/$defs/_Vortran" }, { "$ref": "#/$defs/_Ams_Osram" } ], "title": "Source" }, "rrid": { "anyOf": [ { "$ref": "#/$defs/PIDName" }, { "type": "null" } ], "default": null, "title": "Research Resource ID" }, "lot_number": { "title": "Lot number", "type": "string" }, "expiration_date": { "anyOf": [ { "format": "date", "type": "string" }, { "type": "null" } ], "default": null, "title": "Lot expiration date" } }, "required": [ "name", "source", "lot_number" ], "title": "Reagent", "type": "object" }, "Rotation3dTransform": { "additionalProperties": false, "description": "Values to be vector-added to a 3D position. Often needed to specify a device or tile's origin.", "properties": { "type": { "const": "rotation", "default": "rotation", "title": "Type", "type": "string" }, "rotation": { "items": { "anyOf": [ { "type": "number" }, { "type": "string" } ] }, "maxItems": 9, "minItems": 9, "title": "3D rotation matrix values (3x3) ", "type": "array" } }, "required": [ "rotation" ], "title": "Rotation3dTransform", "type": "object" }, "Scale3dTransform": { "additionalProperties": false, "description": "Values to be vector-multiplied with a 3D position, equivalent to the diagonals of a 3x3 transform matrix.\nRepresents voxel spacing if used as the first applied coordinate transform.", "properties": { "type": { "const": "scale", "default": "scale", "title": "Type", "type": "string" }, "scale": { "items": { "anyOf": [ { "type": "number" }, { "type": "string" } ] }, "maxItems": 3, "minItems": 3, "title": "3D scale parameters", "type": "array" } }, "required": [ "scale" ], "title": "Scale3dTransform", "type": "object" }, "SizeUnit": { "description": "Enumeration of Length Measurements", "enum": [ "meter", "centimeter", "millimeter", "micrometer", "nanometer", "inch", "pixel" ], "title": "SizeUnit", "type": "string" }, "Software": { "additionalProperties": false, "description": "Description of generic software", "properties": { "name": { "title": "Software name", "type": "string" }, "version": { "title": "Software version", "type": "string" }, "url": { "anyOf": [ { "type": "string" }, { "type": "null" } ], "default": null, "title": "URL to commit being used" }, "parameters": { "$ref": "#/$defs/AindGeneric", "default": {}, "title": "Software parameters" } }, "required": [ "name", "version" ], "title": "Software", "type": "object" }, "Translation3dTransform": { "additionalProperties": false, "description": "Values to be vector-added to a 3D position. 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"default": { "name": "Research Organization Registry", "abbreviation": "ROR" }, "discriminator": { "mapping": { "ADDGENE": "#/$defs/aind_data_schema_models__registries___Addgene", "EMAPA": "#/$defs/_Emapa", "MGI": "#/$defs/_Mgi", "NCBI": "#/$defs/_Ncbi", "ORCID": "#/$defs/_Orcid", "ROR": "#/$defs/_Ror", "RRID": "#/$defs/_Rrid" }, "propertyName": "abbreviation" }, "oneOf": [ { "$ref": "#/$defs/aind_data_schema_models__registries___Addgene" }, { "$ref": "#/$defs/_Emapa" }, { "$ref": "#/$defs/_Mgi" }, { "$ref": "#/$defs/_Ncbi" }, { "$ref": "#/$defs/_Orcid" }, { "$ref": "#/$defs/_Ror" }, { "$ref": "#/$defs/_Rrid" } ], "title": "Registry" }, "registry_identifier": { "const": "021sy4w91", "default": "021sy4w91", "title": "Registry Identifier", "type": "string" } }, "title": "_Jackson_Laboratory", "type": "object" }, "_Janelia_Research_Campus": { "description": "Model Janelia Research Campus", "properties": { "name": { "const": "Janelia Research Campus", "default": "Janelia Research Campus", "title": "Name", "type": "string" }, "abbreviation": { "const": "Janelia", "default": "Janelia", "title": "Abbreviation", "type": "string" }, "registry": { "default": { "name": "Research Organization Registry", "abbreviation": "ROR" }, "discriminator": { "mapping": { "ADDGENE": "#/$defs/aind_data_schema_models__registries___Addgene", "EMAPA": "#/$defs/_Emapa", "MGI": "#/$defs/_Mgi", "NCBI": "#/$defs/_Ncbi", "ORCID": "#/$defs/_Orcid", "ROR": "#/$defs/_Ror", "RRID": "#/$defs/_Rrid" }, "propertyName": "abbreviation" }, "oneOf": [ { "$ref": "#/$defs/aind_data_schema_models__registries___Addgene" }, { "$ref": "#/$defs/_Emapa" }, { "$ref": "#/$defs/_Mgi" }, { "$ref": "#/$defs/_Ncbi" }, { "$ref": "#/$defs/_Orcid" }, { "$ref": "#/$defs/_Ror" }, { "$ref": "#/$defs/_Rrid" } ], "title": "Registry" }, "registry_identifier": { "const": "013sk6x84", "default": "013sk6x84", "title": "Registry Identifier", "type": "string" } }, "title": "_Janelia_Research_Campus", "type": "object" }, "_Julabo": { "description": "Model Julabo", "properties": { "name": { "const": "Julabo", "default": "Julabo", "title": "Name", "type": "string" }, "abbreviation": { "const": null, "default": null, "title": "Abbreviation", "type": "null" }, "registry": { "default": null, "title": "Registry", "type": "null" }, "registry_identifier": { "default": null, "title": "Registry Identifier", "type": "null" } }, "title": "_Julabo", "type": "object" }, "_Kowa": { "description": "Model Kowa", "properties": { "name": { "const": "Kowa", "default": "Kowa", "title": "Name", "type": "string" }, "abbreviation": { "const": null, "default": null, "title": "Abbreviation", "type": "null" }, "registry": { "default": { "name": "Research Organization Registry", "abbreviation": "ROR" }, "discriminator": { "mapping": { "ADDGENE": "#/$defs/aind_data_schema_models__registries___Addgene", "EMAPA": "#/$defs/_Emapa", "MGI": "#/$defs/_Mgi", "NCBI": "#/$defs/_Ncbi", "ORCID": "#/$defs/_Orcid", "ROR": "#/$defs/_Ror", "RRID": 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"Registry", "type": "null" }, "registry_identifier": { "default": null, "title": "Registry Identifier", "type": "null" } }, "title": "_Oxxius", "type": "object" }, "_Placid_Industries": { "description": "Model Placid Industries", "properties": { "name": { "const": "Placid Industries", "default": "Placid Industries", "title": "Name", "type": "string" }, "abbreviation": { "const": null, "default": null, "title": "Abbreviation", "type": "null" }, "registry": { "default": null, "title": "Registry", "type": "null" }, "registry_identifier": { "default": null, "title": "Registry Identifier", "type": "null" } }, "title": "_Placid_Industries", "type": "object" }, "_Prizmatix": { "description": "Model Prizmatix", "properties": { "name": { "const": "Prizmatix", "default": "Prizmatix", "title": "Name", "type": "string" }, "abbreviation": { "const": null, "default": null, "title": "Abbreviation", "type": "null" }, "registry": { "default": null, "title": "Registry", "type": "null" }, "registry_identifier": { "default": null, "title": "Registry Identifier", "type": "null" } }, "title": "_Prizmatix", "type": "object" }, "_Quantifi": { "description": "Model Quantifi", "properties": { "name": { "const": "Quantifi", "default": "Quantifi", "title": "Name", "type": "string" }, "abbreviation": { "const": null, "default": null, "title": "Abbreviation", "type": "null" }, "registry": { "default": null, "title": "Registry", "type": "null" }, "registry_identifier": { "default": null, "title": "Registry Identifier", "type": "null" } }, "title": "_Quantifi", "type": "object" }, "_Raspberry_Pi": { "description": "Model Raspberry Pi", "properties": { "name": { "const": "Raspberry Pi", "default": "Raspberry Pi", "title": "Name", "type": "string" }, "abbreviation": { "const": null, "default": null, "title": "Abbreviation", "type": "null" }, "registry": { "default": null, "title": "Registry", "type": "null" }, "registry_identifier": { "default": null, "title": "Registry Identifier", "type": "null" } }, "title": "_Raspberry_Pi", "type": "object" }, "_Ror": { "additionalProperties": false, "description": "Model ROR", "properties": { "name": { "const": "Research Organization Registry", "default": "Research Organization Registry", "title": "Name", "type": "string" }, "abbreviation": { "const": "ROR", "default": "ROR", "title": "Abbreviation", "type": "string" } }, "title": "_Ror", "type": "object" }, "_Rrid": { "additionalProperties": false, "description": "Model RRID", "properties": { "name": { "const": "Research Resource Identifiers", "default": "Research Resource Identifiers", "title": "Name", "type": "string" }, "abbreviation": { "const": "RRID", "default": "RRID", "title": "Abbreviation", "type": "string" } }, "title": "_Rrid", "type": "object" }, "_Same_Sky": { "description": "Model Same Sky", "properties": { "name": { "const": "Same Sky", "default": "Same Sky", "title": "Name", "type": "string" }, "abbreviation": { "const": null, "default": null, "title": "Abbreviation", "type": "null" }, "registry": { "default": null, "title": "Registry", "type": "null" }, "registry_identifier": { "default": null, "title": "Registry Identifier", "type": "null" } }, "title": "_Same_Sky", "type": "object" }, "_Schneider_Kreuznach": { "description": "Model Schneider-Kreuznach", "properties": { "name": { "const": "Schneider-Kreuznach", "default": "Schneider-Kreuznach", "title": "Name", "type": "string" }, "abbreviation": { "const": null, "default": null, "title": "Abbreviation", "type": "null" }, "registry": { "default": null, "title": "Registry", "type": "null" }, "registry_identifier": { "default": null, "title": "Registry Identifier", "type": "null" } }, "title": "_Schneider_Kreuznach", "type": "object" }, "_Second_Order_Effects": { "description": "Model Second Order Effects", "properties": { "name": { "const": "Second Order Effects", "default": "Second Order Effects", "title": "Name", "type": "string" }, "abbreviation": { "const": null, "default": null, "title": "Abbreviation", "type": "null" }, "registry": { "default": null, "title": "Registry", "type": "null" }, "registry_identifier": { "default": null, "title": "Registry Identifier", "type": "null" } }, "title": "_Second_Order_Effects", "type": "object" }, "_Semrock": { "description": "Model Semrock", "properties": { "name": { "const": "Semrock", "default": "Semrock", "title": "Name", "type": "string" }, "abbreviation": { "const": null, "default": null, "title": "Abbreviation", "type": "null" }, "registry": { "default": null, "title": "Registry", "type": "null" }, "registry_identifier": { "default": null, "title": "Registry Identifier", "type": "null" } }, "title": "_Semrock", "type": "object" }, "_Sicgen": { "description": "Model SICGEN", "properties": { "name": { "const": "SICGEN", "default": "SICGEN", "title": "Name", "type": "string" }, "abbreviation": { "const": null, "default": null, "title": "Abbreviation", "type": "null" }, "registry": { "default": null, "title": "Registry", "type": "null" }, "registry_identifier": { "default": null, "title": "Registry Identifier", "type": "null" } }, "title": "_Sicgen", "type": "object" }, "_Sigma_Aldrich": { "description": "Model Sigma-Aldrich", "properties": { "name": { "const": "Sigma-Aldrich", "default": "Sigma-Aldrich", "title": "Name", "type": "string" }, "abbreviation": { "const": null, "default": null, "title": "Abbreviation", "type": "null" }, "registry": { "default": null, "title": "Registry", "type": "null" }, "registry_identifier": { "default": null, "title": "Registry Identifier", "type": "null" } }, "title": "_Sigma_Aldrich", "type": "object" }, "_Simons_Foundation": { "description": "Model Simons Foundation", "properties": { "name": { "const": "Simons Foundation", "default": "Simons Foundation", "title": "Name", "type": "string" }, "abbreviation": { "const": null, "default": null, "title": "Abbreviation", "type": "null" }, "registry": { "default": { "name": "Research Organization Registry", "abbreviation": "ROR" }, "discriminator": { "mapping": { "ADDGENE": "#/$defs/aind_data_schema_models__registries___Addgene", "EMAPA": "#/$defs/_Emapa", "MGI": "#/$defs/_Mgi", "NCBI": "#/$defs/_Ncbi", "ORCID": "#/$defs/_Orcid", "ROR": "#/$defs/_Ror", "RRID": "#/$defs/_Rrid" }, "propertyName": "abbreviation" }, "oneOf": [ { "$ref": "#/$defs/aind_data_schema_models__registries___Addgene" }, { "$ref": "#/$defs/_Emapa" }, { "$ref": "#/$defs/_Mgi" }, { "$ref": "#/$defs/_Ncbi" }, { "$ref": "#/$defs/_Orcid" }, { "$ref": "#/$defs/_Ror" }, { "$ref": "#/$defs/_Rrid" } ], "title": "Registry" }, "registry_identifier": { "const": "01cmst727", "default": "01cmst727", "title": "Registry Identifier", "type": "string" } }, "title": "_Simons_Foundation", "type": "object" }, "_Spinnaker": { "description": "Model Spinnaker", "properties": { "name": { "const": "Spinnaker", "default": "Spinnaker", "title": "Name", "type": "string" }, "abbreviation": { "const": null, "default": null, "title": "Abbreviation", "type": "null" }, "registry": { "default": null, "title": "Registry", "type": "null" }, "registry_identifier": { "default": null, "title": "Registry Identifier", "type": "null" } }, "title": "_Spinnaker", "type": "object" }, "_Tamron": { "description": "Model Tamron", "properties": { "name": { "const": "Tamron", "default": "Tamron", "title": "Name", "type": "string" }, "abbreviation": { "const": null, "default": null, "title": "Abbreviation", "type": "null" }, "registry": { "default": null, "title": "Registry", "type": "null" }, "registry_identifier": { "default": null, "title": "Registry Identifier", "type": "null" } }, "title": "_Tamron", "type": "object" }, "_Technical_Manufacturing_Corporation": { "description": "Model Technical Manufacturing Corporation", "properties": { "name": { "const": "Technical Manufacturing Corporation", "default": "Technical Manufacturing Corporation", "title": "Name", "type": "string" }, "abbreviation": { "const": "TMC", "default": "TMC", "title": "Abbreviation", "type": "string" }, "registry": { "default": null, "title": "Registry", "type": "null" }, "registry_identifier": { "default": null, "title": "Registry Identifier", "type": "null" } }, "title": "_Technical_Manufacturing_Corporation", "type": "object" }, "_Teledyne_Flir": { "description": "Model Teledyne FLIR", "properties": { "name": { "const": "Teledyne FLIR", "default": "Teledyne FLIR", "title": "Name", "type": "string" }, "abbreviation": { "const": "FLIR", "default": "FLIR", "title": "Abbreviation", "type": "string" }, "registry": { "default": { "name": "Research Organization Registry", "abbreviation": "ROR" }, "discriminator": { "mapping": { "ADDGENE": "#/$defs/aind_data_schema_models__registries___Addgene", "EMAPA": "#/$defs/_Emapa", "MGI": "#/$defs/_Mgi", "NCBI": "#/$defs/_Ncbi", "ORCID": "#/$defs/_Orcid", "ROR": "#/$defs/_Ror", "RRID": "#/$defs/_Rrid" }, "propertyName": "abbreviation" }, "oneOf": [ { "$ref": "#/$defs/aind_data_schema_models__registries___Addgene" }, { "$ref": "#/$defs/_Emapa" }, { "$ref": "#/$defs/_Mgi" }, { "$ref": "#/$defs/_Ncbi" }, { "$ref": "#/$defs/_Orcid" }, { "$ref": "#/$defs/_Ror" }, { "$ref": "#/$defs/_Rrid" } ], "title": "Registry" }, "registry_identifier": { "const": "01j1gwp17", "default": "01j1gwp17", "title": "Registry Identifier", "type": "string" } }, "title": "_Teledyne_Flir", "type": "object" }, "_Templeton_World_Charity_Foundation": { "description": "Model Templeton World Charity Foundation", "properties": { "name": { "const": "Templeton World Charity Foundation", "default": "Templeton World Charity Foundation", "title": "Name", "type": "string" }, "abbreviation": { "const": "TWCF", "default": "TWCF", "title": "Abbreviation", "type": "string" }, "registry": { "default": { "name": "Research Organization Registry", "abbreviation": "ROR" }, "discriminator": { "mapping": { "ADDGENE": "#/$defs/aind_data_schema_models__registries___Addgene", "EMAPA": "#/$defs/_Emapa", "MGI": "#/$defs/_Mgi", "NCBI": "#/$defs/_Ncbi", "ORCID": "#/$defs/_Orcid", "ROR": "#/$defs/_Ror", "RRID": "#/$defs/_Rrid" }, "propertyName": "abbreviation" }, "oneOf": [ { "$ref": "#/$defs/aind_data_schema_models__registries___Addgene" }, { "$ref": "#/$defs/_Emapa" }, { "$ref": "#/$defs/_Mgi" }, { "$ref": "#/$defs/_Ncbi" }, { "$ref": "#/$defs/_Orcid" }, { "$ref": "#/$defs/_Ror" }, { "$ref": "#/$defs/_Rrid" } ], "title": "Registry" }, "registry_identifier": { "const": "00x0z1472", "default": "00x0z1472", "title": "Registry Identifier", "type": "string" } }, "title": "_Templeton_World_Charity_Foundation", "type": "object" }, "_The_Imaging_Source": { "description": "Model The Imaging Source", "properties": { "name": { "const": "The Imaging Source", "default": "The Imaging Source", "title": "Name", "type": "string" }, "abbreviation": { "const": null, "default": null, "title": "Abbreviation", "type": "null" }, "registry": { "default": null, "title": "Registry", "type": "null" }, "registry_identifier": { "default": null, "title": "Registry Identifier", "type": "null" } }, "title": "_The_Imaging_Source", "type": "object" }, "_The_Lee_Company": { "description": "Model The Lee Company", "properties": { "name": { "const": "The Lee Company", "default": "The Lee Company", "title": "Name", "type": "string" }, "abbreviation": { "const": null, "default": null, "title": "Abbreviation", "type": "null" }, "registry": { "default": null, "title": "Registry", "type": "null" }, "registry_identifier": { "default": null, "title": "Registry Identifier", "type": "null" } }, "title": "_The_Lee_Company", "type": "object" }, "_Thermo_Fisher_Scientific": { "description": "Model Thermo Fisher Scientific", "properties": { "name": { "const": "Thermo Fisher Scientific", "default": "Thermo Fisher Scientific", "title": "Name", "type": "string" }, "abbreviation": { "const": null, "default": null, "title": "Abbreviation", "type": "null" }, "registry": { "default": { "name": "Research Organization Registry", "abbreviation": "ROR" }, "discriminator": { "mapping": { "ADDGENE": "#/$defs/aind_data_schema_models__registries___Addgene", "EMAPA": "#/$defs/_Emapa", "MGI": "#/$defs/_Mgi", "NCBI": "#/$defs/_Ncbi", "ORCID": "#/$defs/_Orcid", "ROR": "#/$defs/_Ror", "RRID": "#/$defs/_Rrid" }, "propertyName": "abbreviation" }, "oneOf": [ { "$ref": "#/$defs/aind_data_schema_models__registries___Addgene" }, { "$ref": "#/$defs/_Emapa" }, { "$ref": "#/$defs/_Mgi" }, { "$ref": "#/$defs/_Ncbi" }, { "$ref": "#/$defs/_Orcid" }, { "$ref": "#/$defs/_Ror" }, { "$ref": "#/$defs/_Rrid" } ], "title": "Registry" }, "registry_identifier": { "const": "03x1ewr52", "default": "03x1ewr52", "title": "Registry Identifier", "type": "string" } }, "title": "_Thermo_Fisher_Scientific", "type": "object" }, "_Thorlabs": { "description": "Model Thorlabs", "properties": { "name": { "const": "Thorlabs", "default": "Thorlabs", "title": "Name", "type": "string" }, "abbreviation": { "const": null, "default": null, "title": "Abbreviation", "type": "null" }, "registry": { "default": { "name": "Research Organization Registry", "abbreviation": "ROR" }, "discriminator": { "mapping": { "ADDGENE": "#/$defs/aind_data_schema_models__registries___Addgene", "EMAPA": "#/$defs/_Emapa", "MGI": "#/$defs/_Mgi", "NCBI": "#/$defs/_Ncbi", "ORCID": "#/$defs/_Orcid", "ROR": "#/$defs/_Ror", "RRID": "#/$defs/_Rrid" }, "propertyName": "abbreviation" }, "oneOf": [ { "$ref": "#/$defs/aind_data_schema_models__registries___Addgene" }, { "$ref": "#/$defs/_Emapa" }, { "$ref": "#/$defs/_Mgi" }, { "$ref": "#/$defs/_Ncbi" }, { "$ref": "#/$defs/_Orcid" }, { "$ref": "#/$defs/_Ror" }, { "$ref": "#/$defs/_Rrid" } ], "title": "Registry" }, "registry_identifier": { "const": "04gsnvb07", "default": "04gsnvb07", "title": "Registry Identifier", "type": "string" } }, "title": "_Thorlabs", "type": "object" }, "_Transducer_Techniques": { "description": "Model Transducer Techniques", "properties": { "name": { "const": "Transducer Techniques", "default": "Transducer Techniques", "title": "Name", "type": "string" }, "abbreviation": { "const": null, "default": null, "title": "Abbreviation", "type": "null" }, "registry": { "default": null, "title": "Registry", "type": "null" }, "registry_identifier": { "default": null, "title": "Registry Identifier", "type": "null" } }, "title": "_Transducer_Techniques", "type": "object" }, "_Tymphany": { "description": "Model Tymphany", "properties": { "name": { "const": "Tymphany", "default": "Tymphany", "title": "Name", "type": "string" }, "abbreviation": { "const": null, "default": null, "title": "Abbreviation", "type": "null" }, "registry": { "default": null, "title": "Registry", "type": "null" }, "registry_identifier": { "default": null, "title": "Registry Identifier", "type": "null" } }, "title": "_Tymphany", "type": "object" }, "_Vieworks": { "description": "Model Vieworks", "properties": { "name": { "const": "Vieworks", "default": "Vieworks", "title": "Name", "type": "string" }, "abbreviation": { "const": null, "default": null, "title": "Abbreviation", "type": "null" }, "registry": { "default": null, "title": "Registry", "type": "null" }, "registry_identifier": { "default": null, "title": "Registry Identifier", "type": "null" } }, "title": "_Vieworks", "type": "object" }, "_Vortran": { "description": "Model Vortran", "properties": { "name": { "const": "Vortran", "default": "Vortran", "title": "Name", "type": "string" }, "abbreviation": { "const": null, "default": null, "title": "Abbreviation", "type": "null" }, "registry": { "default": null, "title": "Registry", "type": "null" }, "registry_identifier": { "default": null, "title": "Registry Identifier", "type": "null" } }, "title": "_Vortran", "type": "object" }, "aind_data_schema_models__organizations___Addgene": { "description": "Model Addgene", "properties": { "name": { "const": "Addgene", "default": "Addgene", "title": "Name", "type": "string" }, "abbreviation": { "const": null, "default": null, "title": "Abbreviation", "type": "null" }, "registry": { "default": { "name": "Research Organization Registry", "abbreviation": "ROR" }, "discriminator": { "mapping": { "ADDGENE": "#/$defs/aind_data_schema_models__registries___Addgene", "EMAPA": "#/$defs/_Emapa", "MGI": "#/$defs/_Mgi", "NCBI": "#/$defs/_Ncbi", "ORCID": "#/$defs/_Orcid", "ROR": "#/$defs/_Ror", "RRID": "#/$defs/_Rrid" }, "propertyName": "abbreviation" }, "oneOf": [ { "$ref": "#/$defs/aind_data_schema_models__registries___Addgene" }, { "$ref": "#/$defs/_Emapa" }, { "$ref": "#/$defs/_Mgi" }, { "$ref": "#/$defs/_Ncbi" }, { "$ref": "#/$defs/_Orcid" }, { "$ref": "#/$defs/_Ror" }, { "$ref": "#/$defs/_Rrid" } ], "title": "Registry" }, "registry_identifier": { "const": "01nn1pw54", "default": "01nn1pw54", "title": "Registry Identifier", "type": "string" } }, "title": "_Addgene", "type": "object" }, "aind_data_schema_models__registries___Addgene": { "additionalProperties": false, "description": "Model ADDGENE", "properties": { "name": { "const": "Addgene", "default": "Addgene", "title": "Name", "type": "string" }, "abbreviation": { "const": "ADDGENE", "default": "ADDGENE", "title": "Abbreviation", "type": "string" } }, "title": "_Addgene", "type": "object" } }, "additionalProperties": false, "required": [ "experimenter_full_name", "specimen_id", "instrument_id", "session_start_time", "session_end_time", "tiles", "axes", "chamber_immersion" ] }
- Config:
extra: str = forbid
use_enum_values: bool = True
- Fields:
axes (List[aind_data_schema.components.coordinates.ImageAxis])calibrations (List[aind_data_schema.components.devices.Calibration])chamber_immersion (aind_data_schema.core.acquisition.Immersion)maintenance (List[aind_data_schema.components.devices.Maintenance])processing_steps (List[aind_data_schema.core.acquisition.ProcessingSteps])sample_immersion (aind_data_schema.core.acquisition.Immersion | None)session_end_time (pydantic.types.AwareDatetime[pydantic.types.AwareDatetime])session_start_time (pydantic.types.AwareDatetime[pydantic.types.AwareDatetime])software (List[aind_data_schema.components.devices.Software] | None)tiles (List[aind_data_schema.components.tile.AcquisitionTile])
- Validators:
- field active_objectives: List[str] | None = None¶
- Validated by:
- field calibrations: List[Calibration] = []¶
List of calibration measurements taken prior to acquisition.
- Validated by:
- field describedBy: str = 'https://raw.githubusercontent.com/AllenNeuralDynamics/aind-data-schema/main/src/aind_data_schema/core/acquisition.py'¶
- Validated by:
- field experimenter_full_name: List[str] [Required]¶
First and last name of the experimenter(s).
- Validated by:
- field external_storage_directory: str | None = None¶
- Validated by:
- field instrument_id: str [Required]¶
- Validated by:
- field local_storage_directory: str | None = None¶
- Validated by:
- field maintenance: List[Maintenance] = []¶
List of maintenance on rig prior to acquisition.
- Validated by:
- field notes: str | None = None¶
- Validated by:
- field processing_steps: List[ProcessingSteps] = []¶
List of downstream processing steps planned for each channel
- Validated by:
- field protocol_id: List[str] = []¶
DOI for protocols.io
- Validated by:
- field schema_version: Literal['1.0.4'][~typing.Literal['1.0.4']] = '1.0.4'¶
- Validated by:
- field session_end_time: AwareDatetime[AwareDatetime] [Required]¶
- Constraints:
func = <function _coerce_naive_datetime at 0x7f379fb609d0>
json_schema_input_type = PydanticUndefined
- Validated by:
- field session_start_time: AwareDatetime[AwareDatetime] [Required]¶
- Constraints:
func = <function _coerce_naive_datetime at 0x7f379fb609d0>
json_schema_input_type = PydanticUndefined
- Validated by:
- field session_type: str | None = None¶
- Validated by:
- field specimen_id: str [Required]¶
- Validated by:
- field subject_id: str | None = None¶
- Validated by:
- field tiles: List[AcquisitionTile] [Required]¶
- Validated by:
- model_post_init(context: Any, /) None¶
We need to both initialize private attributes and call the user-defined model_post_init method.
- pydantic model aind_data_schema.core.acquisition.Immersion¶
Bases:
AindModelDescription of immersion medium
Show JSON schema
{ "title": "Immersion", "description": "Description of immersion medium", "type": "object", "properties": { "medium": { "$ref": "#/$defs/ImmersionMedium", "title": "Immersion medium" }, "refractive_index": { "anyOf": [ { "type": "number" }, { "type": "string" } ], "title": "Index of refraction" } }, "$defs": { "ImmersionMedium": { "description": "Immersion medium name", "enum": [ "air", "multi", "oil", "PBS", "water", "other", "easy index", "ethyl cinnimate", "aqueous clearing buffer" ], "title": "ImmersionMedium", "type": "string" } }, "additionalProperties": false, "required": [ "medium", "refractive_index" ] }
- Config:
extra: str = forbid
use_enum_values: bool = True
- Fields:
- Validators:
- field medium: ImmersionMedium [Required]¶
- Validated by:
- field refractive_index: Decimal [Required]¶
- Validated by:
- pydantic model aind_data_schema.core.acquisition.ProcessingSteps¶
Bases:
AindModelDescription of downstream processing steps
Show JSON schema
{ "title": "ProcessingSteps", "description": "Description of downstream processing steps", "type": "object", "properties": { "channel_name": { "title": "Channel name", "type": "string" }, "process_name": { "items": { "enum": [ "Image atlas alignment", "Image background subtraction", "Image cell segmentation", "Image destriping", "Image flat-field correction", "Image importing", "Image thresholding", "Image tile alignment", "Image tile fusing", "Image tile projection", "File format conversion" ], "type": "string" }, "title": "Process Name", "type": "array" } }, "additionalProperties": false, "required": [ "channel_name", "process_name" ] }
- Config:
extra: str = forbid
use_enum_values: bool = True
- Fields:
process_name (List[Literal[
- Validators:
- field channel_name: str [Required]¶
- Validated by:
- field process_name: FILE_FORMAT_CONVERSION: 'File format conversion'>]] [Required]¶
- Validated by:
aind_data_schema.core.data_description module¶
Generic metadata classes for data
- pydantic model aind_data_schema.core.data_description.AnalysisDescription¶
Bases:
DataDescriptionA collection of data files as analyzed from an asset
Show JSON schema
{ "title": "AnalysisDescription", "description": "A collection of data files as analyzed from an asset", "type": "object", "properties": { "describedBy": { "const": "https://raw.githubusercontent.com/AllenNeuralDynamics/aind-data-schema/main/src/aind_data_schema/core/data_description.py", "default": "https://raw.githubusercontent.com/AllenNeuralDynamics/aind-data-schema/main/src/aind_data_schema/core/data_description.py", "title": "Describedby", "type": "string" }, "schema_version": { "const": "1.0.4", "default": "1.0.4", "title": "Schema Version", "type": "string" }, "license": { "const": "CC-BY-4.0", "default": "CC-BY-4.0", "title": "License", "type": "string" }, "platform": { "description": "Name for a standardized primary data collection system", "discriminator": { "mapping": { "Behavior platform": "#/$defs/aind_data_schema_models__platforms___Behavior", "Confocal microscopy platform": "#/$defs/aind_data_schema_models__platforms___Confocal", "Electrophysiology platform": "#/$defs/aind_data_schema_models__platforms___Ecephys", "ExaSPIM platform": "#/$defs/_Exaspim", "Frame-projected independent-fiber photometry platform": "#/$defs/_Fip", "Hybridization chain reaction platform": "#/$defs/_Hcr", "Hyperspectral fiber photometry platform": "#/$defs/_Hsfp", "Intrinsic signal imaging platform": "#/$defs/aind_data_schema_models__platforms___Isi", "MERFISH platform": "#/$defs/aind_data_schema_models__platforms___Merfish", "Magnetic resonance imaging platform": "#/$defs/aind_data_schema_models__platforms___Mri", "MesoSPIM platform": "#/$defs/_Mesospim", "Motor observatory platform": "#/$defs/_Motor_Observatory", "Multiplane optical physiology platform": "#/$defs/_Multiplane_Ophys", "SLAP2 platform": "#/$defs/_Slap2", "Single-plane optical physiology platform": "#/$defs/_Single_Plane_Ophys", "SmartSPIM platform": "#/$defs/_Smartspim" }, "propertyName": "name" }, "oneOf": [ { "$ref": "#/$defs/aind_data_schema_models__platforms___Behavior" }, { "$ref": "#/$defs/aind_data_schema_models__platforms___Confocal" }, { "$ref": "#/$defs/aind_data_schema_models__platforms___Ecephys" }, { "$ref": "#/$defs/_Exaspim" }, { "$ref": "#/$defs/_Fip" }, { "$ref": "#/$defs/_Hcr" }, { "$ref": "#/$defs/_Hsfp" }, { "$ref": "#/$defs/aind_data_schema_models__platforms___Isi" }, { "$ref": "#/$defs/aind_data_schema_models__platforms___Merfish" }, { "$ref": "#/$defs/aind_data_schema_models__platforms___Mri" }, { "$ref": "#/$defs/_Mesospim" }, { "$ref": "#/$defs/_Motor_Observatory" }, { "$ref": "#/$defs/_Multiplane_Ophys" }, { "$ref": "#/$defs/_Slap2" }, { "$ref": "#/$defs/_Single_Plane_Ophys" }, { "$ref": "#/$defs/_Smartspim" } ], "title": "Platform" }, "subject_id": { "description": "Unique identifier for the subject of data acquisition", "pattern": "^[^_]+$", "title": "Subject ID", "type": "string" }, "creation_time": { "description": "Time that data files were created, used to uniquely identify the data", "format": "date-time", "title": "Creation Time", "type": "string" }, "label": { "anyOf": [ { "type": "string" }, { "type": "null" } ], "default": null, "description": "A short name for the data, used in file names and labels", "title": "Label" }, "name": { "anyOf": [ { "type": "string" }, { "type": "null" } ], "default": null, "description": "Name of data, conventionally also the name of the directory containing all data and metadata", "title": "Name" }, "institution": { "description": "An established society, corporation, foundation or other organization that collected this data", "discriminator": { "mapping": { "Allen Institute for Brain Science": "#/$defs/_Allen_Institute_For_Brain_Science", "Allen Institute for Neural Dynamics": "#/$defs/_Allen_Institute_For_Neural_Dynamics", "Columbia University": "#/$defs/_Columbia_University", "Huazhong University of Science and Technology": "#/$defs/_Huazhong_University_Of_Science_And_Technology", "Janelia Research Campus": "#/$defs/_Janelia_Research_Campus", "New York University": "#/$defs/_New_York_University", "Other": "#/$defs/_Other" }, "propertyName": "name" }, "oneOf": [ { "$ref": "#/$defs/_Allen_Institute_For_Brain_Science" }, { "$ref": "#/$defs/_Allen_Institute_For_Neural_Dynamics" }, { "$ref": "#/$defs/_Columbia_University" }, { "$ref": "#/$defs/_Huazhong_University_Of_Science_And_Technology" }, { "$ref": "#/$defs/_Janelia_Research_Campus" }, { "$ref": "#/$defs/_New_York_University" }, { "$ref": "#/$defs/_Other" } ], "title": "Institution" }, "funding_source": { "description": "Funding source. If internal funding, select 'Allen Institute'", "items": { "$ref": "#/$defs/Funding" }, "minItems": 1, "title": "Funding source", "type": "array" }, "data_level": { "const": "derived", "default": "derived", "description": "Level of processing that data has undergone", "title": "Data Level", "type": "string" }, "group": { "anyOf": [ { "$ref": "#/$defs/Group" }, { "type": "null" } ], "default": null, "description": "A short name for the group of individuals that collected this data", "title": "Group" }, "investigators": { "description": "Full name(s) of key investigators (e.g. PI, lead scientist, contact person)", "items": { "$ref": "#/$defs/PIDName" }, "minItems": 1, "title": "Investigators", "type": "array" }, "project_name": { "description": "Name of the project the analysis belongs to", "pattern": "^[^<>:;\"/|? \\\\_]+$", "title": "Project name", "type": "string" }, "restrictions": { "anyOf": [ { "type": "string" }, { "type": "null" } ], "default": null, "description": "Detail any restrictions on publishing or sharing these data", "title": "Restrictions" }, "modality": { "description": "A short name for the specific manner, characteristic, pattern of application, or the employmentof any technology or formal procedure to generate data for a study", "items": { "discriminator": { "mapping": { "EMG": "#/$defs/_Emg", "ISI": "#/$defs/aind_data_schema_models__modalities___Isi", "MRI": "#/$defs/aind_data_schema_models__modalities___Mri", "SPIM": "#/$defs/_Spim", "behavior": "#/$defs/aind_data_schema_models__modalities___Behavior", "behavior-videos": "#/$defs/_Behavior_Videos", "confocal": "#/$defs/aind_data_schema_models__modalities___Confocal", "ecephys": "#/$defs/aind_data_schema_models__modalities___Ecephys", "fMOST": "#/$defs/_Fmost", "fib": "#/$defs/_Fib", "icephys": "#/$defs/_Icephys", "merfish": "#/$defs/aind_data_schema_models__modalities___Merfish", "pophys": "#/$defs/_Pophys", "slap": "#/$defs/_Slap" }, "propertyName": "abbreviation" }, "oneOf": [ { "$ref": "#/$defs/aind_data_schema_models__modalities___Behavior" }, { "$ref": "#/$defs/_Behavior_Videos" }, { "$ref": "#/$defs/aind_data_schema_models__modalities___Confocal" }, { "$ref": "#/$defs/_Emg" }, { "$ref": "#/$defs/aind_data_schema_models__modalities___Ecephys" }, { "$ref": "#/$defs/_Fib" }, { "$ref": "#/$defs/_Fmost" }, { "$ref": "#/$defs/_Icephys" }, { "$ref": "#/$defs/aind_data_schema_models__modalities___Isi" }, { "$ref": "#/$defs/aind_data_schema_models__modalities___Mri" }, { "$ref": "#/$defs/aind_data_schema_models__modalities___Merfish" }, { "$ref": "#/$defs/_Pophys" }, { "$ref": "#/$defs/_Slap" }, { "$ref": "#/$defs/_Spim" } ] }, "title": "Modality", "type": "array" }, "related_data": { "default": [], "description": "Path and description of data assets associated with this asset (eg. reference images)", "items": { "$ref": "#/$defs/RelatedData" }, "title": "Related data", "type": "array" }, "data_summary": { "anyOf": [ { "type": "string" }, { "type": "null" } ], "default": null, "description": "Semantic summary of experimental goal", "title": "Data summary" }, "analysis_name": { "description": "Name of the analysis performed", "pattern": "^[^<>:;\"/|? \\\\_]+$", "title": "Analysis name", "type": "string" } }, "$defs": { "BaseName": { "additionalProperties": false, "description": "A simple model associating a name with an abbreviation", "properties": { "name": { "title": "Name", "type": "string" }, "abbreviation": { "anyOf": [ { "type": "string" }, { "type": "null" } ], "default": null, "title": "Abbreviation" } }, "required": [ "name" ], "title": "BaseName", "type": "object" }, "Funding": { "additionalProperties": false, "description": "Description of funding sources", "properties": { "funder": { "discriminator": { "mapping": { "Allen Institute": "#/$defs/_Allen_Institute", "Chan Zuckerberg Initiative": "#/$defs/_Chan_Zuckerberg_Initiative", "MBF Bioscience": "#/$defs/_Mbf_Bioscience", "Michael J. Fox Foundation for Parkinson's Research": "#/$defs/_Michael_J_Fox_Foundation_For_Parkinson_S_Research", "National Center for Complementary and Integrative Health": "#/$defs/_National_Center_For_Complementary_And_Integrative_Health", "National Institute of Mental Health": "#/$defs/_National_Institute_Of_Mental_Health", "National Institute of Neurological Disorders and Stroke": "#/$defs/_National_Institute_Of_Neurological_Disorders_And_Stroke", "Simons Foundation": "#/$defs/_Simons_Foundation", "Templeton World Charity Foundation": "#/$defs/_Templeton_World_Charity_Foundation" }, "propertyName": "name" }, "oneOf": [ { "$ref": "#/$defs/_Allen_Institute" }, { "$ref": "#/$defs/_Chan_Zuckerberg_Initiative" }, { "$ref": "#/$defs/_Mbf_Bioscience" }, { "$ref": "#/$defs/_Michael_J_Fox_Foundation_For_Parkinson_S_Research" }, { "$ref": "#/$defs/_National_Center_For_Complementary_And_Integrative_Health" }, { "$ref": "#/$defs/_National_Institute_Of_Mental_Health" }, { "$ref": "#/$defs/_National_Institute_Of_Neurological_Disorders_And_Stroke" }, { "$ref": "#/$defs/_Simons_Foundation" }, { "$ref": "#/$defs/_Templeton_World_Charity_Foundation" } ], "title": "Funder" }, "grant_number": { "anyOf": [ { "type": "string" }, { "type": "null" } ], "default": null, "title": "Grant number" }, "fundee": { "anyOf": [ { "type": "string" }, { "type": "null" } ], "default": null, "description": "Person(s) funded by this mechanism", "title": "Fundee" } }, "required": [ "funder" ], "title": "Funding", "type": "object" }, "Group": { "description": "Data collection group name", "enum": [ "behavior", "ephys", "MSMA", "ophys", "NBA" ], "title": "Group", "type": "string" }, "PIDName": { "additionalProperties": false, "description": "Model for associate a name with a persistent identifier (PID),\nthe registry for that PID, and abbreviation for that registry", "properties": { "name": { "title": "Name", "type": "string" }, "abbreviation": { "anyOf": [ { "type": "string" }, { "type": "null" } ], "default": null, "title": "Abbreviation" }, "registry": { "anyOf": [ { "$ref": "#/$defs/BaseName" }, { "type": "null" } ], "default": null, "title": "Registry" }, "registry_identifier": { "anyOf": [ { "type": "string" }, { "type": "null" } ], "default": null, "title": "Registry identifier" } }, "required": [ "name" ], "title": "PIDName", "type": "object" }, "RelatedData": { "additionalProperties": false, "description": "Description of related data asset", "properties": { "related_data_path": { "title": "Related data path", "type": "string" }, "relation": { "description": "Relation of data to this asset", "title": "Relation", "type": "string" } }, "required": [ "related_data_path", "relation" ], "title": "RelatedData", "type": "object" }, "_Addgene": { "additionalProperties": false, "description": "Model ADDGENE", "properties": { "name": { "const": "Addgene", "default": "Addgene", "title": "Name", "type": "string" }, "abbreviation": { "const": "ADDGENE", "default": "ADDGENE", "title": "Abbreviation", "type": "string" } }, "title": "_Addgene", "type": "object" }, "_Allen_Institute": { "description": "Model Allen Institute", "properties": { "name": { "const": "Allen Institute", "default": "Allen Institute", "title": "Name", "type": "string" }, "abbreviation": { "const": "AI", "default": "AI", "title": "Abbreviation", "type": "string" }, "registry": { "default": { "name": "Research Organization Registry", "abbreviation": "ROR" }, "discriminator": { "mapping": { "ADDGENE": "#/$defs/_Addgene", "EMAPA": "#/$defs/_Emapa", "MGI": "#/$defs/_Mgi", "NCBI": "#/$defs/_Ncbi", "ORCID": "#/$defs/_Orcid", "ROR": "#/$defs/_Ror", "RRID": "#/$defs/_Rrid" }, "propertyName": "abbreviation" }, "oneOf": [ { "$ref": "#/$defs/_Addgene" }, { "$ref": "#/$defs/_Emapa" }, { "$ref": "#/$defs/_Mgi" }, { "$ref": "#/$defs/_Ncbi" }, { "$ref": "#/$defs/_Orcid" }, { "$ref": "#/$defs/_Ror" }, { "$ref": "#/$defs/_Rrid" } ], "title": "Registry" }, "registry_identifier": { "const": "03cpe7c52", "default": "03cpe7c52", "title": "Registry Identifier", "type": "string" } }, "title": "_Allen_Institute", "type": "object" }, "_Allen_Institute_For_Brain_Science": { "description": "Model Allen Institute for Brain Science", "properties": { "name": { "const": "Allen Institute for Brain Science", "default": "Allen Institute for Brain Science", "title": "Name", "type": "string" }, "abbreviation": { "const": "AIBS", "default": "AIBS", "title": "Abbreviation", "type": "string" }, "registry": { "default": { "name": "Research Organization Registry", "abbreviation": "ROR" }, "discriminator": { "mapping": { "ADDGENE": "#/$defs/_Addgene", "EMAPA": "#/$defs/_Emapa", "MGI": "#/$defs/_Mgi", "NCBI": "#/$defs/_Ncbi", "ORCID": "#/$defs/_Orcid", "ROR": "#/$defs/_Ror", "RRID": "#/$defs/_Rrid" }, "propertyName": "abbreviation" }, "oneOf": [ { "$ref": "#/$defs/_Addgene" }, { "$ref": "#/$defs/_Emapa" }, { "$ref": "#/$defs/_Mgi" }, { "$ref": "#/$defs/_Ncbi" }, { "$ref": "#/$defs/_Orcid" }, { "$ref": "#/$defs/_Ror" }, { "$ref": "#/$defs/_Rrid" } ], "title": "Registry" }, "registry_identifier": { "const": "00dcv1019", "default": "00dcv1019", "title": "Registry Identifier", "type": "string" } }, "title": "_Allen_Institute_For_Brain_Science", "type": "object" }, "_Allen_Institute_For_Neural_Dynamics": { "description": "Model Allen Institute for Neural Dynamics", "properties": { "name": { "const": "Allen Institute for Neural Dynamics", "default": "Allen Institute for Neural Dynamics", "title": "Name", "type": "string" }, "abbreviation": { "const": "AIND", "default": "AIND", "title": "Abbreviation", "type": "string" }, "registry": { "default": { "name": "Research Organization Registry", "abbreviation": "ROR" }, "discriminator": { "mapping": { "ADDGENE": "#/$defs/_Addgene", "EMAPA": "#/$defs/_Emapa", "MGI": "#/$defs/_Mgi", "NCBI": "#/$defs/_Ncbi", "ORCID": "#/$defs/_Orcid", "ROR": "#/$defs/_Ror", "RRID": "#/$defs/_Rrid" }, "propertyName": "abbreviation" }, "oneOf": [ { "$ref": "#/$defs/_Addgene" }, { "$ref": "#/$defs/_Emapa" }, { "$ref": "#/$defs/_Mgi" }, { "$ref": "#/$defs/_Ncbi" }, { "$ref": "#/$defs/_Orcid" }, { "$ref": "#/$defs/_Ror" }, { "$ref": "#/$defs/_Rrid" } ], "title": "Registry" }, "registry_identifier": { "const": "04szwah67", "default": "04szwah67", "title": "Registry Identifier", "type": "string" } }, "title": "_Allen_Institute_For_Neural_Dynamics", "type": "object" }, "_Behavior_Videos": { "additionalProperties": false, "description": "Model behavior-videos", "properties": { "name": { "const": "Behavior videos", "default": "Behavior videos", "title": "Name", "type": "string" }, "abbreviation": { "const": "behavior-videos", "default": "behavior-videos", "title": "Abbreviation", "type": "string" } }, "title": "_Behavior_Videos", "type": "object" }, "_Chan_Zuckerberg_Initiative": { "description": "Model Chan Zuckerberg Initiative", "properties": { "name": { "const": "Chan Zuckerberg Initiative", "default": "Chan Zuckerberg Initiative", "title": "Name", "type": "string" }, "abbreviation": { "const": "CZI", "default": "CZI", "title": "Abbreviation", "type": "string" }, "registry": { "default": { "name": "Research Organization Registry", "abbreviation": "ROR" }, "discriminator": { "mapping": { "ADDGENE": "#/$defs/_Addgene", "EMAPA": "#/$defs/_Emapa", "MGI": "#/$defs/_Mgi", "NCBI": "#/$defs/_Ncbi", "ORCID": "#/$defs/_Orcid", "ROR": "#/$defs/_Ror", "RRID": "#/$defs/_Rrid" }, "propertyName": "abbreviation" }, "oneOf": [ { "$ref": "#/$defs/_Addgene" }, { "$ref": "#/$defs/_Emapa" }, { "$ref": "#/$defs/_Mgi" }, { "$ref": "#/$defs/_Ncbi" }, { "$ref": "#/$defs/_Orcid" }, { "$ref": "#/$defs/_Ror" }, { "$ref": "#/$defs/_Rrid" } ], "title": "Registry" }, "registry_identifier": { "const": "02qenvm24", "default": "02qenvm24", "title": "Registry Identifier", "type": "string" } }, "title": "_Chan_Zuckerberg_Initiative", "type": "object" }, "_Columbia_University": { "description": "Model Columbia University", "properties": { "name": { "const": "Columbia University", "default": "Columbia University", "title": "Name", "type": "string" }, "abbreviation": { "const": "Columbia", "default": "Columbia", "title": "Abbreviation", "type": "string" }, "registry": { "default": { "name": "Research Organization Registry", "abbreviation": "ROR" }, "discriminator": { "mapping": { "ADDGENE": "#/$defs/_Addgene", "EMAPA": "#/$defs/_Emapa", "MGI": "#/$defs/_Mgi", "NCBI": "#/$defs/_Ncbi", "ORCID":