Add cell matching schemas and CellTypeReferenceUser

emannotationschemas/__init__.py

@@ -26,7 +26,11 @@
 from emannotationschemas.schemas.braincircuits import (
     BrainCircuitsBoundTagAnnotationUser,
 )
-from emannotationschemas.schemas.cell_type_local import CellTypeLocal, CellTypeReference
+from emannotationschemas.schemas.cell_type_local import (
+    CellTypeLocal,
+    CellTypeReference,
+    CellTypeReferenceUser,
+)
 from emannotationschemas.schemas.contact import Contact
 from emannotationschemas.schemas.derived_spatial_point import (
     DerivedNumeric,
@@ -41,9 +45,12 @@
     FunctionalCoregistration,
     FunctionalUnitCoregistration,
     FunctionalUnitCoregistrationExtended,
-    V1DDFunctionalUnitCoregistration
+    V1DDFunctionalUnitCoregistration,
+)
+from emannotationschemas.schemas.functional_props import (
+    FunctionalPropertiesBCM,
+    DigitalTwinPropertiesBCM,
 )
-from emannotationschemas.schemas.functional_props import FunctionalPropertiesBCM, DigitalTwinPropertiesBCM
 from emannotationschemas.schemas.glia_contact import GliaContact
 from emannotationschemas.schemas.groups import SimpleGroup
 from emannotationschemas.schemas.neuropil import FlyNeuropil
@@ -59,6 +66,11 @@
 from emannotationschemas.schemas.reference_text_float import (
     ReferenceTagFloat,
 )
+from emannotationschemas.schemas.matching import (
+    CellMatch,
+    CellSimilarity,
+    CellMatchReference,
+)
 from emannotationschemas.schemas.synapse import (
     BuhmannEcksteinSynapseSchema,
     BuhmannSynapseSchema,
@@ -89,6 +101,7 @@
     "reference_tag": ReferenceTagAnnotation,
     "cell_type_local": CellTypeLocal,
     "cell_type_reference": CellTypeReference,
+    "cell_type_reference_user": CellTypeReferenceUser,
     "nucleus_detection": NucleusDetection,
     "bound_tag": BoundTagAnnotation,
     "bound_double_tag": BoundDoubleTagAnnotation,
@@ -122,7 +135,10 @@
     "reference_tag_float": ReferenceTagFloat,
     "compartment_proofread_status_strategy": CompartmentProofreadStatusStrategy,
     "reference_tag_with_confidence": ReferenceTagWithConfidence,
-    "digital_twin_properties": DigitalTwinPropertiesBCM
+    "digital_twin_properties": DigitalTwinPropertiesBCM,
+    "cell_match": CellMatch,
+    "cell_similarity": CellSimilarity,
+    "cell_match_reference": CellMatchReference,
 }
 
 

emannotationschemas/schemas/cell_type_local.py

@@ -1,5 +1,9 @@
 import marshmallow as mm
-from emannotationschemas.schemas.base import AnnotationSchema, BoundSpatialPoint, ReferenceAnnotation
+from emannotationschemas.schemas.base import (
+    AnnotationSchema,
+    BoundSpatialPoint,
+    ReferenceAnnotation,
+)
 
 allowed_types = dict(
     valence=["e", "i", "g", "uncertain"],
@@ -77,15 +81,13 @@ def validate_type(self, item, **kwargs):
         return item
 
 
-
 class CellTypeReference(ReferenceAnnotation):
 
     classification_system = mm.fields.String(
         required=True, description="Classification system followed"
     )
     cell_type = mm.fields.String(required=True, description="Cell type name")
 
-
     @mm.post_load
     def validate_type(self, item, **kwargs):
 
@@ -99,3 +101,11 @@ def validate_type(self, item, **kwargs):
             item["valid"] = True
 
         return item
+
+
+class CellTypeReferenceUser(CellTypeReference):
+    """CellTypeReference schema with user tracking"""
+
+    user_id = mm.fields.Int(
+        required=True, description="User who created the cell type classification."
+    )

emannotationschemas/schemas/matching.py

@@ -0,0 +1,85 @@
+import marshmallow as mm
+from emannotationschemas.schemas.base import (
+    AnnotationSchema,
+    BoundSpatialPoint,
+    NumericField,
+    ReferenceAnnotation,
+)
+
+
+class CellMatch(AnnotationSchema):
+    """Schema for matching cells between datasets"""
+
+    pt = mm.fields.Nested(
+        BoundSpatialPoint,
+        required=True,
+        description="Source cell identity (pt_root_id, pt_supervoxel_id, pt_position)",
+    )
+    query_root_id = NumericField(
+        required=True,
+        description="Static root ID used for score calculation",
+    )
+    match_id = mm.fields.Str(
+        required=True,
+        description="Unique identifier for cell from another dataset",
+        index=True,
+    )
+    score = mm.fields.Float(
+        required=True,
+        description="Normalised NBLAST similarity score [for CAVE schema, could be any numeric score]",
+    )
+    validation = mm.fields.Bool(
+        required=False,
+        default=False,
+        description="False if not separately validated, True if separately validated",
+    )
+
+
+class CellSimilarity(AnnotationSchema):
+    """Schema for cell similarity scoring between two cells"""
+
+    pt = mm.fields.Nested(
+        BoundSpatialPoint,
+        required=True,
+        description="Query cell identity (pt_root_id, pt_supervoxel_id, pt_position)",
+    )
+    match_pt = mm.fields.Nested(
+        BoundSpatialPoint,
+        required=True,
+        description="Target cell identity (match_root_id, match_supervoxel_id, match_position)",
+    )
+    query_root_id = NumericField(
+        required=True,
+        description="Static root ID for query cell at time of score calculation",
+    )
+    match_root_id = NumericField(
+        required=True,
+        description="Static root ID for target cell at time of score calculation",
+    )
+    score = mm.fields.Float(
+        required=True,
+        description="Numeric similarity score between the two cells",
+    )
+
+
+class CellMatchReference(ReferenceAnnotation):
+    """Reference annotation version of CellMatch schema"""
+
+    query_root_id = NumericField(
+        required=True,
+        description="Static root ID used for score calculation",
+    )
+    match_id = mm.fields.Str(
+        required=True,
+        description="Unique identifier for cell from another dataset",
+        index=True,
+    )
+    score = mm.fields.Float(
+        required=True,
+        description="Normalized NBLAST similarity score [for CAVE schema, could be any numeric score]",
+    )
+    validation = mm.fields.Bool(
+        required=False,
+        default=False,
+        description="False if not validated by a human, True if validated by a human",
+    )