aind-data-schema 2.5.0__tar.gz → 2.6.0__tar.gz

{aind_data_schema-2.5.0/src/aind_data_schema.egg-info → aind_data_schema-2.6.0}/PKG-INFO

@@ -1,13 +1,13 @@
 Metadata-Version: 2.4
 Name: aind-data-schema
-Version: 2.5.0
+Version: 2.6.0
 Summary: A library that defines AIND data schema and validates JSON files.
 License: MIT
 Classifier: Programming Language :: Python :: 3
 Requires-Python: >=3.10
 Description-Content-Type: text/markdown
 License-File: LICENSE
-Requires-Dist: aind-data-schema-models<6,>=5
+Requires-Dist: aind-data-schema-models<6,>=5.4.1
 Requires-Dist: pydantic<2.12,>=2.7
 Requires-Dist: pydantic-extra-types
 Provides-Extra: dev

{aind_data_schema-2.5.0 → aind_data_schema-2.6.0}/docs/base/core/procedures.md

@@ -8,7 +8,9 @@ The `procedures.json` file contains anything done to the subject or specimen pri
 
 **Subject** procedures are performed on a live subject (e.g. injections, surgeries, implants, perfusions, etc.) whereas **specimen** procedures are performed on tissue extracted after perfusion (e.g. tissue processing, immunolabeling, sectioning, etc.).
 
-Sectioned specimens must have a unique number appended as a suffix to the subject ID: `<subject_id>_<###>`.
+### SpecimenProcedure.specimen_id
+
+After perfusion or death we refer to specimens by the `specimen_id` field. When the tissue has not been sectioned in some way the `specimen_id` should be identical to the `subject_id`. Sectioned specimens should have a unique number appended as a suffix to the subject ID: `<subject_id>_<###>`. 
 
 ## Examples
 

{aind_data_schema-2.5.0 → aind_data_schema-2.6.0}/docs/source/acquisition.md

@@ -80,7 +80,7 @@ while the StimulusEpoch represents all stimuli being presented.
 | `subject_id` | `str` | Subject ID (Unique identifier for the subject) |
 | `specimen_id` | `Optional[str]` | Specimen ID (Specimen ID is required for in vitro imaging modalities) |
 | `acquisition_start_time` | `datetime (timezone-aware)` | Acquisition start time (During validation, timezone information will be moved into the acquisition_start_tz field.) |
-| `acquisition_start_tz` | `Optional[pydantic_extra_types.timezone_name.TimeZoneName]` | Acquisition start timezone (Automatically populated by a validator based on acquisition_start_time.) |
+| `acquisition_start_tz` | `int or pydantic_extra_types.timezone_name.TimeZoneName or NoneType` | Acquisition start timezone (Automatically populated by a validator based on acquisition_start_time. Will be a TimeZoneName (IANA name) when the datetime uses a ZoneInfo timezone, or an integer UTC offset in hours for fixed-offset timezones. Use ZoneInfo (from the zoneinfo standard library) to preserve the named timezone.) |
 | `acquisition_end_time` | `datetime (timezone-aware)` | Acquisition end time  |
 | `experimenters` | `List[str]` | experimenter(s)  |
 | `protocol_id` | `Optional[List[str]]` | Protocol ID (DOI for protocols.io) |
@@ -127,7 +127,7 @@ same time.
 | `code` | Optional[List[[Code](components/identifiers.md#code)]] | Acquisition code  |
 | `notes` | `Optional[str]` | Notes  |
 | `active_devices` | `List[str]` | Active devices (Device names must match devices in the Instrument) |
-| `configurations` | List[[LightEmittingDiodeConfig](components/configs.md#lightemittingdiodeconfig) or [LaserConfig](components/configs.md#laserconfig) or [ManipulatorConfig](components/configs.md#manipulatorconfig) or [DetectorConfig](components/configs.md#detectorconfig) or [PatchCordConfig](components/configs.md#patchcordconfig) or [FiberAssemblyConfig](components/configs.md#fiberassemblyconfig) or [MISCameraConfig](components/configs.md#miscameraconfig) or [MRIScan](components/configs.md#mriscan) or [LickSpoutConfig](components/configs.md#lickspoutconfig) or [AirPuffConfig](components/configs.md#airpuffconfig) or [ImagingConfig](components/configs.md#imagingconfig) or [SlapPlane](components/configs.md#slapplane) or [SampleChamberConfig](components/configs.md#samplechamberconfig) or [ProbeConfig](components/configs.md#probeconfig) or [EphysAssemblyConfig](components/configs.md#ephysassemblyconfig) or [CatheterConfig](components/configs.md#catheterconfig)] | Device configurations (Configurations are parameters controlling active devices during this stream) |
+| `configurations` | List[[LightEmittingDiodeConfig](components/configs.md#lightemittingdiodeconfig) or [LaserConfig](components/configs.md#laserconfig) or [ManipulatorConfig](components/configs.md#manipulatorconfig) or [DetectorConfig](components/configs.md#detectorconfig) or [PatchCordConfig](components/configs.md#patchcordconfig) or [FiberAssemblyConfig](components/configs.md#fiberassemblyconfig) or [MISCameraConfig](components/configs.md#miscameraconfig) or [MRIScan](components/configs.md#mriscan) or [LickSpoutConfig](components/configs.md#lickspoutconfig) or [AirPuffConfig](components/configs.md#airpuffconfig) or [ImagingConfig](components/configs.md#imagingconfig) or [SampleChamberConfig](components/configs.md#samplechamberconfig) or [ProbeConfig](components/configs.md#probeconfig) or [EphysAssemblyConfig](components/configs.md#ephysassemblyconfig) or [CatheterConfig](components/configs.md#catheterconfig)] | Device configurations (Configurations are parameters controlling active devices during this stream) |
 | `connections` | List[[Connection](components/connections.md#connection)] | Connections (Connections are links between devices that are specific to this acquisition (i.e. not already defined in the Instrument)) |
 
 

{aind_data_schema-2.5.0 → aind_data_schema-2.6.0}/docs/source/aind_data_schema_models/devices.md

@@ -95,6 +95,7 @@ Detector type name
 |------|-------|
 | `CAMERA` | `Camera` |
 | `PMT` | `Photomultiplier Tube` |
+| `SiPM` | `Silicon Photomultiplier` |
 | `OTHER` | `Other` |
 
 

{aind_data_schema-2.5.0 → aind_data_schema-2.6.0}/docs/source/aind_data_schema_models/organizations.md

@@ -9,97 +9,98 @@ Organization
 | Name | abbreviation | name | registry | registry_identifier |
 |------|------|------|------|------|
 | `AA_OPTO_ELECTRONIC` | `None` | `AA Opto Electronic` | `None` | `None` |
-| `ABCAM` | `None` | `Abcam` | `Registry.ROR` | `02e1wjw63` |
-| `ADDGENE` | `None` | `Addgene` | `Registry.ROR` | `01nn1pw54` |
-| `AI` | `AI` | `Allen Institute` | `Registry.ROR` | `03cpe7c52` |
-| `AIBS` | `AIBS` | `Allen Institute for Brain Science` | `Registry.ROR` | `00dcv1019` |
+| `ABCAM` | `None` | `Abcam` | `Research Organization Registry (ROR)` | `02e1wjw63` |
+| `ADDGENE` | `None` | `Addgene` | `Research Organization Registry (ROR)` | `01nn1pw54` |
+| `AI` | `AI` | `Allen Institute` | `Research Organization Registry (ROR)` | `03cpe7c52` |
+| `AIBS` | `AIBS` | `Allen Institute for Brain Science` | `Research Organization Registry (ROR)` | `00dcv1019` |
 | `AILIPU` | `Ailipu` | `Ailipu Technology Co` | `None` | `None` |
-| `AIND` | `AIND` | `Allen Institute for Neural Dynamics` | `Registry.ROR` | `04szwah67` |
-| `AMS_OSRAM` | `None` | `ams OSRAM` | `Registry.ROR` | `045d0h266` |
+| `AIND` | `AIND` | `Allen Institute for Neural Dynamics` | `Research Organization Registry (ROR)` | `04szwah67` |
+| `AMS_OSRAM` | `None` | `ams OSRAM` | `Research Organization Registry (ROR)` | `045d0h266` |
 | `ARDUINO` | `None` | `Arduino` | `None` | `None` |
 | `ARECONT_VISION_COSTAR` | `None` | `Arecont Vision Costar` | `None` | `None` |
 | `ASI` | `ASI` | `Applied Scientific Instrumentation` | `None` | `None` |
-| `ASUS` | `None` | `ASUS` | `Registry.ROR` | `00bxkz165` |
+| `ASUS` | `None` | `ASUS` | `Research Organization Registry (ROR)` | `00bxkz165` |
 | `BASLER` | `None` | `Basler` | `None` | `None` |
-| `BCM` | `BCM` | `Baylor College of Medicine` | `Registry.ROR` | `02pttbw34` |
-| `BU` | `BU` | `Boston University` | `Registry.ROR` | `05qwgg493` |
-| `CAJAL` | `Cajal` | `Cajal Neuroscience` | `Registry.ROR` | `05pdc0q70` |
+| `BCM` | `BCM` | `Baylor College of Medicine` | `Research Organization Registry (ROR)` | `02pttbw34` |
+| `BRUKER` | `None` | `Bruker` | `Research Organization Registry (ROR)` | `04r739x86` |
+| `BU` | `BU` | `Boston University` | `Research Organization Registry (ROR)` | `05qwgg493` |
+| `CAJAL` | `Cajal` | `Cajal Neuroscience` | `Research Organization Registry (ROR)` | `05pdc0q70` |
 | `CAMBRIDGE_TECHNOLOGY` | `None` | `Cambridge Technology` | `None` | `None` |
-| `CARL_ZEISS` | `None` | `Carl Zeiss` | `Registry.ROR` | `01xk5xs43` |
+| `CARL_ZEISS` | `None` | `Carl Zeiss` | `Research Organization Registry (ROR)` | `01xk5xs43` |
 | `CATHETER_IMPLANT_INSTITUTIONS` | `N/A` | `N/A` | `N/A` | `N/A` |
-| `CHAMPALIMAUD` | `Champalimaud` | `Champalimaud Foundation` | `Registry.ROR` | `03g001n57` |
+| `CHAMPALIMAUD` | `Champalimaud` | `Champalimaud Foundation` | `Research Organization Registry (ROR)` | `03g001n57` |
 | `CHROMA` | `None` | `Chroma` | `None` | `None` |
-| `COHERENT_SCIENTIFIC` | `None` | `Coherent Scientific` | `Registry.ROR` | `031tysd23` |
-| `COLUMBIA` | `Columbia` | `Columbia University` | `Registry.ROR` | `00hj8s172` |
+| `COHERENT_SCIENTIFIC` | `None` | `Coherent Scientific` | `Research Organization Registry (ROR)` | `031tysd23` |
+| `COLUMBIA` | `Columbia` | `Columbia University` | `Research Organization Registry (ROR)` | `00hj8s172` |
 | `COMPUTAR` | `None` | `Computar` | `None` | `None` |
 | `CONOPTICS` | `None` | `Conoptics` | `None` | `None` |
 | `CRESTOPTICS` | `None` | `CrestOptics` | `None` | `None` |
-| `CRL` | `CRL` | `Charles River Laboratories` | `Registry.ROR` | `03ndmsg87` |
+| `CRL` | `CRL` | `Charles River Laboratories` | `Research Organization Registry (ROR)` | `03ndmsg87` |
 | `CUSTOM` | `None` | `Custom` | `None` | `None` |
-| `CZI` | `CZI` | `Chan Zuckerberg Initiative` | `Registry.ROR` | `02qenvm24` |
+| `CZI` | `CZI` | `Chan Zuckerberg Initiative` | `Research Organization Registry (ROR)` | `02qenvm24` |
 | `DAQ_DEVICE_MANUFACTURERS` | `N/A` | `N/A` | `N/A` | `N/A` |
 | `DETECTOR_MANUFACTURERS` | `N/A` | `N/A` | `N/A` | `N/A` |
 | `DIGIKEY` | `None` | `DigiKey` | `None` | `None` |
 | `DODOTRONIC` | `None` | `Dodotronic` | `None` | `None` |
-| `DORIC` | `None` | `Doric` | `Registry.ROR` | `059n53q30` |
+| `DORIC` | `None` | `Doric` | `Research Organization Registry (ROR)` | `059n53q30` |
 | `EALING` | `None` | `Ealing` | `None` | `None` |
-| `EDMUND_OPTICS` | `None` | `Edmund Optics` | `Registry.ROR` | `01j1gwp17` |
-| `EMORY` | `Emory` | `Emory University` | `Registry.ROR` | `03czfpz43` |
+| `EDMUND_OPTICS` | `None` | `Edmund Optics` | `Research Organization Registry (ROR)` | `01j1gwp17` |
+| `EMORY` | `Emory` | `Emory University` | `Research Organization Registry (ROR)` | `03czfpz43` |
 | `EURESYS` | `None` | `Euresys` | `None` | `None` |
 | `FILTER_MANUFACTURERS` | `N/A` | `N/A` | `N/A` | `N/A` |
-| `FLIR` | `FLIR` | `Teledyne FLIR` | `Registry.ROR` | `01j1gwp17` |
+| `FLIR` | `FLIR` | `Teledyne FLIR` | `Research Organization Registry (ROR)` | `01j1gwp17` |
 | `FUJINON` | `None` | `Fujinon` | `None` | `None` |
 | `FUNDERS` | `N/A` | `N/A` | `N/A` | `N/A` |
-| `HAMAMATSU` | `None` | `Hamamatsu` | `Registry.ROR` | `03natb733` |
+| `HAMAMATSU` | `None` | `Hamamatsu` | `Research Organization Registry (ROR)` | `03natb733` |
 | `HAMILTON` | `None` | `Hamilton` | `None` | `None` |
-| `HUST` | `HUST` | `Huazhong University of Science and Technology` | `Registry.ROR` | `00p991c53` |
-| `IDT` | `IDT` | `Integrated DNA Technologies` | `Registry.ROR` | `009jvpf03` |
-| `IMEC` | `IMEC` | `Interuniversity Microelectronics Center` | `Registry.ROR` | `02kcbn207` |
+| `HUST` | `HUST` | `Huazhong University of Science and Technology` | `Research Organization Registry (ROR)` | `00p991c53` |
+| `IDT` | `IDT` | `Integrated DNA Technologies` | `Research Organization Registry (ROR)` | `009jvpf03` |
+| `IMEC` | `IMEC` | `Interuniversity Microelectronics Center` | `Research Organization Registry (ROR)` | `02kcbn207` |
 | `INFINITY_PHOTO_OPTICAL` | `None` | `Infinity Photo-Optical` | `None` | `None` |
-| `INVITROGEN` | `None` | `Invitrogen` | `Registry.ROR` | `03x1ewr52` |
+| `INVITROGEN` | `None` | `Invitrogen` | `Research Organization Registry (ROR)` | `03x1ewr52` |
 | `IR_ROBOT_CO` | `None` | `IR Robot Co` | `None` | `None` |
 | `ISL` | `ISL` | `ISL Products International` | `None` | `None` |
 | `ITEM` | `None` | `Item` | `None` | `None` |
-| `JANELIA` | `Janelia` | `Janelia Research Campus` | `Registry.ROR` | `013sk6x84` |
-| `JAX` | `JAX` | `Jackson Laboratory` | `Registry.ROR` | `021sy4w91` |
-| `JENOPTIK` | `None` | `Jenoptik` | `Registry.ROR` | `05g7t5c49` |
-| `JHU` | `JHU` | `Johns Hopkins University` | `Registry.ROR` | `00za53h95` |
+| `JANELIA` | `Janelia` | `Janelia Research Campus` | `Research Organization Registry (ROR)` | `013sk6x84` |
+| `JAX` | `JAX` | `Jackson Laboratory` | `Research Organization Registry (ROR)` | `021sy4w91` |
+| `JENOPTIK` | `None` | `Jenoptik` | `Research Organization Registry (ROR)` | `05g7t5c49` |
+| `JHU` | `JHU` | `Johns Hopkins University` | `Research Organization Registry (ROR)` | `00za53h95` |
 | `JULABO` | `None` | `Julabo` | `None` | `None` |
-| `KOWA` | `None` | `Kowa` | `Registry.ROR` | `03zbwg482` |
+| `KOWA` | `None` | `Kowa` | `Research Organization Registry (ROR)` | `03zbwg482` |
 | `LASER_MANUFACTURERS` | `N/A` | `N/A` | `N/A` | `N/A` |
 | `LASOS` | `LASOS` | `LASOS Lasertechnik` | `None` | `None` |
 | `LED_MANUFACTURERS` | `N/A` | `N/A` | `N/A` | `N/A` |
 | `LEICA` | `None` | `Leica` | `None` | `None` |
 | `LENS_MANUFACTURERS` | `N/A` | `N/A` | `N/A` | `N/A` |
-| `LG` | `None` | `LG` | `Registry.ROR` | `02b948n83` |
+| `LG` | `None` | `LG` | `Research Organization Registry (ROR)` | `02b948n83` |
 | `LIFECANVAS` | `None` | `LifeCanvas` | `None` | `None` |
 | `LUMENCOR` | `None` | `Lumencor` | `None` | `None` |
 | `LUMEN_DYNAMICS` | `None` | `Lumen Dynamics` | `None` | `None` |
 | `MANIPULATOR_MANUFACTURERS` | `N/A` | `N/A` | `N/A` | `N/A` |
-| `MBF` | `MBF` | `MBF Bioscience` | `Registry.ROR` | `02zynam48` |
-| `MEADOWLARK_OPTICS` | `None` | `Meadowlark Optics` | `Registry.ROR` | `00n8qbq54` |
-| `MIBR` | `MIBR` | `McGovern Institute for Brain Research` | `Registry.ROR` | `05ymca674` |
+| `MBF` | `MBF` | `MBF Bioscience` | `Research Organization Registry (ROR)` | `02zynam48` |
+| `MEADOWLARK_OPTICS` | `None` | `Meadowlark Optics` | `Research Organization Registry (ROR)` | `00n8qbq54` |
+| `MIBR` | `MIBR` | `McGovern Institute for Brain Research` | `Research Organization Registry (ROR)` | `05ymca674` |
 | `MIDOPT` | `MidOpt` | `Midwest Optical Systems, Inc.` | `None` | `None` |
-| `MIT` | `MIT` | `Massachusetts Institute of Technology` | `Registry.ROR` | `042nb2s44` |
+| `MIT` | `MIT` | `Massachusetts Institute of Technology` | `Research Organization Registry (ROR)` | `042nb2s44` |
 | `MITUTUYO` | `None` | `Mitutuyo` | `None` | `None` |
 | `MIT_BCS` | `MIT-BCS` | `MIT Department of Brain and Cognitive Sciences` | `None` | `None` |
-| `MJFF` | `MJFF` | `Michael J. Fox Foundation for Parkinson's Research` | `Registry.ROR` | `03arq3225` |
-| `MKS_NEWPORT` | `None` | `MKS Newport` | `Registry.ROR` | `00k17f049` |
+| `MJFF` | `MJFF` | `Michael J. Fox Foundation for Parkinson's Research` | `Research Organization Registry (ROR)` | `03arq3225` |
+| `MKS_NEWPORT` | `None` | `MKS Newport` | `Research Organization Registry (ROR)` | `00k17f049` |
 | `MONITOR_MANUFACTURERS` | `N/A` | `N/A` | `N/A` | `N/A` |
 | `MPI` | `MPI` | `MPI` | `None` | `None` |
-| `NATIONAL_INSTRUMENTS` | `None` | `National Instruments` | `Registry.ROR` | `026exqw73` |
+| `NATIONAL_INSTRUMENTS` | `None` | `National Instruments` | `Research Organization Registry (ROR)` | `026exqw73` |
 | `NAVITAR` | `None` | `Navitar` | `None` | `None` |
-| `NCCIH` | `NCCIH` | `National Center for Complementary and Integrative Health` | `Registry.ROR` | `00190t495` |
+| `NCCIH` | `NCCIH` | `National Center for Complementary and Integrative Health` | `Research Organization Registry (ROR)` | `00190t495` |
 | `NEURALYNX` | `None` | `NeuraLynx` | `None` | `None` |
 | `NEUROPHOTOMETRICS` | `None` | `Neurophotometrics` | `None` | `None` |
 | `NEW_SCALE_TECHNOLOGIES` | `None` | `New Scale Technologies` | `None` | `None` |
-| `NIKON` | `None` | `Nikon` | `Registry.ROR` | `0280y9h11` |
-| `NIMH` | `NIMH` | `National Institute of Mental Health` | `Registry.ROR` | `04xeg9z08` |
-| `NINDS` | `NINDS` | `National Institute of Neurological Disorders and Stroke` | `Registry.ROR` | `01s5ya894` |
+| `NIKON` | `None` | `Nikon` | `Research Organization Registry (ROR)` | `0280y9h11` |
+| `NIMH` | `NIMH` | `National Institute of Mental Health` | `Research Organization Registry (ROR)` | `04xeg9z08` |
+| `NINDS` | `NINDS` | `National Institute of Neurological Disorders and Stroke` | `Research Organization Registry (ROR)` | `01s5ya894` |
 | `NRESEARCH_INC` | `None` | `NResearch Inc` | `None` | `None` |
-| `NYU` | `NYU` | `New York University` | `Registry.ROR` | `0190ak572` |
-| `OEPS` | `OEPS` | `Open Ephys Production Site` | `Registry.ROR` | `007rkz355` |
-| `OLYMPUS` | `None` | `Olympus` | `Registry.ROR` | `02vcdte90` |
+| `NYU` | `NYU` | `New York University` | `Research Organization Registry (ROR)` | `0190ak572` |
+| `OEPS` | `OEPS` | `Open Ephys Production Site` | `Research Organization Registry (ROR)` | `007rkz355` |
+| `OLYMPUS` | `None` | `Olympus` | `Research Organization Registry (ROR)` | `02vcdte90` |
 | `OPTOTUNE` | `None` | `Optotune` | `None` | `None` |
 | `OTHER` | `None` | `Other` | `None` | `None` |
 | `OXXIUS` | `None` | `Oxxius` | `None` | `None` |
@@ -114,25 +115,25 @@ Organization
 | `SEMROCK` | `None` | `Semrock` | `None` | `None` |
 | `SICGEN` | `None` | `SICGEN` | `None` | `None` |
 | `SIGMA_ALDRICH` | `None` | `Sigma-Aldrich` | `None` | `None` |
-| `SIMONS_FOUNDATION` | `None` | `Simons Foundation` | `Registry.ROR` | `01cmst727` |
+| `SIMONS_FOUNDATION` | `None` | `Simons Foundation` | `Research Organization Registry (ROR)` | `01cmst727` |
 | `SPEAKER_MANUFACTURERS` | `N/A` | `N/A` | `N/A` | `N/A` |
-| `SPECTRA_PHYSICS` | `None` | `Spectra-Physics` | `Registry.ROR` | `02ad9kp97` |
+| `SPECTRA_PHYSICS` | `None` | `Spectra-Physics` | `Research Organization Registry (ROR)` | `02ad9kp97` |
 | `SPINNAKER` | `None` | `Spinnaker` | `None` | `None` |
 | `SUBJECT_SOURCES` | `N/A` | `N/A` | `N/A` | `N/A` |
 | `TAMRON` | `None` | `Tamron` | `None` | `None` |
 | `TELEDYNE_VISION_SOLUTIONS` | `None` | `Teledyne Vision Solutions` | `None` | `None` |
-| `TE_CONNECTIVITY` | `None` | `TE Connectivity` | `Registry.ROR` | `034frgp20` |
-| `THERMO_FISHER_SCIENTIFIC` | `None` | `Thermo Fisher Scientific` | `Registry.ROR` | `03x1ewr52` |
+| `TE_CONNECTIVITY` | `None` | `TE Connectivity` | `Research Organization Registry (ROR)` | `034frgp20` |
+| `THERMO_FISHER_SCIENTIFIC` | `None` | `Thermo Fisher Scientific` | `Research Organization Registry (ROR)` | `03x1ewr52` |
 | `THE_IMAGING_SOURCE` | `None` | `The Imaging Source` | `None` | `None` |
 | `THE_LEE_COMPANY` | `None` | `The Lee Company` | `None` | `None` |
-| `THORLABS` | `None` | `Thorlabs` | `Registry.ROR` | `04gsnvb07` |
+| `THORLABS` | `None` | `Thorlabs` | `Research Organization Registry (ROR)` | `04gsnvb07` |
 | `TMC` | `TMC` | `Technical Manufacturing Corporation` | `None` | `None` |
 | `TRANSDUCER_TECHNIQUES` | `None` | `Transducer Techniques` | `None` | `None` |
-| `TWCF` | `TWCF` | `Templeton World Charity Foundation` | `Registry.ROR` | `00x0z1472` |
+| `TWCF` | `TWCF` | `Templeton World Charity Foundation` | `Research Organization Registry (ROR)` | `00x0z1472` |
 | `TYMPHANY` | `None` | `Tymphany` | `None` | `None` |
-| `UCSD` | `UCSD` | `University of California, San Diego` | `Registry.ROR` | `0168r3w48` |
+| `UCSD` | `UCSD` | `University of California, San Diego` | `Research Organization Registry (ROR)` | `0168r3w48` |
 | `UNKNOWN` | `UNKNOWN` | `Unknown` | `None` | `None` |
-| `UPENN` | `UPENN` | `University of Pennsylvania` | `Registry.ROR` | `00b30xv10` |
+| `UPENN` | `UPENN` | `University of Pennsylvania` | `Research Organization Registry (ROR)` | `00b30xv10` |
 | `VIEWORKS` | `None` | `Vieworks` | `None` | `None` |
 | `VORTRAN` | `None` | `Vortran` | `None` | `None` |
 

aind_data_schema-2.6.0/docs/source/aind_data_schema_models/species.md

@@ -0,0 +1,35 @@
+# Species
+
+## Model definitions
+
+### Species
+
+Species
+
+| Name | name | common_name | registry | registry_identifier |
+|------|------|------|------|------|
+| `ALPACA` | `Vicuna pacos` | `Alpaca` | `National Center for Biotechnology Information (NCBI)` | `NCBI:txid30538` |
+| `CHICKEN` | `Gallus gallus` | `Chicken` | `National Center for Biotechnology Information (NCBI)` | `NCBI:txid9031` |
+| `COMMON_MARMOSET` | `Callithrix jacchus` | `Common marmoset` | `National Center for Biotechnology Information (NCBI)` | `NCBI:txid9483` |
+| `DONKEY` | `Equus asinus` | `Donkey` | `National Center for Biotechnology Information (NCBI)` | `NCBI:txid9793` |
+| `EUROPEAN_RABBIT` | `Oryctolagus cuniculus` | `European rabbit` | `National Center for Biotechnology Information (NCBI)` | `NCBI:txid9986` |
+| `GOAT` | `Carpa hircus` | `Goat` | `National Center for Biotechnology Information (NCBI)` | `NCBI:txid9925` |
+| `GUINEA_PIG` | `Cavia porcellus` | `Guinea pig` | `National Center for Biotechnology Information (NCBI)` | `NCBI:txid10141` |
+| `HOUSE_MOUSE` | `Mus musculus` | `House mouse` | `National Center for Biotechnology Information (NCBI)` | `NCBI:txid10090` |
+| `HUMAN` | `Homo sapiens` | `Human` | `National Center for Biotechnology Information (NCBI)` | `NCBI:txid9606` |
+| `LLAMA` | `Lama glama` | `Llama` | `National Center for Biotechnology Information (NCBI)` | `NCBI:txid9844` |
+| `NORWAY_RAT` | `Rattus norvegicus` | `Norway rat` | `National Center for Biotechnology Information (NCBI)` | `NCBI:txid10116` |
+| `RHESUS_MACAQUE` | `Macaca mulatta` | `Rhesus macaque` | `National Center for Biotechnology Information (NCBI)` | `NCBI:txid9544` |
+
+
+### Strain
+
+Strain
+
+| Name | name | species | registry | registry_identifier |
+|------|------|------|------|------|
+| `BALB_C` | `BALB/c` | `Mus musculus` | `Mouse Genome Informatics (MGI)` | `MGI:2159737` |
+| `C57BL_6J` | `C57BL/6J` | `Mus musculus` | `Mouse Genome Informatics (MGI)` | `MGI:3028467` |
+| `UNKNOWN` | `Unknown` | `Mus musculus` | `None` | `None` |
+
+

{aind_data_schema-2.5.0 → aind_data_schema-2.6.0}/docs/source/components/configs.md

@@ -68,10 +68,15 @@ Configuration of detector settings
 
 | Field | Type | Title (Description) |
 |-------|------|-------------|
-| `exposure_time` | `float` | Exposure time  |
+| `exposure_time` | `Optional[float]` | Exposure time  |
 | `exposure_time_unit` | [TimeUnit](../aind_data_schema_models/units.md#timeunit) | Exposure time unit  |
 | `trigger_type` | [TriggerType](#triggertype) | Trigger type  |
 | `compression` | Optional[[Code](identifiers.md#code)] | Compression (Compression algorithm used during acquisition) |
+| `crop_offset_x` | `Optional[int]` | Crop offset x (Overrides any value set in the Instrument metadata) |
+| `crop_offset_y` | `Optional[int]` | Crop offset y (Overrides any value set in the Instrument metadata) |
+| `crop_width` | `Optional[int]` | Crop width (Overrides any value set in the Instrument metadata) |
+| `crop_height` | `Optional[int]` | Crop height (Overrides any value set in the Instrument metadata) |
+| `crop_unit` | Optional[[SizeUnit](../aind_data_schema_models/units.md#sizeunit)] | Crop size unit  |
 | `device_name` | `str` | Device name (Must match a device defined in the instrument.json) |
 
 
@@ -143,7 +148,7 @@ Configuration of an imaging instrument
 
 | Field | Type | Title (Description) |
 |-------|------|-------------|
-| `channels` | List[[Channel](#channel) or [SlapChannel](#slapchannel)] |   |
+| `channels` | `List[typing.Annotated[aind_data_schema.components.configs.Channel, FieldInfo(annotation=NoneType, required=True, discriminator='object_type')]]` |   |
 | `coordinate_system` | Optional[[CoordinateSystem](coordinates.md#coordinatesystem)] | Coordinate system (Required for ImageSPIM objects and when the imaging coordinate system differs from the Acquisition.coordinate_system) |
 | `images` | List[[PlanarImage](#planarimage) or [PlanarImageStack](#planarimagestack) or [ImageSPIM](#imagespim)] | Images  |
 | `sampling_strategy` | Optional[[SamplingStrategy](#samplingstrategy)] | Sampling strategy  |
@@ -312,6 +317,18 @@ Configuration for mouse platforms
 | `device_name` | `str` | Device name (Must match a device defined in the instrument.json) |
 
 
+### NeuronStructure
+
+Neuronal structures captured in imaging planes
+
+| Name | Value |
+|------|-------|
+| `SOMA` | `Soma` |
+| `DENDRITE` | `Dendrite` |
+| `AXON` | `Axon` |
+| `OTHER` | `Other` |
+
+
 ### OlfactometerChannelInfo
 
 Configuration of a channel in an olfactometer
@@ -350,7 +367,7 @@ Description of an N-D image acquired in a specific imaging plane
 
 | Field | Type | Title (Description) |
 |-------|------|-------------|
-| `planes` | List[[Plane](#plane) or [CoupledPlane](#coupledplane) or [SlapPlane](#slapplane)] | Imaging planes  |
+| `planes` | List[[Plane](#plane) or [CoupledPlane](#coupledplane) or [Slap2Plane](#slap2plane)] | Imaging planes  |
 | `channel_name` | `str` | Channel name  |
 | `dimensions_unit` | [SizeUnit](../aind_data_schema_models/units.md#sizeunit) | Dimensions unit  |
 | `image_to_acquisition_transform` | List[[Translation](coordinates.md#translation) or [Rotation](coordinates.md#rotation) or [Scale](coordinates.md#scale) or [Affine](coordinates.md#affine)] | Image to acquisition transform (Position, rotation, and scale of the image. Note that depth should be in the planes.) |
@@ -368,7 +385,7 @@ Description of a stack of images acquired in a specific imaging plane
 | `depth_end` | `float` | Ending depth  |
 | `depth_step` | `float` | Step size  |
 | `depth_unit` | [SizeUnit](../aind_data_schema_models/units.md#sizeunit) | Depth unit  |
-| `planes` | List[[Plane](#plane) or [CoupledPlane](#coupledplane) or [SlapPlane](#slapplane)] | Imaging planes  |
+| `planes` | List[[Plane](#plane) or [CoupledPlane](#coupledplane) or [Slap2Plane](#slap2plane)] | Imaging planes  |
 | `channel_name` | `str` | Channel name  |
 | `dimensions_unit` | [SizeUnit](../aind_data_schema_models/units.md#sizeunit) | Dimensions unit  |
 | `image_to_acquisition_transform` | List[[Translation](coordinates.md#translation) or [Rotation](coordinates.md#rotation) or [Scale](coordinates.md#scale) or [Affine](coordinates.md#affine)] | Image to acquisition transform (Position, rotation, and scale of the image. Note that depth should be in the planes.) |
@@ -449,50 +466,21 @@ Description of an image sampling strategy
 | `frame_rate_unit` | [FrequencyUnit](../aind_data_schema_models/units.md#frequencyunit) | Frame rate unit  |
 
 
-### SlapAcquisitionType
-
-Type of slap acquisition
-
-| Name | Value |
-|------|-------|
-| `PARENT` | `Parent` |
-| `BRANCH` | `Branch` |
-
-
-### SlapChannel
-
-Configuration of a channel for Slap
-
-| Field | Type | Title (Description) |
-|-------|------|-------------|
-| `dilation` | `int` | Dilation  |
-| `dilation_unit` | [SizeUnit](../aind_data_schema_models/units.md#sizeunit) | Dilation unit  |
-| `description` | `Optional[str]` | Description  |
-| `channel_name` | `str` | Channel  |
-| `intended_measurement` | `Optional[str]` | Intended measurement (What signal is this channel measuring) |
-| `detector` | [DetectorConfig](#detectorconfig) | Detector configuration  |
-| `additional_device_names` | Optional[List[[DeviceConfig](#deviceconfig)]] | Additional device names (Mirrors, dichroics, etc) |
-| `light_sources` | List[[LaserConfig](#laserconfig) or [LightEmittingDiodeConfig](#lightemittingdiodeconfig)] | Light source configurations  |
-| `variable_power` | `Optional[bool]` | Variable power (Set to true when the power varies across Planes -- put the power in the Plane.power field) |
-| `excitation_filters` | Optional[List[[DeviceConfig](#deviceconfig)]] | Excitation filters  |
-| `emission_filters` | Optional[List[[DeviceConfig](#deviceconfig)]] | Emission filters  |
-| `emission_wavelength` | `Optional[int]` | Emission wavelength  |
-| `emission_wavelength_unit` | Optional[[SizeUnit](../aind_data_schema_models/units.md#sizeunit)] | Emission wavelength unit  |
-
-
-### SlapPlane
+### Slap2Plane
 
-Configuration of an imagine plane on a Slap microscope
+Configuration of a SLAP2 imaging plane (all imaging ROIs of a specific acquisition type at a particular depth)
 
 | Field | Type | Title (Description) |
 |-------|------|-------------|
-| `dmd_dilation_x` | `int` | DMD Dilation X (pixels)  |
-| `dmd_dilation_y` | `int` | DMD Dilation Y (pixels)  |
-| `dilation_unit` | [SizeUnit](../aind_data_schema_models/units.md#sizeunit) | Dilation unit  |
-| `slap_acquisition_type` | [SlapAcquisitionType](#slapacquisitiontype) | Slap experiment type  |
-| `target_neuron` | `Optional[str]` | Target neuron  |
-| `target_branch` | `Optional[str]` | Target branch  |
-| `path_to_array_of_frame_rates` | `AssetPath` | Array of frame rates (Relative path from metadata json to file) |
+| `slap2_acquisition_type` | {Slap2AcquisitionType} | SLAP2 ROI acquisition type  |
+| `specimen_id` | `Optional[str]` | Specimen ID (Unique index identifying the cell being imaged: <subject_id>_###) |
+| `fov_index` | `Optional[int]` | Field of view index (For FOVs that are imaged multiple times, assign a shared index to each instance of the FOV) |
+| `structure_types` | Optional[List[[NeuronStructure](#neuronstructure)]] | Structure type  |
+| `target_name` | `Optional[str]` | Name of imaged target  |
+| `y_dilations` | `List[int]` | Unique Y dilations  |
+| `y_dilations_unit` | [SizeUnit](../aind_data_schema_models/units.md#sizeunit) | Dilation unit  |
+| `frame_rates` | `List[float]` | Unique frame rates  |
+| `frame_rates_unit` | [FrequencyUnit](../aind_data_schema_models/units.md#frequencyunit) | Frame rate unit  |
 | `depth` | `float` | Depth  |
 | `depth_unit` | [SizeUnit](../aind_data_schema_models/units.md#sizeunit) | Depth unit  |
 | `power` | `float` | Power  |
@@ -541,6 +529,7 @@ Types of detector triggers
 |------|-------|
 | `INTERNAL` | `Internal` |
 | `EXTERNAL` | `External` |
+| `ANALOG` | `Analog` |
 
 
 ### Valence

{aind_data_schema-2.5.0 → aind_data_schema-2.6.0}/docs/source/components/devices.md

@@ -275,19 +275,15 @@ Description of a Digital Micromirror Device (DMD)
 | Field | Type | Title (Description) |
 |-------|------|-------------|
 | `max_dmd_patterns` | `int` | Max DMD patterns  |
-| `double_bounce_design` | `bool` | Double bounce design  |
 | `invert_pixel_values` | `bool` | Invert pixel values  |
 | `motion_padding_x` | `int` | Motion padding X (pixels)  |
 | `motion_padding_y` | `int` | Motion padding Y (pixels)  |
 | `padding_unit` | [SizeUnit](../aind_data_schema_models/units.md#sizeunit) | Padding unit  |
-| `pixel_size` | `decimal.Decimal` | DMD Pixel size  |
-| `pixel_size_unit` | [SizeUnit](../aind_data_schema_models/units.md#sizeunit) | Pixel size unit  |
-| `start_phase` | `decimal.Decimal` | DMD Start phase (fraction of cycle)  |
-| `dmd_flip` | `bool` | DMD Flip  |
-| `dmd_curtain` | `List[decimal.Decimal]` | DMD Curtain  |
-| `dmd_curtain_unit` | [SizeUnit](../aind_data_schema_models/units.md#sizeunit) | dmd_curtain_unit  |
-| `line_shear` | `List[int]` | Line shear (pixels)  |
-| `line_shear_unit` | [SizeUnit](../aind_data_schema_models/units.md#sizeunit) | Line shear unit  |
+| `pixel_size` | `float` | DMD Pixel size (fraction of line scan period)  |
+| `start_phase` | `float` | DMD Start phase (fraction of line scan period)  |
+| `dmd_curtain` | `List[float]` | DMD Curtain (fraction of DMD scan period)  |
+| `line_shear_anchors` | `List[float]` | Line shear anchors at top and bottom of field of view (pixels)  |
+| `line_shear_anchors_unit` | [SizeUnit](../aind_data_schema_models/units.md#sizeunit) | Line shear anchors unit  |
 | `name` | `str` | Device name  |
 | `serial_number` | `Optional[str]` | Serial number  |
 | `manufacturer` | Optional[[Organization](../aind_data_schema_models/organizations.md#organization)] | Manufacturer  |
@@ -340,7 +336,7 @@ Description of an enclosure
 
 ### EphysAssembly
 
-Named assembly for combining a manipulator and ephys probes
+Named assembly for combining a manipulator and extracellular ephys probes
 
 | Field | Type | Title (Description) |
 |-------|------|-------------|
@@ -351,7 +347,7 @@ Named assembly for combining a manipulator and ephys probes
 
 ### EphysProbe
 
-Probe used in an ephys experiment
+Probe used in an extracellular ephys experiment
 
 | Field | Type | Title (Description) |
 |-------|------|-------------|
@@ -760,7 +756,7 @@ description of a Olfactometer channel
 |-------|------|-------------|
 | `channel_index` | `int` | Channel index  |
 | `channel_type` | [OlfactometerChannelType](#olfactometerchanneltype) | Channel type  |
-| `flow_capacity` | `100 or 1000` | Flow capacity  |
+| `flow_capacity` | `int` | Flow capacity  |
 | `flow_unit` | `str` | Flow unit  |
 
 
@@ -781,7 +777,7 @@ Multichannel electrophysiology DAQ
 | Field | Type | Title (Description) |
 |-------|------|-------------|
 | `ports` | List[[ProbePort](#probeport)] | Acquisition board ports  |
-| `data_interface` | `"DataInterface.USB"` |   |
+| `data_interface` | `"USB"` |   |
 | `manufacturer` | [Organization](../aind_data_schema_models/organizations.md#organization) |   |
 | `channels` | List[[DAQChannel](#daqchannel)] | DAQ channels  |
 | `firmware_version` | `Optional[str]` | Firmware version  |
@@ -793,6 +789,17 @@ Multichannel electrophysiology DAQ
 | `notes` | `Optional[str]` | Notes  |
 
 
+### PatchClampEphysAssembly
+
+Assembly combining a manipulator and headstage used for Patch clamp ephys
+
+| Field | Type | Title (Description) |
+|-------|------|-------------|
+| `name` | `str` | Patch clamp Assembly Name  |
+| `manipulator` | [Manipulator](#manipulator) | Manipulator  |
+| `headstage` | [Device](#device) | Headstage  |
+
+
 ### PockelsCell
 
 Description of a Pockels Cell

{aind_data_schema-2.5.0 → aind_data_schema-2.6.0}/docs/source/components/identifiers.md

@@ -12,7 +12,7 @@ Code or script identifier
 | `name` | `Optional[str]` | Name  |
 | `version` | `Optional[str]` | Code version  |
 | `container` | Optional[[Container](#container)] | Container  |
-| `run_script` | `Optional[pathlib._local.Path]` | Run script (Path to run script) |
+| `run_script` | `Optional[pathlib.Path]` | Run script (Path to run script) |
 | `language` | `Optional[str]` | Programming language (Programming language used) |
 | `language_version` | `Optional[str]` | Programming language version  |
 | `input_data` | Optional[List[[DataAsset](#dataasset) or [CombinedData](#combineddata)]] | Input data (Input data used in the code or script) |

{aind_data_schema-2.5.0 → aind_data_schema-2.6.0}/docs/source/components/subjects.md

@@ -58,6 +58,7 @@ Description of a human subject
 
 | Field | Type | Title (Description) |
 |-------|------|-------------|
+| `species` | `aind_data_schema_models.species.SpeciesModel` | Species  |
 | `sex` | [Sex](#sex) | Sex  |
 | `year_of_birth` | `int` | Year of birth  |
 | `source` | [Organization](../aind_data_schema_models/organizations.md#organization) | Source (Where the subject was acquired from.) |
@@ -73,6 +74,17 @@ Description of vivarium light cycle times
 | `lights_off_time` | `datetime.time` | Lights off time (Time in UTC that lights were turned off) |
 
 
+### MatingStatus
+
+Subject mating status
+
+| Name | Value |
+|------|-------|
+| `MATED` | `Mated` |
+| `UNMATED` | `Un-mated` |
+| `UNKNOWN` | `Unknown` |
+
+
 ### MouseSubject
 
 Description of a mouse subject
@@ -93,6 +105,20 @@ Description of a mouse subject
 | `rrid` | Optional[[PIDName](../aind_data_schema_models/pid_names.md#pidname)] | RRID (RRID of mouse if acquired from supplier) |
 
 
+### NonHumanPrimateSubject
+
+Description of a non-human primate subject
+
+| Field | Type | Title (Description) |
+|-------|------|-------------|
+| `species` | [Species](../aind_data_schema_models/species.md#species) | species  |
+| `sex` | [Sex](#sex) | Sex  |
+| `date_of_birth` | `Optional[datetime.date]` | Date of birth  |
+| `year_of_birth` | `int` | Year of birth  |
+| `mating_status` | [MatingStatus](#matingstatus) | Mating status  |
+| `source` | [Organization](../aind_data_schema_models/organizations.md#organization) | Source (Where the subject was acquired from.) |
+
+
 ### Sex
 
 Subject sex name

{aind_data_schema-2.5.0 → aind_data_schema-2.6.0}/docs/source/instrument.md

@@ -64,4 +64,4 @@ Description of an instrument
 | `temperature_control` | `Optional[bool]` | Temperature control (Does the instrument maintain a constant temperature?) |
 | `notes` | `Optional[str]` | Notes  |
 | `connections` | List[[Connection](components/connections.md#connection)] | Connections (List of all connections between devices in the instrument) |
-| `components` | List[[Monitor](components/devices.md#monitor) or [Olfactometer](components/devices.md#olfactometer) or [LickSpout](components/devices.md#lickspout) or [LickSpoutAssembly](components/devices.md#lickspoutassembly) or [AirPuffDevice](components/devices.md#airpuffdevice) or [Speaker](components/devices.md#speaker) or [CameraAssembly](components/devices.md#cameraassembly) or [Enclosure](components/devices.md#enclosure) or [EphysAssembly](components/devices.md#ephysassembly) or [FiberAssembly](components/devices.md#fiberassembly) or [LaserAssembly](components/devices.md#laserassembly) or [FiberPatchCord](components/devices.md#fiberpatchcord) or [Laser](components/devices.md#laser) or [LightEmittingDiode](components/devices.md#lightemittingdiode) or [Lamp](components/devices.md#lamp) or [Detector](components/devices.md#detector) or [Camera](components/devices.md#camera) or [Objective](components/devices.md#objective) or [Scanner](components/devices.md#scanner) or [Filter](components/devices.md#filter) or [Lens](components/devices.md#lens) or [DigitalMicromirrorDevice](components/devices.md#digitalmicromirrordevice) or [PolygonalScanner](components/devices.md#polygonalscanner) or [PockelsCell](components/devices.md#pockelscell) or [HarpDevice](components/devices.md#harpdevice) or [NeuropixelsBasestation](components/devices.md#neuropixelsbasestation) or [OpenEphysAcquisitionBoard](components/devices.md#openephysacquisitionboard) or [MotorizedStage](components/devices.md#motorizedstage) or [ScanningStage](components/devices.md#scanningstage) or [AdditionalImagingDevice](components/devices.md#additionalimagingdevice) or [Disc](components/devices.md#disc) or [Wheel](components/devices.md#wheel) or [Tube](components/devices.md#tube) or [Treadmill](components/devices.md#treadmill) or [Arena](components/devices.md#arena) or [DAQDevice](components/devices.md#daqdevice) or [Computer](components/devices.md#computer) or [Microscope](components/devices.md#microscope) or [Device](components/devices.md#device)] | Components (List of all devices in the instrument) |
+| `components` | List[[Monitor](components/devices.md#monitor) or [Olfactometer](components/devices.md#olfactometer) or [LickSpout](components/devices.md#lickspout) or [LickSpoutAssembly](components/devices.md#lickspoutassembly) or [AirPuffDevice](components/devices.md#airpuffdevice) or [Speaker](components/devices.md#speaker) or [CameraAssembly](components/devices.md#cameraassembly) or [Enclosure](components/devices.md#enclosure) or [EphysAssembly](components/devices.md#ephysassembly) or [FiberAssembly](components/devices.md#fiberassembly) or [LaserAssembly](components/devices.md#laserassembly) or [FiberPatchCord](components/devices.md#fiberpatchcord) or [Laser](components/devices.md#laser) or [LightEmittingDiode](components/devices.md#lightemittingdiode) or [Lamp](components/devices.md#lamp) or [Detector](components/devices.md#detector) or [Camera](components/devices.md#camera) or [Objective](components/devices.md#objective) or [Scanner](components/devices.md#scanner) or [Filter](components/devices.md#filter) or [Lens](components/devices.md#lens) or [DigitalMicromirrorDevice](components/devices.md#digitalmicromirrordevice) or [PatchClampEphysAssembly](components/devices.md#patchclampephysassembly) or [PolygonalScanner](components/devices.md#polygonalscanner) or [PockelsCell](components/devices.md#pockelscell) or [HarpDevice](components/devices.md#harpdevice) or [NeuropixelsBasestation](components/devices.md#neuropixelsbasestation) or [OpenEphysAcquisitionBoard](components/devices.md#openephysacquisitionboard) or [MotorizedStage](components/devices.md#motorizedstage) or [ScanningStage](components/devices.md#scanningstage) or [AdditionalImagingDevice](components/devices.md#additionalimagingdevice) or [Disc](components/devices.md#disc) or [Wheel](components/devices.md#wheel) or [Tube](components/devices.md#tube) or [Treadmill](components/devices.md#treadmill) or [Arena](components/devices.md#arena) or [DAQDevice](components/devices.md#daqdevice) or [Computer](components/devices.md#computer) or [Microscope](components/devices.md#microscope) or [Device](components/devices.md#device)] | Components (List of all devices in the instrument) |

{aind_data_schema-2.5.0 → aind_data_schema-2.6.0}/docs/source/procedures.md

@@ -8,7 +8,9 @@ The `procedures.json` file contains anything done to the subject or specimen pri
 
 **Subject** procedures are performed on a live subject (e.g. injections, surgeries, implants, perfusions, etc.) whereas **specimen** procedures are performed on tissue extracted after perfusion (e.g. tissue processing, immunolabeling, sectioning, etc.).
 
-Sectioned specimens must have a unique number appended as a suffix to the subject ID: `<subject_id>_<###>`.
+### SpecimenProcedure.specimen_id
+
+After perfusion or death we refer to specimens by the `specimen_id` field. When the tissue has not been sectioned in some way the `specimen_id` should be identical to the `subject_id`. Sectioned specimens should have a unique number appended as a suffix to the subject ID: `<subject_id>_<###>`. 
 
 ## Examples
 

{aind_data_schema-2.5.0 → aind_data_schema-2.6.0}/docs/source/validation.md

@@ -4,7 +4,15 @@ To ensure that your metadata is valid you need to construct the full [Metadata](
 
 ## Instrument and Acquisition
 
-If you are validating your `Instrument` and `Acquisition` on your rig, you may not have access to the other metadata files like the procedures. To allow for partial validation of these files we include an `InstrumentAcquisitionCompatibility` class. Construct it as follows:
+If you are validating your `Instrument` and `Acquisition` on your rig, you may not have access to the other metadata files like the procedures. To allow for partial validation of these files we include an `InstrumentAcquisitionCompatibility` class.
+
+The following consistency rules are enforced:
+
+- `Acquisition.instrument_id` must match `Instrument.instrument_id`
+- Device names in `DataStream.active_devices` must match device names in the `Instrument`
+- Device names in `StimulusEpoch.active_devices` must match device names in the `Instrument`
+
+Construct it as follows:
 
 ```{python}
 from aind_data_schema.utils.compatibility_check import InstrumentAcquisitionCompatibility

{aind_data_schema-2.5.0 → aind_data_schema-2.6.0}/examples/aibs_smartspim_instrument.py

@@ -1,4 +1,4 @@
-""" example SmartSPIM instrument """
+"""example SmartSPIM instrument"""
 
 import argparse
 import datetime

{aind_data_schema-2.5.0 → aind_data_schema-2.6.0}/examples/aibs_smartspim_procedures.py

@@ -1,4 +1,4 @@
-""" example for specimen procedures """
+"""example for specimen procedures"""
 
 import argparse
 from datetime import date

{aind_data_schema-2.5.0 → aind_data_schema-2.6.0}/examples/aind_smartspim_instrument.py

@@ -1,4 +1,4 @@
-""" example SmartSPIM instrument """
+"""example SmartSPIM instrument"""
 
 import argparse
 from datetime import date