aind-data-schema 2.4.0__tar.gz → 2.5.1__tar.gz

{aind_data_schema-2.4.0 → aind_data_schema-2.5.1}/.github/workflows/update_docs.yml

@@ -62,9 +62,6 @@ jobs:
         run: |
           sudo apt install graphviz libgraphviz-dev -y
           python -m pip install -e .[dev] -e .[docs] --no-cache-dir
-      - name: Generate new rst files
-        run: |
-          sphinx-apidoc -o docs/source/ src
       - name: Commit changes
         uses: EndBug/add-and-commit@v9
         with:

{aind_data_schema-2.4.0 → aind_data_schema-2.5.1}/CONTRIBUTING.md

@@ -179,6 +179,6 @@ When you are ready to open a pull request, please link any relevant issues and r
 - Manually increment the major/minor/patch versions of the core files as needed
 - Push the branch and open a PR into main
 - After this push, any last minute changes to the release-vX.Y.Z will have to done to via a PR
-- After review, use a merge commit to merge into main
-- Open a PR from main back into dev so they're synced again
+- After review, use a **merge commit** to merge into main, DO NOT SQUASH INTO MAIN
+- Open a PR from main back into dev so they're synced again, bypass the rules to use a **merge commit**, DO NOT SQUASH MAIN INTO DEV
 - Create a Github release with the corresponding tag, modify the auto-generated release notes to focus on the major changes that occurred

{aind_data_schema-2.4.0/src/aind_data_schema.egg-info → aind_data_schema-2.5.1}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: aind-data-schema
-Version: 2.4.0
+Version: 2.5.1
 Summary: A library that defines AIND data schema and validates JSON files.
 License: MIT
 Classifier: Programming Language :: Python :: 3
@@ -9,12 +9,14 @@ Description-Content-Type: text/markdown
 License-File: LICENSE
 Requires-Dist: aind-data-schema-models<6,>=5
 Requires-Dist: pydantic<2.12,>=2.7
+Requires-Dist: pydantic-extra-types
 Provides-Extra: dev
 Requires-Dist: aind_data_schema[linters]; extra == "dev"
 Requires-Dist: pydantic!=2.9.0,!=2.9.1,>=2.7; extra == "dev"
 Requires-Dist: scipy; extra == "dev"
 Requires-Dist: dictdiffer; extra == "dev"
 Requires-Dist: semver; extra == "dev"
+Requires-Dist: argparse; extra == "dev"
 Provides-Extra: linters
 Requires-Dist: codespell; extra == "linters"
 Requires-Dist: black; extra == "linters"

{aind_data_schema-2.4.0 → aind_data_schema-2.5.1}/docs/source/acquisition.md

@@ -79,7 +79,8 @@ 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  |
+| `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` | `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) |
@@ -108,7 +109,7 @@ Details about the subject during an acquisition
 | `animal_weight_post` | `Optional[decimal.Decimal]` | Animal weight (g) (Animal weight after procedure) |
 | `weight_unit` | [MassUnit](aind_data_schema_models/units.md#massunit) | Weight unit  |
 | `anaesthesia` | Optional[[Anaesthetic](components/surgery_procedures.md#anaesthetic)] | Anaesthesia (Anaesthesia present during entire acquisition, use Manipulation for partial anaesthesia) |
-| `mouse_platform_name` | `str` | Mouse platform  |
+| `mouse_platform_name` | `str` | Mouse platform (The surface that the mouse is on during the acquisition) |
 | `reward_consumed_total` | `Optional[decimal.Decimal]` | Total reward consumed (mL)  |
 | `reward_consumed_unit` | Optional[[VolumeUnit](aind_data_schema_models/units.md#volumeunit)] | Reward consumed unit  |
 
@@ -126,7 +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 [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 [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) |
 | `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)) |
 
 
@@ -149,7 +150,7 @@ Summary of a StimulusEpoch
 
 | Field | Type | Title (Description) |
 |-------|------|-------------|
-| `output_parameters` | `dict` | Additional metrics  |
+| `output_parameters` | `Optional[dict]` | Additional metrics  |
 | `reward_consumed_during_epoch` | `Optional[decimal.Decimal]` | Reward consumed during training (uL)  |
 | `reward_consumed_unit` | Optional[[VolumeUnit](aind_data_schema_models/units.md#volumeunit)] | Reward consumed unit  |
 | `trials_total` | `Optional[int]` | Total trials  |

{aind_data_schema-2.4.0 → aind_data_schema-2.5.1}/docs/source/aind_data_schema_models/coordinates.md

@@ -64,13 +64,14 @@ Origin positions for coordinate systems
 | `ORIGIN` | `Origin` |
 | `BREGMA` | `Bregma` |
 | `LAMBDA` | `Lambda` |
-| `C1` | `C1` |
-| `C2` | `C2` |
-| `C3` | `C3` |
-| `C4` | `C4` |
-| `C5` | `C5` |
-| `C6` | `C6` |
-| `C7` | `C7` |
+| `BETWEEN_C1_C2` | `Between_C1-C2` |
+| `BETWEEN_C2_C3` | `Between_C2-C3` |
+| `BETWEEN_C3_C4` | `Between_C3-C4` |
+| `BETWEEN_C4_C5` | `Between_C4-C5` |
+| `BETWEEN_C6_C7` | `Between_C6-C7` |
+| `BETWEEN_C7_C8` | `Between_C7-C8` |
+| `BETWEEN_C8_T1` | `Between_C8-T1` |
+| `BETWEEN_T1_T2` | `Between_T1-T2` |
 | `TIP` | `Tip` |
 | `FRONT_CENTER` | `Front_center` |
 | `ARENA_CENTER` | `Arena_center` |

{aind_data_schema-2.4.0 → aind_data_schema-2.5.1}/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-2.4.0 → aind_data_schema-2.5.1}/docs/source/aind_data_schema_models/modalities.md

@@ -8,19 +8,25 @@ Modalities
 
 | Name | name | abbreviation |
 |------|------|------|
+| `BARSEQ` | `Barcoded anatomy resolved by sequencing` | `BARseq` |
 | `BEHAVIOR` | `Behavior` | `behavior` |
 | `BEHAVIOR_VIDEOS` | `Behavior videos` | `behavior-videos` |
+| `BRIGHTFIELD` | `Brightfield microscopy` | `brightfield` |
 | `CONFOCAL` | `Confocal microscopy` | `confocal` |
 | `ECEPHYS` | `Extracellular electrophysiology` | `ecephys` |
+| `EM` | `Electron microscopy` | `EM` |
 | `EMG` | `Electromyography` | `EMG` |
 | `FIB` | `Fiber photometry` | `fib` |
 | `FMOST` | `Fluorescence micro-optical sectioning tomography` | `fMOST` |
 | `ICEPHYS` | `Intracellular electrophysiology` | `icephys` |
 | `ISI` | `Intrinsic signal imaging` | `ISI` |
+| `MAPSEQ` | `Multiplexed analysis of projections by sequencing` | `MAPseq` |
 | `MERFISH` | `Multiplexed error-robust fluorescence in situ hybridization` | `merfish` |
 | `MRI` | `Magnetic resonance imaging` | `MRI` |
 | `POPHYS` | `Planar optical physiology` | `pophys` |
-| `SLAP` | `Scanned line projection imaging` | `slap` |
+| `SCRNASEQ` | `Single cell RNA sequencing` | `scRNAseq` |
+| `SLAP2` | `Random access projection microscopy` | `slap2` |
 | `SPIM` | `Selective plane illumination microscopy` | `SPIM` |
+| `STPT` | `Serial two-photon tomogrophy` | `STPT` |
 
 

aind_data_schema-2.5.1/docs/source/aind_data_schema_models/organizations.md

@@ -0,0 +1,140 @@
+# Organizations
+
+## Model definitions
+
+### Organization
+
+Organization
+
+| Name | abbreviation | name | registry | registry_identifier |
+|------|------|------|------|------|
+| `AA_OPTO_ELECTRONIC` | `None` | `AA Opto Electronic` | `None` | `None` |
+| `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` | `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` | `Research Organization Registry (ROR)` | `00bxkz165` |
+| `BASLER` | `None` | `Basler` | `None` | `None` |
+| `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` | `Research Organization Registry (ROR)` | `01xk5xs43` |
+| `CATHETER_IMPLANT_INSTITUTIONS` | `N/A` | `N/A` | `N/A` | `N/A` |
+| `CHAMPALIMAUD` | `Champalimaud` | `Champalimaud Foundation` | `Research Organization Registry (ROR)` | `03g001n57` |
+| `CHROMA` | `None` | `Chroma` | `None` | `None` |
+| `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` | `Research Organization Registry (ROR)` | `03ndmsg87` |
+| `CUSTOM` | `None` | `Custom` | `None` | `None` |
+| `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` | `Research Organization Registry (ROR)` | `059n53q30` |
+| `EALING` | `None` | `Ealing` | `None` | `None` |
+| `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` | `Research Organization Registry (ROR)` | `01j1gwp17` |
+| `FUJINON` | `None` | `Fujinon` | `None` | `None` |
+| `FUNDERS` | `N/A` | `N/A` | `N/A` | `N/A` |
+| `HAMAMATSU` | `None` | `Hamamatsu` | `Research Organization Registry (ROR)` | `03natb733` |
+| `HAMILTON` | `None` | `Hamilton` | `None` | `None` |
+| `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` | `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` | `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` | `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` | `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` | `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` | `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` | `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` | `Research Organization Registry (ROR)` | `026exqw73` |
+| `NAVITAR` | `None` | `Navitar` | `None` | `None` |
+| `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` | `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` | `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` |
+| `PLACID_INDUSTRIES` | `None` | `Placid Industries` | `None` | `None` |
+| `PRIZMATIX` | `None` | `Prizmatix` | `None` | `None` |
+| `QUANTIFI` | `None` | `Quantifi` | `None` | `None` |
+| `RASPBERRY_PI` | `None` | `Raspberry Pi` | `None` | `None` |
+| `RESEARCH_INSTITUTIONS` | `N/A` | `N/A` | `N/A` | `N/A` |
+| `SAME_SKY` | `None` | `Same Sky` | `None` | `None` |
+| `SCHNEIDER_KREUZNACH` | `None` | `Schneider-Kreuznach` | `None` | `None` |
+| `SECOND_ORDER_EFFECTS` | `None` | `Second Order Effects` | `None` | `None` |
+| `SEMROCK` | `None` | `Semrock` | `None` | `None` |
+| `SICGEN` | `None` | `SICGEN` | `None` | `None` |
+| `SIGMA_ALDRICH` | `None` | `Sigma-Aldrich` | `None` | `None` |
+| `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` | `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` | `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` | `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` | `Research Organization Registry (ROR)` | `00x0z1472` |
+| `TYMPHANY` | `None` | `Tymphany` | `None` | `None` |
+| `UCSD` | `UCSD` | `University of California, San Diego` | `Research Organization Registry (ROR)` | `0168r3w48` |
+| `UNKNOWN` | `UNKNOWN` | `Unknown` | `None` | `None` |
+| `UPENN` | `UPENN` | `University of Pennsylvania` | `Research Organization Registry (ROR)` | `00b30xv10` |
+| `VIEWORKS` | `None` | `Vieworks` | `None` | `None` |
+| `VORTRAN` | `None` | `Vortran` | `None` | `None` |
+
+

{aind_data_schema-2.4.0 → aind_data_schema-2.5.1}/docs/source/aind_data_schema_models/process_names.md

@@ -37,6 +37,7 @@ Process names
 | `IMAGE_TILE_PROJECTION` | `Image tile projection` |
 | `MODEL_EVALUATION` | `Model evaluation` |
 | `MODEL_TRAINING` | `Model training` |
+| `NEURON_SKELETON_PROCESSING` | `Neuron skeleton processing` |
 | `NEUROPIL_SUBTRACTION` | `Neuropil subtraction` |
 | `OTHER` | `Other` |
 | `PIPELINE` | `Pipeline` |

{aind_data_schema-2.4.0 → aind_data_schema-2.5.1}/docs/source/aind_data_schema_models/registries.md

@@ -9,8 +9,10 @@ Registries
 | Name | Value |
 |------|-------|
 | `ADDGENE` | `Addgene (ADDGENE)` |
+| `DOI` | `Digital Object Identifier (DOI)` |
 | `EMAPA` | `Edinburgh Mouse Atlas Project (EMAPA)` |
 | `MGI` | `Mouse Genome Informatics (MGI)` |
+| `GENBANK` | `NCBI GenBank (GENBANK)` |
 | `NCBI` | `National Center for Biotechnology Information (NCBI)` |
 | `ORCID` | `Open Researcher and Contributor ID (ORCID)` |
 | `ROR` | `Research Organization Registry (ROR)` |

aind_data_schema-2.5.1/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-2.4.0 → aind_data_schema-2.5.1}/docs/source/components/configs.md

@@ -227,6 +227,20 @@ Solution names
 | `OTHER` | `Other` |
 
 
+### MISCameraConfig
+
+Configuration for a camera used in a New Scale modular insertion system
+
+| Field | Type | Title (Description) |
+|-------|------|-------------|
+| `detector_config` | [DetectorConfig](#detectorconfig) | Detector configuration  |
+| `module` | [MISModuleConfig](#mismoduleconfig) | Module  |
+| `device_name` | `str` | Device name (Must match a device defined in the instrument.json) |
+| `relative_position` | List[[AnatomicalRelative](../aind_data_schema_models/coordinates.md#anatomicalrelative)] | Relative position  |
+| `coordinate_system` | Optional[[CoordinateSystem](coordinates.md#coordinatesystem)] | Device coordinate system  |
+| `transform` | Optional[List[[Translation](coordinates.md#translation) or [Rotation](coordinates.md#rotation) or [Scale](coordinates.md#scale) or [Affine](coordinates.md#affine)]] | Device to instrument transform (Position and orientation of the device in the instrument coordinate system) |
+
+
 ### MISModuleConfig
 
 Modular insertion system module configuration
@@ -240,28 +254,38 @@ Modular insertion system module configuration
 | `notes` | `Optional[str]` | Notes  |
 
 
+### MRAcquisitionType
+
+MRI acquisition type
+
+| Name | Value |
+|------|-------|
+| `SCAN_2D` | `2D` |
+| `SCAN_3D` | `3D` |
+
+
 ### MRIScan
 
 Configuration of a 3D scan
 
 | Field | Type | Title (Description) |
 |-------|------|-------------|
-| `scan_index` | `int` | Scan index  |
-| `scan_type` | [ScanType](#scantype) | Scan type  |
-| `primary_scan` | `bool` | Primary scan (Indicates the primary scan used for downstream analysis) |
-| `scan_sequence_type` | [MriScanSequence](#mriscansequence) | Scan sequence  |
+| `index` | `int` | Index (Index of the scan in the session, starting at 1) |
+| `setup` | `bool` | Setup (Positioning, shim, and other pre-scan adjustments) |
+| `pulse_sequence_type` | [PulseSequenceType](#pulsesequencetype) | Scan sequence (BIDS PulseSequenceType) |
+| `mr_acquisition_type` | [MRAcquisitionType](#mracquisitiontype) | MR acquisition type (BIDS MRAcquisitionType / DICOM Tag 0018,0023) |
+| `resolution` | Optional[[Scale](coordinates.md#scale)] | Voxel resolution  |
+| `resolution_unit` | Optional[[SizeUnit](../aind_data_schema_models/units.md#sizeunit)] | Voxel resolution unit  |
+| `additional_scan_parameters` | `Optional[dict]` | Parameters  |
 | `rare_factor` | `Optional[int]` | RARE factor  |
-| `echo_time` | `decimal.Decimal` | Echo time  |
+| `echo_time` | `decimal.Decimal` | Echo time (s) (BIDS EchoTime / DICOM Tag 0018,0081) |
 | `echo_time_unit` | [TimeUnit](../aind_data_schema_models/units.md#timeunit) | Echo time unit  |
 | `effective_echo_time` | `Optional[decimal.Decimal]` | Effective echo time  |
-| `repetition_time` | `decimal.Decimal` | Repetition time  |
+| `repetition_time` | `decimal.Decimal` | Repetition time (s) (BIDS RepetitionTime / DICOM Tag 0018,0080) |
 | `repetition_time_unit` | [TimeUnit](../aind_data_schema_models/units.md#timeunit) | Repetition time unit  |
-| `scan_coordinate_system` | Optional[[CoordinateSystem](coordinates.md#coordinatesystem)] | Scanner coordinate system  |
-| `scan_affine_transform` | Optional[List[[Translation](coordinates.md#translation) or [Rotation](coordinates.md#rotation) or [Scale](coordinates.md#scale) or [Affine](coordinates.md#affine)]] | MRI Scan affine transform (NIFTI sform/qform, Bruker vc_transform, etc) |
+| `scanner_coordinate_system` | Optional[[CoordinateSystem](coordinates.md#coordinatesystem)] | Scanner coordinate system  |
+| `affine_transform` | Optional[List[[Translation](coordinates.md#translation) or [Rotation](coordinates.md#rotation) or [Scale](coordinates.md#scale) or [Affine](coordinates.md#affine)]] | MRI Scan affine transform (NIFTI sform/qform, Bruker vc_transform, etc) |
 | `subject_position` | [SubjectPosition](#subjectposition) | Subject position  |
-| `resolution` | Optional[[Scale](coordinates.md#scale)] | Voxel resolution  |
-| `resolution_unit` | Optional[[SizeUnit](../aind_data_schema_models/units.md#sizeunit)] | Voxel resolution unit  |
-| `additional_scan_parameters` | `dict` | Parameters  |
 | `notes` | `Optional[str]` | Notes  |
 | `device_name` | `str` | Device name (Must match a device defined in the instrument.json) |
 
@@ -288,16 +312,6 @@ Configuration for mouse platforms
 | `device_name` | `str` | Device name (Must match a device defined in the instrument.json) |
 
 
-### MriScanSequence
-
-MRI scan sequence
-
-| Name | Value |
-|------|-------|
-| `RARE` | `RARE` |
-| `OTHER` | `Other` |
-
-
 ### OlfactometerChannelInfo
 
 Configuration of a channel in an olfactometer
@@ -402,6 +416,18 @@ Configuration for a device inserted into a brain
 | `device_name` | `str` | Device name (Must match a device defined in the instrument.json) |
 
 
+### PulseSequenceType
+
+MRI pulse sequence type
+
+| Name | Value |
+|------|-------|
+| `RARE` | `RARE` |
+| `FLASH` | `FLASH` |
+| `MSME` | `MSME` |
+| `OTHER` | `Other` |
+
+
 ### SampleChamberConfig
 
 Configuration of a sample chamber
@@ -423,16 +449,6 @@ Description of an image sampling strategy
 | `frame_rate_unit` | [FrequencyUnit](../aind_data_schema_models/units.md#frequencyunit) | Frame rate unit  |
 
 
-### ScanType
-
-Type of scan
-
-| Name | Value |
-|------|-------|
-| `SETUP` | `Set Up` |
-| `SCAN_3D` | `3D Scan` |
-
-
 ### SlapAcquisitionType
 
 Type of slap acquisition

{aind_data_schema-2.4.0 → aind_data_schema-2.5.1}/docs/source/components/devices.md

@@ -340,7 +340,7 @@ 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 +351,7 @@ 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) |
 |-------|------|-------------|
@@ -622,9 +622,9 @@ Description of visual display for visual stimuli
 | `viewing_distance` | `decimal.Decimal` | Viewing distance (cm)  |
 | `viewing_distance_unit` | [SizeUnit](../aind_data_schema_models/units.md#sizeunit) | Viewing distance unit  |
 | `contrast` | `Optional[int]` | Contrast (Monitor's contrast setting) |
-| `contrast_unit` | `Optional[UnitlessUnit]` | Contrast unit |
+| `contrast_unit` | Optional[[UnitlessUnit](../aind_data_schema_models/units.md#unitlessunit)] | Contrast unit  |
 | `brightness` | `Optional[int]` | Brightness (Monitor's brightness setting) |
-| `brightness_unit` | `Optional[UnitlessUnit]` | Brightness unit |
+| `brightness_unit` | Optional[[UnitlessUnit](../aind_data_schema_models/units.md#unitlessunit)] | Brightness unit  |
 | `name` | `str` | Device name  |
 | `serial_number` | `Optional[str]` | Serial number  |
 | `model` | `Optional[str]` | Model  |
@@ -781,7 +781,7 @@ 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 +793,17 @@ 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-2.4.0 → aind_data_schema-2.5.1}/docs/source/components/measurements.md

@@ -13,10 +13,10 @@ Generic calibration class
 | `protocol_id` | `Optional[str]` | Protocol ID (DOI for protocols.io) |
 | `measured_at` | `Optional[str]` | Measurement location  |
 | `input` | `List[float or str]` | Inputs (Calibration input) |
-| `input_unit` | [SizeUnit](../aind_data_schema_models/units.md#sizeunit) or [MassUnit](../aind_data_schema_models/units.md#massunit) or [FrequencyUnit](../aind_data_schema_models/units.md#frequencyunit) or [SpeedUnit](../aind_data_schema_models/units.md#speedunit) or [VolumeUnit](../aind_data_schema_models/units.md#volumeunit) or [AngleUnit](../aind_data_schema_models/units.md#angleunit) or [TimeUnit](../aind_data_schema_models/units.md#timeunit) or [PowerUnit](../aind_data_schema_models/units.md#powerunit) or [CurrentUnit](../aind_data_schema_models/units.md#currentunit) or [ConcentrationUnit](../aind_data_schema_models/units.md#concentrationunit) or [TemperatureUnit](../aind_data_schema_models/units.md#temperatureunit) or [SoundIntensityUnit](../aind_data_schema_models/units.md#soundintensityunit) or [VoltageUnit](../aind_data_schema_models/units.md#voltageunit) or [MemoryUnit](../aind_data_schema_models/units.md#memoryunit) or [UnitlessUnit](../aind_data_schema_models/units.md#unitlessunit) or [MagneticFieldUnit](../aind_data_schema_models/units.md#magneticfieldunit) or [PressureUnit](../aind_data_schema_models/units.md#pressureunit) | Input unit  |
+| `input_unit` | [SizeUnit](../aind_data_schema_models/units.md#sizeunit) or [MassUnit](../aind_data_schema_models/units.md#massunit) or [FrequencyUnit](../aind_data_schema_models/units.md#frequencyunit) or [SpeedUnit](../aind_data_schema_models/units.md#speedunit) or [VolumeUnit](../aind_data_schema_models/units.md#volumeunit) or [AngleUnit](../aind_data_schema_models/units.md#angleunit) or [TimeUnit](../aind_data_schema_models/units.md#timeunit) or [PowerUnit](../aind_data_schema_models/units.md#powerunit) or [CurrentUnit](../aind_data_schema_models/units.md#currentunit) or [ConcentrationUnit](../aind_data_schema_models/units.md#concentrationunit) or [TemperatureUnit](../aind_data_schema_models/units.md#temperatureunit) or [SoundIntensityUnit](../aind_data_schema_models/units.md#soundintensityunit) or [VoltageUnit](../aind_data_schema_models/units.md#voltageunit) or [MemoryUnit](../aind_data_schema_models/units.md#memoryunit) or [UnitlessUnit](../aind_data_schema_models/units.md#unitlessunit) or [MagneticFieldUnit](../aind_data_schema_models/units.md#magneticfieldunit) or [PressureUnit](../aind_data_schema_models/units.md#pressureunit) or {TorqueUnit} | Input unit  |
 | `repeats` | `Optional[int]` | Number of repeats (If each input was repeated multiple times, provide the number of repeats) |
 | `output` | `List[float or str]` | Outputs (Calibration output (provide the average if repeated)) |
-| `output_unit` | [SizeUnit](../aind_data_schema_models/units.md#sizeunit) or [MassUnit](../aind_data_schema_models/units.md#massunit) or [FrequencyUnit](../aind_data_schema_models/units.md#frequencyunit) or [SpeedUnit](../aind_data_schema_models/units.md#speedunit) or [VolumeUnit](../aind_data_schema_models/units.md#volumeunit) or [AngleUnit](../aind_data_schema_models/units.md#angleunit) or [TimeUnit](../aind_data_schema_models/units.md#timeunit) or [PowerUnit](../aind_data_schema_models/units.md#powerunit) or [CurrentUnit](../aind_data_schema_models/units.md#currentunit) or [ConcentrationUnit](../aind_data_schema_models/units.md#concentrationunit) or [TemperatureUnit](../aind_data_schema_models/units.md#temperatureunit) or [SoundIntensityUnit](../aind_data_schema_models/units.md#soundintensityunit) or [VoltageUnit](../aind_data_schema_models/units.md#voltageunit) or [MemoryUnit](../aind_data_schema_models/units.md#memoryunit) or [UnitlessUnit](../aind_data_schema_models/units.md#unitlessunit) or [MagneticFieldUnit](../aind_data_schema_models/units.md#magneticfieldunit) or [PressureUnit](../aind_data_schema_models/units.md#pressureunit) | Output unit  |
+| `output_unit` | [SizeUnit](../aind_data_schema_models/units.md#sizeunit) or [MassUnit](../aind_data_schema_models/units.md#massunit) or [FrequencyUnit](../aind_data_schema_models/units.md#frequencyunit) or [SpeedUnit](../aind_data_schema_models/units.md#speedunit) or [VolumeUnit](../aind_data_schema_models/units.md#volumeunit) or [AngleUnit](../aind_data_schema_models/units.md#angleunit) or [TimeUnit](../aind_data_schema_models/units.md#timeunit) or [PowerUnit](../aind_data_schema_models/units.md#powerunit) or [CurrentUnit](../aind_data_schema_models/units.md#currentunit) or [ConcentrationUnit](../aind_data_schema_models/units.md#concentrationunit) or [TemperatureUnit](../aind_data_schema_models/units.md#temperatureunit) or [SoundIntensityUnit](../aind_data_schema_models/units.md#soundintensityunit) or [VoltageUnit](../aind_data_schema_models/units.md#voltageunit) or [MemoryUnit](../aind_data_schema_models/units.md#memoryunit) or [UnitlessUnit](../aind_data_schema_models/units.md#unitlessunit) or [MagneticFieldUnit](../aind_data_schema_models/units.md#magneticfieldunit) or [PressureUnit](../aind_data_schema_models/units.md#pressureunit) or {TorqueUnit} | Output unit  |
 | `fit` | Optional[[CalibrationFit](#calibrationfit)] | Fit (Fit equation for the calibration data used during data acquisition) |
 | `notes` | `Optional[str]` | Notes  |
 | `device_name` | `str` | Device name (Must match a device defined in the instrument.json) |

{aind_data_schema-2.4.0 → aind_data_schema-2.5.1}/docs/source/components/specimen_procedures.md

@@ -29,31 +29,49 @@ Description of an HCR staining round
 | `probe_concentration_unit` | `str` | Probe concentration unit  |
 
 
+### PlanarSection
+
+Description of a single planar section of brain tissue
+
+| Field | Type | Title (Description) |
+|-------|------|-------------|
+| `coordinate_system_name` | `str` | Coordinate system name  |
+| `start_coordinate` | [Translation](coordinates.md#translation) | Start coordinate  |
+| `end_coordinate` | Optional[[Translation](coordinates.md#translation)] | End coordinate  |
+| `thickness` | `Optional[float]` | Slice thickness  |
+| `thickness_unit` | Optional[[SizeUnit](../aind_data_schema_models/units.md#sizeunit)] | Slice thickness unit  |
+| `partial_slice` | Optional[List[[AnatomicalRelative](../aind_data_schema_models/coordinates.md#anatomicalrelative)]] | Partial slice (If sectioning does not include the entire slice, indicate which part of the slice is retained.) |
+| `output_specimen_id` | `str` | Specimen ID  |
+| `targeted_structure` | Optional[[BrainAtlas](../aind_data_schema_models/brain_atlas.md#ccfv3)] | Targeted structure  |
+| `includes_surrounding_tissue` | `Optional[bool]` | Includes surrounding tissue (Whether the section includes additional tissue surrounding the targeted structure.) |
+
+
 ### PlanarSectioning
 
 Description of a sectioning procedure performed on the coronal, sagittal, or transverse/axial plane
 
 | Field | Type | Title (Description) |
 |-------|------|-------------|
-| `coordinate_system` | Optional[[CoordinateSystem](coordinates.md#coordinatesystem)] | Sectioning coordinate system (Only required if different from the Procedures.coordinate_system) |
-| `sections` | List[[Section](#section)] | Sections  |
+| `coordinate_system` | [CoordinateSystem](coordinates.md#coordinatesystem) or [Atlas](coordinates.md#atlas) or NoneType | Sectioning coordinate system (Only required if different from the Procedures.coordinate_system) |
+| `sections` | List[[Section](#section) or [PlanarSection](#planarsection)] | Planar sections (Use PlanarSection for new implementations) |
 | `section_orientation` | [SectionOrientation](#sectionorientation) | Sectioning orientation  |
 
 
 ### Section
 
-Description of a slice of brain tissue
+Description of a single section of brain tissue. Slices should use PlanarSection.
 
 | Field | Type | Title (Description) |
 |-------|------|-------------|
 | `output_specimen_id` | `str` | Specimen ID  |
 | `targeted_structure` | Optional[[BrainAtlas](../aind_data_schema_models/brain_atlas.md#ccfv3)] | Targeted structure  |
-| `coordinate_system_name` | `str` | Coordinate system name  |
-| `start_coordinate` | [Translation](coordinates.md#translation) | Start coordinate  |
-| `end_coordinate` | Optional[[Translation](coordinates.md#translation)] | End coordinate  |
-| `thickness` | `Optional[float]` | Slice thickness  |
-| `thickness_unit` | Optional[[SizeUnit](../aind_data_schema_models/units.md#sizeunit)] | Slice thickness unit  |
-| `partial_slice` | Optional[List[[AnatomicalRelative](../aind_data_schema_models/coordinates.md#anatomicalrelative)]] | Partial slice (If sectioning does not include the entire slice, indicate which part of the slice is retained.) |
+| `includes_surrounding_tissue` | `Optional[bool]` | Includes surrounding tissue (Whether the section includes additional tissue surrounding the targeted structure.) |
+| <del>`coordinate_system_name`</del> | `Optional[str]` | **[DEPRECATED]** Use PlanarSection instead. Coordinate system name  |
+| <del>`start_coordinate`</del> | Optional[[Translation](coordinates.md#translation)] | **[DEPRECATED]** Use PlanarSection instead. Start coordinate  |
+| <del>`end_coordinate`</del> | Optional[[Translation](coordinates.md#translation)] | **[DEPRECATED]** Use PlanarSection instead. End coordinate  |
+| <del>`thickness`</del> | `Optional[float]` | **[DEPRECATED]** Use PlanarSection instead. Slice thickness  |
+| <del>`thickness_unit`</del> | Optional[[SizeUnit](../aind_data_schema_models/units.md#sizeunit)] | **[DEPRECATED]** Use PlanarSection instead. Slice thickness unit  |
+| <del>`partial_slice`</del> | Optional[List[[AnatomicalRelative](../aind_data_schema_models/coordinates.md#anatomicalrelative)]] | **[DEPRECATED]** Use PlanarSection instead. Partial slice (If sectioning does not include the entire slice, indicate which part of the slice is retained.) |
 
 
 ### SectionOrientation
@@ -67,6 +85,15 @@ Orientation of sectioning
 | `TRANSVERSE` | `Transverse` |
 
 
+### Sectioning
+
+Description of a sectioning procedure targeting a specific structure
+
+| Field | Type | Title (Description) |
+|-------|------|-------------|
+| `sections` | List[[Section](#section)] | Sections  |
+
+
 ### SpecimenProcedure
 
 Description of surgical or other procedure performed on a specimen
@@ -75,13 +102,13 @@ Description of surgical or other procedure performed on a specimen
 |-------|------|-------------|
 | `procedure_type` | [SpecimenProcedureType](../aind_data_schema_models/specimen_procedure_types.md#specimenproceduretype) | Procedure type  |
 | `procedure_name` | `Optional[str]` | Procedure name  |
-| `specimen_id` | `str` | Specimen ID  |
+| `specimen_id` | `str or List[str]` | Specimen ID(s)  |
 | `start_date` | `datetime.date` | Start date  |
 | `end_date` | `datetime.date` | End date  |
 | `experimenters` | `List[str]` | experimenter(s)  |
 | `protocol_id` | `Optional[List[str]]` | Protocol ID (DOI for protocols.io) |
 | `protocol_parameters` | `Optional[Dict[str, str]]` | Protocol parameters (Parameters defined in the protocol and their value during this procedure) |
-| `procedure_details` | List[[HCRSeries](#hcrseries) or [FluorescentStain](reagent.md#fluorescentstain) or [PlanarSectioning](#planarsectioning) or [ProbeReagent](reagent.md#probereagent) or [Reagent](reagent.md#reagent) or [GeneProbeSet](reagent.md#geneprobeset)] | Procedure details (Details of the procedures, including reagents and sectioning information.) |
+| `procedure_details` | List[[HCRSeries](#hcrseries) or [FluorescentStain](reagent.md#fluorescentstain) or [Sectioning](#sectioning) or [PlanarSectioning](#planarsectioning) or [ProbeReagent](reagent.md#probereagent) or [Reagent](reagent.md#reagent) or [GeneProbeSet](reagent.md#geneprobeset)] | Procedure details (Details of the procedures, including reagents and sectioning information.) |
 | `notes` | `Optional[str]` | Notes  |