Create new ElectrodesTable neurodata type (#539)

rly · mavaylon1 · web-flow · commit f3cd9f8d6a98 · 2025-05-01T08:30:35.000-07:00
* Create new ElectrodesTable neurodata type

* clean up

* Update core/nwb.ecephys.yaml

* Update format_release_notes.rst

* Update format_release_notes.rst

* Update nwb.file.yaml

* Update format_release_notes.rst

---------

Co-authored-by: Matthew Avaylon &lt;mavaylon1@berkeley.edu&gt;
Co-authored-by: Matthew Avaylon &lt;avaylonmatthew@gmail.com&gt;
diff --git a/core/nwb.ecephys.yaml b/core/nwb.ecephys.yaml
@@ -257,6 +257,75 @@ groups:
     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 2.8.0. 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
   neurodata_type_inc: NWBDataInterface
diff --git a/core/nwb.file.yaml b/core/nwb.file.yaml
@@ -292,72 +292,10 @@ 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 2.9.0 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: '?'
diff --git a/docs/format/source/format_release_notes.rst b/docs/format/source/format_release_notes.rst
@@ -4,7 +4,11 @@ Release Notes
 =============
 
 2.9.0 (Upcoming)
-----------------
+------------------------
+
+Major changes
+^^^^^^^^^^^^^
+- Changed ``NWBFile.electrodes`` from a generic ``DynamicTable`` with added columns to an ``ElectrodesTable`` that extends ``DynamicTable`` with added columns. (#539)
 
 Major changes
 ^^^^^^^^^^^^^
