feat: add MISCameraConfig

docs/source/acquisition.md

@@ -126,7 +126,7 @@ 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)) |
 
 

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

docs/source/components/specimen_procedures.md

@@ -35,7 +35,7 @@ Description of a sectioning procedure performed on the coronal, sagittal, or tra
 
 | Field | Type | Title (Description) |
 |-------|------|-------------|
-| `coordinate_system` | Optional[[CoordinateSystem](coordinates.md#coordinatesystem)] | Sectioning coordinate system (Only required if different from the Procedures.coordinate_system) |
+| `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)] | Sections  |
 | `section_orientation` | [SectionOrientation](#sectionorientation) | Sectioning orientation  |
 

src/aind_data_schema/components/configs.py

@@ -30,6 +30,7 @@
     Scale,
     Translation,
 )
+from aind_data_schema.components.devices import DevicePosition
 from aind_data_schema.components.identifiers import Code
 from aind_data_schema.components.wrappers import AssetPath
 
@@ -505,6 +506,13 @@ class EphysAssemblyConfig(DeviceConfig):
     )
 
 
+class MISCameraConfig(DeviceConfig, DevicePosition):
+    """Configuration for a camera used in a New Scale modular insertion system"""
+
+    detector_config: DetectorConfig = Field(..., title="Detector configuration")
+    module: MISModuleConfig = Field(..., title="Module")
+
+
 class FiberAssemblyConfig(DeviceConfig):
     """Inserted fiber photometry probe recorded in a stream"""
 

src/aind_data_schema/core/acquisition.py

@@ -24,6 +24,7 @@
     LightEmittingDiodeConfig,
     ManipulatorConfig,
     MousePlatformConfig,
+    MISCameraConfig,
     MRIScan,
     OlfactometerConfig,
     PatchCordConfig,
@@ -126,6 +127,7 @@ class DataStream(DataModel):
         | DetectorConfig
         | PatchCordConfig
         | FiberAssemblyConfig
+        | MISCameraConfig
         | MRIScan
         | LickSpoutConfig
         | AirPuffConfig