anatomical coordinates and reference (#1016)

* anatomical coordinates and reference * whitespace * literal? * fixing indents maybe * example
AllenNeuralDynamics · Aug 6, 2024 · c5deee5 · c5deee5
1 parent 5aeea41
commit c5deee5
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Showing 2 changed files with 14 additions and 6 deletions.
diff --git a/examples/ephys_session.json b/examples/ephys_session.json
@@ -54,7 +54,8 @@
                   "z": "11087.5",
                   "unit": "micrometer"
                },
-               "bregma_coordinates": null,
+               "anatomical_coordinates": null,
+               "anatomical_reference": null,
                "surface_z": null,
                "surface_z_unit": "micrometer",
                "dye": null,
@@ -86,7 +87,8 @@
                   "z": "13262",
                   "unit": "micrometer"
                },
-               "bregma_coordinates": null,
+               "anatomical_coordinates": null,
+               "anatomical_reference": null,
                "surface_z": null,
                "surface_z_unit": "micrometer",
                "dye": null,
@@ -187,7 +189,8 @@
                   "z": "11087.5",
                   "unit": "micrometer"
                },
-               "bregma_coordinates": null,
+               "anatomical_coordinates": null,
+               "anatomical_reference": null,
                "surface_z": null,
                "surface_z_unit": "micrometer",
                "dye": null,
@@ -219,7 +222,8 @@
                   "z": "13262",
                   "unit": "micrometer"
                },
-               "bregma_coordinates": null,
+               "anatomical_coordinates": null,
+               "anatomical_reference": null,
                "surface_z": null,
                "surface_z_unit": "micrometer",
                "dye": null,

diff --git a/src/aind_data_schema/core/session.py b/src/aind_data_schema/core/session.py
@@ -39,7 +39,7 @@
     VisualStimulation,
 )
 from aind_data_schema.components.tile import Channel
-from aind_data_schema.core.procedures import Anaesthetic
+from aind_data_schema.core.procedures import Anaesthetic, CoordinateReferenceLocation
 
 
 class StimulusModality(str, Enum):
@@ -217,7 +217,11 @@ class ManipulatorModule(DomeModule):
         ...,
         title="Manipulator coordinates",
     )
-    bregma_coordinates: Optional[Coordinates3d] = Field(default=None, title="Bregma coordinates")
+    anatomical_coordinates: Optional[Coordinates3d] = Field(default=None, title="Anatomical coordinates")
+    anatomical_reference: Optional[Literal[CoordinateReferenceLocation.BREGMA,
+                                           CoordinateReferenceLocation.LAMBDA]] = Field(
+                                               default=None, title="Anatomical coordinate reference"
+                                               )
     surface_z: Optional[Decimal] = Field(default=None, title="Surface z")
     surface_z_unit: SizeUnit = Field(SizeUnit.UM, title="Surface z unit")
     dye: Optional[str] = Field(default=None, title="Dye")