diff --git a/docs/source/aind_data_schema_models/harp_types.md b/docs/source/aind_data_schema_models/harp_types.md index f89b1bad1..56297cc39 100644 --- a/docs/source/aind_data_schema_models/harp_types.md +++ b/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` | diff --git a/docs/source/aind_data_schema_models/organizations.md b/docs/source/aind_data_schema_models/organizations.md index 6a7fd7db5..2587f75b8 100644 --- a/docs/source/aind_data_schema_models/organizations.md +++ b/docs/source/aind_data_schema_models/organizations.md @@ -47,6 +47,7 @@ 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` | diff --git a/docs/source/aind_data_schema_models/process_names.md b/docs/source/aind_data_schema_models/process_names.md index 45a1b3028..557b8d904 100644 --- a/docs/source/aind_data_schema_models/process_names.md +++ b/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` | @@ -28,6 +29,7 @@ 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` | diff --git a/docs/source/aind_data_schema_models/specimen_procedure_types.md b/docs/source/aind_data_schema_models/specimen_procedure_types.md index d7b3895ba..6b9956d60 100644 --- a/docs/source/aind_data_schema_models/specimen_procedure_types.md +++ b/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` | diff --git a/docs/source/components/reagent.md b/docs/source/components/reagent.md index d442a13b6..72f92ff56 100644 --- a/docs/source/components/reagent.md +++ b/docs/source/components/reagent.md @@ -115,3 +115,13 @@ Description of a small molecule probe | `mass_unit` | [MassUnit](../aind_data_schema_models/units.md#massunit) | Mass unit | +### Solution + +Description of a solution made in house. Should match a solution named in protocol. + +| Field | Type | Title (Description) | +|-------|------|-------------| +| `name` | `str` | Name | +| `lot_number` | `Optional[str]` | Lot number | + + diff --git a/docs/source/components/specimen_procedures.md b/docs/source/components/specimen_procedures.md index c61eaed70..cf2f72c17 100644 --- a/docs/source/components/specimen_procedures.md +++ b/docs/source/components/specimen_procedures.md @@ -108,7 +108,7 @@ Description of surgical or other procedure performed on a specimen | `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 [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.) | +| `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) or [Solution](reagent.md#solution)] | Procedure details (Details of the procedures, including reagents and sectioning information.) | | `notes` | `Optional[str]` | Notes | diff --git a/src/aind_data_schema/components/reagent.py b/src/aind_data_schema/components/reagent.py index 3ed148a85..cdd8f5603 100644 --- a/src/aind_data_schema/components/reagent.py +++ b/src/aind_data_schema/components/reagent.py @@ -31,6 +31,13 @@ class Reagent(DataModel): expiration_date: Optional[date] = Field(default=None, title="Lot expiration date") +class Solution(DataModel): + """Description of a solution made in house. Should match a solution named in protocol.""" + + name: str = Field(..., title="Name") + lot_number: Optional[str] = Field(default=None, title="Lot number") + + class OligoProbe(DataModel): """Description of an oligonucleotide probe""" diff --git a/src/aind_data_schema/components/specimen_procedures.py b/src/aind_data_schema/components/specimen_procedures.py index d0b196249..64a587359 100644 --- a/src/aind_data_schema/components/specimen_procedures.py +++ b/src/aind_data_schema/components/specimen_procedures.py @@ -13,7 +13,7 @@ from aind_data_schema.base import AwareDatetimeWithDefault, DataModel, DiscriminatedList from aind_data_schema.components.coordinates import Atlas, CoordinateSystem, Translation -from aind_data_schema.components.reagent import FluorescentStain, GeneProbeSet, ProbeReagent, Reagent +from aind_data_schema.components.reagent import FluorescentStain, GeneProbeSet, ProbeReagent, Reagent, Solution from aind_data_schema.utils.exceptions import OneOfError @@ -178,7 +178,7 @@ class SpecimenProcedure(DataModel): ) procedure_details: DiscriminatedList[ - HCRSeries | FluorescentStain | Sectioning | PlanarSectioning | ProbeReagent | Reagent | GeneProbeSet + HCRSeries | FluorescentStain | Sectioning | PlanarSectioning | ProbeReagent | Reagent | GeneProbeSet | Solution ] = Field( default=[], title="Procedure details",