Create new ElectrodesTable neurodata type

NeurodataWithoutBorders · Apr 28, 2023 · 5109e61 · 5109e61
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Showing 2 changed files with 71 additions and 65 deletions.
diff --git a/core/nwb.ecephys.yaml b/core/nwb.ecephys.yaml
@@ -257,6 +257,74 @@ groups:
   - name: device
     target_type: Device
     doc: Link to the device that was used to record from this electrode group.
+- neurodata_type_def: ElectrodesTable
+  neurodata_type_inc: DynamicTable
+  doc: A table of all electrodes (i.e. channels) used for recording. Introduced in NWB 2.7.0. Replaces the "electrodes"
+    table (neurodata_type_inc DynamicTable, no neurodata_type_def) that is part of NWBFile.
+  datasets:
+  - name: location
+    neurodata_type_inc: VectorData
+    dtype: text
+    doc: Location of the electrode (channel). Specify the area, layer, comments
+      on estimation of area/layer, stereotaxic coordinates if in vivo, etc. Use
+      standard atlas names for anatomical regions when possible.
+  - name: group
+    neurodata_type_inc: VectorData
+    dtype:
+      target_type: ElectrodeGroup
+      reftype: object
+    doc: Reference to the ElectrodeGroup this electrode is a part of.
+  - name: group_name
+    neurodata_type_inc: VectorData
+    dtype: text
+    doc: Name of the ElectrodeGroup this electrode is a part of.
+    quantity: '?'
+  - name: x
+    neurodata_type_inc: VectorData
+    dtype: float32
+    doc: x coordinate of the channel location in the brain (+x is posterior).
+    quantity: '?'
+  - name: y
+    neurodata_type_inc: VectorData
+    dtype: float32
+    doc: y coordinate of the channel location in the brain (+y is inferior).
+    quantity: '?'
+  - name: z
+    neurodata_type_inc: VectorData
+    dtype: float32
+    doc: z coordinate of the channel location in the brain (+z is right).
+    quantity: '?'
+  - name: imp
+    neurodata_type_inc: VectorData
+    dtype: float32
+    doc: Impedance of the channel, in ohms.
+    quantity: '?'
+  - name: filtering
+    neurodata_type_inc: VectorData
+    dtype: text
+    doc: Description of hardware filtering, including the filter name and frequency cutoffs.
+    quantity: '?'
+  - name: rel_x
+    neurodata_type_inc: VectorData
+    dtype: float32
+    doc: x coordinate in electrode group
+    quantity: '?'
+  - name: rel_y
+    neurodata_type_inc: VectorData
+    dtype: float32
+    doc: y coordinate in electrode group
+    quantity: '?'
+  - name: rel_z
+    neurodata_type_inc: VectorData
+    dtype: float32
+    doc: z coordinate in electrode group
+    quantity: '?'
+  - name: reference
+    neurodata_type_inc: VectorData
+    dtype: text
+    doc: Description of the reference electrode and/or reference scheme used for this electrode, e.g.,
+      "stainless steel skull screw" or "online common average referencing".
+    quantity: '?'
 
 # The types below have been deprecated
 - neurodata_type_def: ClusterWaveforms

diff --git a/core/nwb.file.yaml b/core/nwb.file.yaml
@@ -270,72 +270,10 @@ groups:
         doc: Physical group of electrodes.
         quantity: '*'
       - name: electrodes
-        neurodata_type_inc: DynamicTable
-        doc: A table of all electrodes (i.e. channels) used for recording.
+        neurodata_type_inc: ElectrodesTable
+        doc: A table of all electrodes (i.e. channels) used for recording. Changed in NWB 2.7.0 to use the newly added
+          ElectrodesTable neurodata type instead of a DynamicTable with added columns.
         quantity: '?'
-        datasets:
-        - name: x
-          neurodata_type_inc: VectorData
-          dtype: float32
-          doc: x coordinate of the channel location in the brain (+x is posterior).
-          quantity: '?'
-        - name: y
-          neurodata_type_inc: VectorData
-          dtype: float32
-          doc: y coordinate of the channel location in the brain (+y is inferior).
-          quantity: '?'
-        - name: z
-          neurodata_type_inc: VectorData
-          dtype: float32
-          doc: z coordinate of the channel location in the brain (+z is right).
-          quantity: '?'
-        - name: imp
-          neurodata_type_inc: VectorData
-          dtype: float32
-          doc: Impedance of the channel, in ohms.
-          quantity: '?'
-        - name: location
-          neurodata_type_inc: VectorData
-          dtype: text
-          doc: Location of the electrode (channel). Specify the area, layer, comments
-            on estimation of area/layer, stereotaxic coordinates if in vivo, etc. Use
-            standard atlas names for anatomical regions when possible.
-        - name: filtering
-          neurodata_type_inc: VectorData
-          dtype: text
-          doc: Description of hardware filtering, including the filter name and frequency cutoffs.
-          quantity: '?'
-        - name: group
-          neurodata_type_inc: VectorData
-          dtype:
-            target_type: ElectrodeGroup
-            reftype: object
-          doc: Reference to the ElectrodeGroup this electrode is a part of.
-        - name: group_name
-          neurodata_type_inc: VectorData
-          dtype: text
-          doc: Name of the ElectrodeGroup this electrode is a part of.
-        - name: rel_x
-          neurodata_type_inc: VectorData
-          dtype: float32
-          doc: x coordinate in electrode group
-          quantity: '?'
-        - name: rel_y
-          neurodata_type_inc: VectorData
-          dtype: float32
-          doc: y coordinate in electrode group
-          quantity: '?'
-        - name: rel_z
-          neurodata_type_inc: VectorData
-          dtype: float32
-          doc: z coordinate in electrode group
-          quantity: '?'
-        - name: reference
-          neurodata_type_inc: VectorData
-          dtype: text
-          doc: Description of the reference electrode and/or reference scheme used for this electrode, e.g.,
-            "stainless steel skull screw" or "online common average referencing".
-          quantity: '?'
     - name: intracellular_ephys
       doc: Metadata related to intracellular electrophysiology.
       quantity: '?'