Merge pull request #1850 from AllenNeuralDynamics/release-v2.8.0

Release v2.8.0

Author: dbirman

.gitignore

@@ -146,3 +146,4 @@ examples/*.json
 *.json
 docs/base/models/*
 .github/copilot-instructions.md
+uv.lock

docs/source/acquisition.md

@@ -83,7 +83,6 @@ while the StimulusEpoch represents all stimuli being presented.
 | `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) |
 | `ethics_review_id` | `Optional[List[str]]` | Ethics review ID  |
 | `instrument_id` | `Optional[str]` | Instrument ID (Should match the Instrument.instrument_id. Required when instrument metadata is available.) |
 | `acquisition_type` | `str` | Acquisition type (Descriptive string detailing the type of acquisition, should be consistent across similar acquisitions for the same experiment.) |
@@ -95,6 +94,7 @@ while the StimulusEpoch represents all stimuli being presented.
 | `stimulus_epochs` | List[[StimulusEpoch](acquisition.md#stimulusepoch)] | Stimulus (A stimulus epoch captures all stimuli being presented during an acquisition. Epochs should be split when the purpose of the stimulus changes.) |
 | `manipulations` | List[[Manipulation](acquisition.md#manipulation)] | Manipulations (Procedures performed during the acquisition.) |
 | `subject_details` | Optional[[AcquisitionSubjectDetails](acquisition.md#acquisitionsubjectdetails)] | Subject details (Required for in vivo acquisitions.) |
+| `protocol_id` | `Optional[List[str]]` | Protocol ID (DOI for protocols.io) |
 
 
 ## Model definitions
@@ -151,9 +151,10 @@ Description of procedures performed during an acquisition.
 |-------|------|-------------|
 | `start_time` | `datetime (timezone-aware)` | Manipulation start time (Must be between the acquisition start and end times) |
 | `end_time` | `datetime (timezone-aware)` | Manipulation end time (Must be between the acquisition start and end times) |
-| `procedures` | Optional[List[[Injection](components/injection_procedures.md#injection) or [BrainInjection](components/surgery_procedures.md#braininjection)]] | Procedures (Procedures performed during the manipulation) |
+| `procedures` | Optional[List[[Injection](components/injection_procedures.md#injection) or [BrainInjection](components/surgery_procedures.md#braininjection) or [Reagent](components/reagent.md#reagent)]] | Procedures (Procedures performed during the manipulation) |
 | `anaesthesia` | Optional[[Anaesthetic](components/surgery_procedures.md#anaesthetic)] | Anaesthesia  |
 | `notes` | `Optional[str]` | Notes  |
+| `protocol_id` | `Optional[List[str]]` | Protocol ID (DOI for protocols.io) |
 
 
 ### PerformanceMetrics

docs/source/aind_data_schema_models/harp_types.md

@@ -18,6 +18,7 @@ Harp device types
 | `CURRENTDRIVER` | `CurrentDriver` | `1282` |
 | `CUTTLEFISH` | `cuTTLefish` | `1403` |
 | `CUTTLEFISHFIP` | `cuTTLefishFip` | `1407` |
+| `DELUXDRIVER` | `deLuxDriver` | `1410` |
 | `DRIVER12VOLTS` | `Driver12Volts` | `1072` |
 | `ENVIRONMENTSENSOR` | `EnvironmentSensor` | `1405` |
 | `FLYPAD` | `FlyPad` | `1200` |

docs/source/aind_data_schema_models/organizations.md

@@ -22,6 +22,7 @@ Organization
 | `ASUS` | `None` | `ASUS` | `Research Organization Registry (ROR)` | `00bxkz165` |
 | `BASLER` | `None` | `Basler` | `None` | `None` |
 | `BCM` | `BCM` | `Baylor College of Medicine` | `Research Organization Registry (ROR)` | `02pttbw34` |
+| `BROADCOM` | `None` | `Broadcom` | `Research Organization Registry (ROR)` | `035gt5s03` |
 | `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` |
@@ -47,6 +48,7 @@ Organization
 | `EDMUND_OPTICS` | `None` | `Edmund Optics` | `Research Organization Registry (ROR)` | `01j1gwp17` |
 | `EMORY` | `Emory` | `Emory University` | `Research Organization Registry (ROR)` | `03czfpz43` |
 | `EURESYS` | `None` | `Euresys` | `None` | `None` |
+| `EXCELITAS_TECHNOLOGIES` | `None` | `Excelitas Technologies` | `Research Organization Registry (ROR)` | `01tpbbf75` |
 | `FILTER_MANUFACTURERS` | `N/A` | `N/A` | `N/A` | `N/A` |
 | `FLIR` | `FLIR` | `Teledyne FLIR` | `Research Organization Registry (ROR)` | `01j1gwp17` |
 | `FUJINON` | `None` | `Fujinon` | `None` | `None` |
@@ -66,6 +68,7 @@ Organization
 | `JENOPTIK` | `None` | `Jenoptik` | `Research Organization Registry (ROR)` | `05g7t5c49` |
 | `JHU` | `JHU` | `Johns Hopkins University` | `Research Organization Registry (ROR)` | `00za53h95` |
 | `JULABO` | `None` | `Julabo` | `None` | `None` |
+| `KENT_SCIENTIFIC_CORPORATION` | `None` | `Kent Scientific Corporation` | `Research Organization Registry (ROR)` | `03xkj6a08` |
 | `KOWA` | `None` | `Kowa` | `Research Organization Registry (ROR)` | `03zbwg482` |
 | `LASER_MANUFACTURERS` | `N/A` | `N/A` | `N/A` | `N/A` |
 | `LASOS` | `LASOS` | `LASOS Lasertechnik` | `None` | `None` |
@@ -104,6 +107,7 @@ Organization
 | `OLYMPUS` | `None` | `Olympus` | `Research Organization Registry (ROR)` | `02vcdte90` |
 | `OPTOTUNE` | `None` | `Optotune` | `None` | `None` |
 | `OTHER` | `None` | `Other` | `None` | `None` |
+| `OXFORD_INSTRUMENTS` | `None` | `Oxford Instruments` | `Research Organization Registry (ROR)` | `01age2z78` |
 | `OXXIUS` | `None` | `Oxxius` | `None` | `None` |
 | `PLACID_INDUSTRIES` | `None` | `Placid Industries` | `None` | `None` |
 | `PRIZMATIX` | `None` | `Prizmatix` | `None` | `None` |
@@ -112,6 +116,7 @@ Organization
 | `RESEARCH_INSTITUTIONS` | `N/A` | `N/A` | `N/A` | `N/A` |
 | `SAME_SKY` | `None` | `Same Sky` | `None` | `None` |
 | `SCHNEIDER_KREUZNACH` | `None` | `Schneider-Kreuznach` | `None` | `None` |
+| `SCIENTIFICA` | `None` | `Scientifica` | `Research Organization Registry (ROR)` | `00z72df47` |
 | `SECOND_ORDER_EFFECTS` | `None` | `Second Order Effects` | `None` | `None` |
 | `SEMROCK` | `None` | `Semrock` | `None` | `None` |
 | `SICGEN` | `None` | `SICGEN` | `None` | `None` |
@@ -137,5 +142,6 @@ Organization
 | `UPENN` | `UPENN` | `University of Pennsylvania` | `Research Organization Registry (ROR)` | `00b30xv10` |
 | `VIEWORKS` | `None` | `Vieworks` | `None` | `None` |
 | `VORTRAN` | `None` | `Vortran` | `None` | `None` |
+| `WPI` | `WPI` | `World Precision Intstruments` | `Research Organization Registry (ROR)` | `03st5df34` |
 
 

docs/source/aind_data_schema_models/process_names.md

@@ -17,6 +17,7 @@ Process names
 | `EPHYS_VISUALIZATION` | `Ephys visualization` |
 | `FIDUCIAL_SEGMENTATION` | `Fiducial segmentation` |
 | `FILE_FORMAT_CONVERSION` | `File format conversion` |
+| `FIX_COLOR_RANGE` | `Fix color range` |
 | `FLUORESCENCE_EVENT_DETECTION` | `Fluorescence event detection` |
 | `IMAGE_ATLAS_ALIGNMENT` | `Image atlas alignment` |
 | `IMAGE_BACKGROUND_SUBTRACTION` | `Image background subtraction` |
@@ -28,13 +29,15 @@ Process names
 | `IMAGE_FLAT_FIELD_CORRECTION` | `Image flat-field correction` |
 | `IMAGE_IMPORTING` | `Image importing` |
 | `IMAGE_MIP_VISUALIZATION` | `Image mip visualization` |
+| `IMAGE_MULTISCALING` | `Image multiscaling` |
 | `IMAGE_RADIAL_CORRECTION` | `Image radial correction` |
 | `IMAGE_SPOT_DETECTION` | `Image spot detection` |
 | `IMAGE_SPOT_SPECTRAL_UNMIXING` | `Image spot spectral unmixing` |
 | `IMAGE_THRESHOLDING` | `Image thresholding` |
 | `IMAGE_TILE_ALIGNMENT` | `Image tile alignment` |
 | `IMAGE_TILE_FUSING` | `Image tile fusing` |
 | `IMAGE_TILE_PROJECTION` | `Image tile projection` |
+| `MANUAL_CURATION` | `Manual curation` |
 | `MODEL_EVALUATION` | `Model evaluation` |
 | `MODEL_TRAINING` | `Model training` |
 | `NEURON_SKELETON_PROCESSING` | `Neuron skeleton processing` |

docs/source/aind_data_schema_models/specimen_procedure_types.md

@@ -25,6 +25,5 @@ Specimen procedures
 | `SOAK` | `Soak` |
 | `STORAGE` | `Storage` |
 | `STRIPPING` | `Stripping` |
-| `TAMOXIFEN_INDUCTION` | `Tamoxifen induction` |
 
 

docs/source/components/devices.md

@@ -57,7 +57,7 @@ Camera Detector
 | Field | Type | Title (Description) |
 |-------|------|-------------|
 | `detector_type` | [DetectorType](../aind_data_schema_models/devices.md#detectortype) |   |
-| `manufacturer` | [Organization](../aind_data_schema_models/organizations.md#organization) |   |
+| `manufacturer` | [Organization](../aind_data_schema_models/organizations.md#organization) | Manufacturer  |
 | `data_interface` | [DataInterface](../aind_data_schema_models/devices.md#datainterface) | Data interface  |
 | `cooling` | [Cooling](../aind_data_schema_models/devices.md#cooling) | Cooling  |
 | `frame_rate` | `Optional[decimal.Decimal]` | Frame rate (Hz) (Frame rate being used) |
@@ -192,7 +192,7 @@ Data acquisition device containing multiple I/O channels
 | Field | Type | Title (Description) |
 |-------|------|-------------|
 | `data_interface` | [DataInterface](../aind_data_schema_models/devices.md#datainterface) | Type of connection to PC  |
-| `manufacturer` | [Organization](../aind_data_schema_models/organizations.md#organization) |   |
+| `manufacturer` | [Organization](../aind_data_schema_models/organizations.md#organization) | Manufacturer  |
 | `channels` | List[[DAQChannel](#daqchannel)] | DAQ channels  |
 | `firmware_version` | `Optional[str]` | Firmware version  |
 | `hardware_version` | `Optional[str]` | Hardware version  |
@@ -210,7 +210,7 @@ Description of a generic detector
 | Field | Type | Title (Description) |
 |-------|------|-------------|
 | `detector_type` | [DetectorType](../aind_data_schema_models/devices.md#detectortype) | Detector Type  |
-| `manufacturer` | [Organization](../aind_data_schema_models/organizations.md#organization) |   |
+| `manufacturer` | [Organization](../aind_data_schema_models/organizations.md#organization) | Manufacturer  |
 | `data_interface` | [DataInterface](../aind_data_schema_models/devices.md#datainterface) | Data interface  |
 | `cooling` | [Cooling](../aind_data_schema_models/devices.md#cooling) | Cooling  |
 | `frame_rate` | `Optional[decimal.Decimal]` | Frame rate (Hz) (Frame rate being used) |
@@ -417,7 +417,7 @@ Filter used in a light path
 | Field | Type | Title (Description) |
 |-------|------|-------------|
 | `filter_type` | [FilterType](../aind_data_schema_models/devices.md#filtertype) | Type of filter  |
-| `manufacturer` | [Organization](../aind_data_schema_models/organizations.md#organization) |   |
+| `manufacturer` | [Organization](../aind_data_schema_models/organizations.md#organization) | Manufacturer  |
 | `cut_off_wavelength` | `Optional[int]` | Cut-off wavelength (nm)  |
 | `cut_on_wavelength` | `Optional[int]` | Cut-on wavelength (nm)  |
 | `center_wavelength` | `int or List[int] or NoneType` | Center wavelength (nm) (Single wavelength or list of wavelengths for MULTIBAND or MULTI_NOTCH filters) |
@@ -435,7 +435,7 @@ DAQ that uses the Harp protocol for synchronization and data transmission
 
 | Field | Type | Title (Description) |
 |-------|------|-------------|
-| `manufacturer` | [Organization](../aind_data_schema_models/organizations.md#organization) |   |
+| `manufacturer` | [Organization](../aind_data_schema_models/organizations.md#organization) | Manufacturer  |
 | `harp_device_type` | [HarpDeviceType](../aind_data_schema_models/harp_types.md#harpdevicetype) | Type of Harp device  |
 | `core_version` | `Optional[str]` | Core version  |
 | `tag_version` | `Optional[str]` | Tag version  |
@@ -476,7 +476,7 @@ Laser module with a specific wavelength (may be a sub-component of a larger asse
 
 | Field | Type | Title (Description) |
 |-------|------|-------------|
-| `manufacturer` | [Organization](../aind_data_schema_models/organizations.md#organization) |   |
+| `manufacturer` | [Organization](../aind_data_schema_models/organizations.md#organization) | Manufacturer  |
 | `wavelength` | `int` | Wavelength (nm)  |
 | `wavelength_unit` | [SizeUnit](../aind_data_schema_models/units.md#sizeunit) | Wavelength unit  |
 | `coupling` | Optional[[Coupling](../aind_data_schema_models/devices.md#coupling)] | Coupling  |
@@ -508,7 +508,7 @@ Lens
 
 | Field | Type | Title (Description) |
 |-------|------|-------------|
-| `manufacturer` | [Organization](../aind_data_schema_models/organizations.md#organization) |   |
+| `manufacturer` | [Organization](../aind_data_schema_models/organizations.md#organization) | Manufacturer  |
 | `name` | `str` | Device name  |
 | `serial_number` | `Optional[str]` | Serial number  |
 | `model` | `Optional[str]` | Model  |
@@ -564,7 +564,7 @@ Description of a Light Emitting Diode (LED) device
 
 | Field | Type | Title (Description) |
 |-------|------|-------------|
-| `manufacturer` | [Organization](../aind_data_schema_models/organizations.md#organization) |   |
+| `manufacturer` | [Organization](../aind_data_schema_models/organizations.md#organization) | Manufacturer  |
 | `wavelength` | `int` | Wavelength (nm)  |
 | `wavelength_unit` | [SizeUnit](../aind_data_schema_models/units.md#sizeunit) | Wavelength unit  |
 | `bandwidth` | `Optional[int]` | Bandwidth (FWHM)  |
@@ -582,7 +582,7 @@ Manipulator used on a dome module
 
 | Field | Type | Title (Description) |
 |-------|------|-------------|
-| `manufacturer` | [Organization](../aind_data_schema_models/organizations.md#organization) |   |
+| `manufacturer` | [Organization](../aind_data_schema_models/organizations.md#organization) | Manufacturer  |
 | `name` | `str` | Device name  |
 | `serial_number` | `Optional[str]` | Serial number  |
 | `model` | `Optional[str]` | Model  |
@@ -610,7 +610,7 @@ Description of visual display for visual stimuli
 
 | Field | Type | Title (Description) |
 |-------|------|-------------|
-| `manufacturer` | [Organization](../aind_data_schema_models/organizations.md#organization) |   |
+| `manufacturer` | [Organization](../aind_data_schema_models/organizations.md#organization) | Manufacturer  |
 | `refresh_rate` | `int` | Refresh rate (Hz)  |
 | `width` | `int` | Width (pixels)  |
 | `height` | `int` | Height (pixels)  |
@@ -732,7 +732,7 @@ Description of an olfactometer for odor stimuli
 
 | Field | Type | Title (Description) |
 |-------|------|-------------|
-| `manufacturer` | [Organization](../aind_data_schema_models/organizations.md#organization) |   |
+| `manufacturer` | [Organization](../aind_data_schema_models/organizations.md#organization) | Manufacturer  |
 | `harp_device_type` | [HarpDeviceType](../aind_data_schema_models/harp_types.md#harpdevicetype) | Type of Harp device  |
 | `channels` | List[[OlfactometerChannel](#olfactometerchannel)] |   |
 | `core_version` | `Optional[str]` | Core version  |
@@ -888,7 +888,7 @@ Description of a speaker for auditory stimuli
 
 | Field | Type | Title (Description) |
 |-------|------|-------------|
-| `manufacturer` | [Organization](../aind_data_schema_models/organizations.md#organization) |   |
+| `manufacturer` | [Organization](../aind_data_schema_models/organizations.md#organization) | Manufacturer  |
 | `name` | `str` | Device name  |
 | `serial_number` | `Optional[str]` | Serial number  |
 | `model` | `Optional[str]` | Model  |

docs/source/components/identifiers.md

@@ -50,7 +50,8 @@ Description of a single data asset
 
 | Field | Type | Title (Description) |
 |-------|------|-------------|
-| `url` | `str` | Asset location (URL pointing to the data asset) |
+| `name` | `Optional[str]` | Asset name (Name of the data asset) |
+| `url` | `Optional[str]` | Asset location (URL pointing to the data asset) |
 
 
 ### Database

docs/source/components/injection_procedures.md

@@ -12,7 +12,7 @@ Description of an injection procedure
 | `targeted_structure` | Optional[[MouseAnatomyModel](../aind_data_schema_models/external.md#mouseanatomymodel)] | Injection target (Use InjectionTargets) |
 | `relative_position` | Optional[List[[AnatomicalRelative](../aind_data_schema_models/coordinates.md#anatomicalrelative)]] | Relative position  |
 | `dynamics` | List[[InjectionDynamics](#injectiondynamics)] | Injection dynamics (List of injection events, one per location/depth) |
-| <del>`protocol_id`</del> | `Optional[str]` | **[DEPRECATED]** Use protocol_id in Surgery or NonSurgicalInjection instead. Protocol ID (DOI for protocols.io) |
+| `protocol_id` | `Optional[str]` | Protocol ID (DOI for protocols.io) |
 
 
 ### InjectionDynamics